Starting phenix.real_space_refine on Sat Mar 16 21:20:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7niv_12366/03_2024/7niv_12366_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7niv_12366/03_2024/7niv_12366.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7niv_12366/03_2024/7niv_12366.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7niv_12366/03_2024/7niv_12366.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7niv_12366/03_2024/7niv_12366_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7niv_12366/03_2024/7niv_12366_updated.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 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: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 54 5.16 5 C 10092 2.51 5 N 2607 2.21 5 O 2970 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D GLU 106": "OE1" <-> "OE2" Residue "D GLU 144": "OE1" <-> "OE2" Residue "D GLU 188": "OE1" <-> "OE2" Residue "D GLU 196": "OE1" <-> "OE2" Residue "E ARG 101": "NH1" <-> "NH2" Residue "A GLU 112": "OE1" <-> "OE2" Residue "A ARG 115": "NH1" <-> "NH2" Residue "A ARG 278": "NH1" <-> "NH2" Residue "A GLU 288": "OE1" <-> "OE2" Residue "A ARG 383": "NH1" <-> "NH2" Residue "A GLU 395": "OE1" <-> "OE2" Residue "A ARG 590": "NH1" <-> "NH2" Residue "A GLU 604": "OE1" <-> "OE2" Residue "A GLU 616": "OE1" <-> "OE2" Residue "A GLU 734": "OE1" <-> "OE2" Residue "A ARG 831": "NH1" <-> "NH2" Residue "A ARG 884": "NH1" <-> "NH2" Residue "A ARG 971": "NH1" <-> "NH2" Residue "A ARG 1013": "NH1" <-> "NH2" Residue "A GLU 1022": "OE1" <-> "OE2" Residue "A GLU 1118": "OE1" <-> "OE2" Residue "A ARG 1137": "NH1" <-> "NH2" Residue "A ARG 1232": "NH1" <-> "NH2" Residue "B ARG 109": "NH1" <-> "NH2" Residue "B GLU 162": "OE1" <-> "OE2" Residue "B GLU 188": "OE1" <-> "OE2" Residue "C GLU 4": "OE1" <-> "OE2" Residue "C ARG 41": "NH1" <-> "NH2" Residue "C GLU 49": "OE1" <-> "OE2" Residue "C TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 101": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 15724 Number of models: 1 Model: "" Number of chains: 6 Chain: "D" Number of atoms: 1584 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 208, 1578 Classifications: {'peptide': 208} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 197} Conformer: "B" Number of residues, atoms: 208, 1575 Classifications: {'peptide': 208} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 197} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 1598 Chain: "E" Number of atoms: 1702 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 229, 1702 Classifications: {'peptide': 229} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 217} Chain: "A" Number of atoms: 8815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1138, 8815 Classifications: {'peptide': 1138} Link IDs: {'PTRANS': 27, 'TRANS': 1110} Chain breaks: 2 Chain: "B" Number of atoms: 1616 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 211, 1610 Classifications: {'peptide': 211} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 200} Conformer: "B" Number of residues, atoms: 211, 1607 Classifications: {'peptide': 211} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 200} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 1631 Chain: "C" Number of atoms: 1757 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 234, 1757 Classifications: {'peptide': 234} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 222} Chain: "A" Number of atoms: 250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 250 Unusual residues: {'CLR': 7, 'DLP': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Time building chain proxies: 10.53, per 1000 atoms: 0.67 Number of scatterers: 15724 At special positions: 0 Unit cell: (159.06, 132, 127.38, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 54 16.00 P 1 15.00 O 2970 8.00 N 2607 7.00 C 10092 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS D 24 " - pdb=" SG CYS D 89 " distance=2.03 Simple disulfide: pdb=" SG CYS D 135 " - pdb=" SG CYS D 195 " distance=2.04 Simple disulfide: pdb=" SG CYS E 25 " - pdb=" SG CYS E 99 " distance=2.03 Simple disulfide: pdb=" SG CYS E 153 " - pdb=" SG CYS E 209 " distance=2.03 Simple disulfide: pdb=" SG CYS B 24 " - pdb=" SG CYS B 89 " distance=2.04 Simple disulfide: pdb=" SG CYS B 135 " - pdb=" SG CYS B 195 " distance=2.03 Simple disulfide: pdb=" SG CYS C 25 " - pdb=" SG CYS C 99 " distance=2.03 Simple disulfide: pdb=" SG CYS C 160 " - pdb=" SG CYS C 216 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.88 Conformation dependent library (CDL) restraints added in 3.8 seconds 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3732 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 50 helices and 20 sheets defined 33.0% alpha, 13.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.85 Creating SS restraints... Processing helix chain 'D' and resid 123 through 126 No H-bonds generated for 'chain 'D' and resid 123 through 126' Processing helix chain 'D' and resid 184 through 187 No H-bonds generated for 'chain 'D' and resid 184 through 187' Processing helix chain 'E' and resid 32 through 34 No H-bonds generated for 'chain 'E' and resid 32 through 34' Processing helix chain 'E' and resid 214 through 216 No H-bonds generated for 'chain 'E' and resid 214 through 216' Processing helix chain 'A' and resid 51 through 91 removed outlier: 4.869A pdb=" N GLY A 70 " --> pdb=" O ALA A 66 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N LEU A 71 " --> pdb=" O HIS A 67 " (cutoff:3.500A) Proline residue: A 72 - end of helix Processing helix chain 'A' and resid 108 through 159 Processing helix chain 'A' and resid 163 through 167 Processing helix chain 'A' and resid 170 through 189 removed outlier: 4.961A pdb=" N ILE A 181 " --> pdb=" O LEU A 177 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N SER A 182 " --> pdb=" O THR A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 210 Processing helix chain 'A' and resid 215 through 243 removed outlier: 3.639A pdb=" N ILE A 223 " --> pdb=" O VAL A 219 " (cutoff:3.500A) Proline residue: A 225 - end of helix removed outlier: 3.835A pdb=" N LEU A 238 " --> pdb=" O TRP A 234 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N SER A 239 " --> pdb=" O ALA A 235 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N SER A 242 " --> pdb=" O LEU A 238 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ASP A 243 " --> pdb=" O SER A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 260 removed outlier: 4.454A pdb=" N ALA A 254 " --> pdb=" O LYS A 251 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU A 257 " --> pdb=" O ALA A 254 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLU A 258 " --> pdb=" O VAL A 255 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N ALA A 259 " --> pdb=" O ALA A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 321 removed outlier: 4.484A pdb=" N ASN A 285 " --> pdb=" O LYS A 281 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ILE A 289 " --> pdb=" O ASN A 285 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N LYS A 292 " --> pdb=" O GLU A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 348 Processing helix chain 'A' and resid 351 through 372 removed outlier: 3.741A pdb=" N ALA A 358 " --> pdb=" O ILE A 354 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N VAL A 366 " --> pdb=" O GLY A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 441 Processing helix chain 'A' and resid 465 through 468 No H-bonds generated for 'chain 'A' and resid 465 through 468' Processing helix chain 'A' and resid 486 through 493 removed outlier: 3.835A pdb=" N TYR A 492 " --> pdb=" O GLU A 488 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N GLY A 493 " --> pdb=" O ASN A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 507 Processing helix chain 'A' and resid 513 through 516 No H-bonds generated for 'chain 'A' and resid 513 through 516' Processing helix chain 'A' and resid 539 through 548 removed outlier: 5.165A pdb=" N ARG A 545 " --> pdb=" O ALA A 542 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ALA A 546 " --> pdb=" O ILE A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 576 removed outlier: 5.170A pdb=" N ALA A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N ALA A 574 " --> pdb=" O GLU A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 617 No H-bonds generated for 'chain 'A' and resid 614 through 617' Processing helix chain 'A' and resid 624 through 627 No H-bonds generated for 'chain 'A' and resid 624 through 627' Processing helix chain 'A' and resid 697 through 704 removed outlier: 4.494A pdb=" N ASN A 704 " --> pdb=" O VAL A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 720 Processing helix chain 'A' and resid 724 through 738 removed outlier: 3.966A pdb=" N ILE A 736 " --> pdb=" O PHE A 732 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ALA A 737 " --> pdb=" O SER A 733 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 796 removed outlier: 3.662A pdb=" N CYS A 751 " --> pdb=" O LYS A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 810 through 840 removed outlier: 3.659A pdb=" N ALA A 821 " --> pdb=" O LEU A 817 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N ALA A 822 " --> pdb=" O ALA A 818 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N GLY A 829 " --> pdb=" O GLN A 825 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N ARG A 831 " --> pdb=" O ALA A 827 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N LEU A 832 " --> pdb=" O THR A 828 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASN A 838 " --> pdb=" O LEU A 834 " (cutoff:3.500A) Processing helix chain 'A' and resid 842 through 852 Processing helix chain 'A' and resid 854 through 867 removed outlier: 3.772A pdb=" N VAL A 863 " --> pdb=" O LEU A 859 " (cutoff:3.500A) Proline residue: A 865 - end of helix Processing helix chain 'A' and resid 870 through 874 Processing helix chain 'A' and resid 882 through 901 removed outlier: 5.391A pdb=" N ILE A 895 " --> pdb=" O ALA A 891 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ALA A 896 " --> pdb=" O ALA A 892 " (cutoff:3.500A) Processing helix chain 'A' and resid 903 through 906 No H-bonds generated for 'chain 'A' and resid 903 through 906' Processing helix chain 'A' and resid 913 through 965 removed outlier: 4.943A pdb=" N GLY A 925 " --> pdb=" O GLU A 921 " (cutoff:3.500A) Proline residue: A 926 - end of helix removed outlier: 3.630A pdb=" N TYR A 949 " --> pdb=" O GLN A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 970 through 991 removed outlier: 3.895A pdb=" N SER A 978 " --> pdb=" O ILE A 974 " (cutoff:3.500A) Processing helix chain 'A' and resid 997 through 1012 removed outlier: 4.415A pdb=" N LEU A1002 " --> pdb=" O ALA A 998 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER A1003 " --> pdb=" O LYS A 999 " (cutoff:3.500A) Processing helix chain 'A' and resid 1079 through 1082 No H-bonds generated for 'chain 'A' and resid 1079 through 1082' Processing helix chain 'A' and resid 1105 through 1109 Processing helix chain 'A' and resid 1131 through 1133 No H-bonds generated for 'chain 'A' and resid 1131 through 1133' Processing helix chain 'A' and resid 1141 through 1150 Processing helix chain 'A' and resid 1154 through 1159 removed outlier: 3.839A pdb=" N GLU A1158 " --> pdb=" O HIS A1154 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N THR A1159 " --> pdb=" O PRO A1155 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1154 through 1159' Processing helix chain 'A' and resid 1180 through 1182 No H-bonds generated for 'chain 'A' and resid 1180 through 1182' Processing helix chain 'A' and resid 1184 through 1189 removed outlier: 3.598A pdb=" N ALA A1188 " --> pdb=" O ALA A1184 " (cutoff:3.500A) Processing helix chain 'A' and resid 1207 through 1214 removed outlier: 4.187A pdb=" N LYS A1211 " --> pdb=" O THR A1207 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N VAL A1212 " --> pdb=" O GLU A1208 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N VAL A1213 " --> pdb=" O SER A1209 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N GLN A1214 " --> pdb=" O GLU A1210 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1207 through 1214' Processing helix chain 'A' and resid 1236 through 1238 No H-bonds generated for 'chain 'A' and resid 1236 through 1238' Processing helix chain 'B' and resid 123 through 126 No H-bonds generated for 'chain 'B' and resid 123 through 126' Processing helix chain 'B' and resid 184 through 187 No H-bonds generated for 'chain 'B' and resid 184 through 187' Processing helix chain 'C' and resid 32 through 34 No H-bonds generated for 'chain 'C' and resid 32 through 34' Processing helix chain 'C' and resid 175 through 177 No H-bonds generated for 'chain 'C' and resid 175 through 177' Processing helix chain 'C' and resid 221 through 223 No H-bonds generated for 'chain 'C' and resid 221 through 223' Processing sheet with id= A, first strand: chain 'D' and resid 20 through 25 removed outlier: 3.794A pdb=" N THR D 73 " --> pdb=" O SER D 66 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N SER D 66 " --> pdb=" O THR D 73 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N SER D 64 " --> pdb=" O THR D 75 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'D' and resid 86 through 91 removed outlier: 4.022A pdb=" N TRP D 36 " --> pdb=" O ILE D 49 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ILE D 49 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N GLN D 38 " --> pdb=" O LEU D 47 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N LEU D 47 " --> pdb=" O GLN D 38 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'D' and resid 115 through 119 removed outlier: 3.786A pdb=" N PHE D 119 " --> pdb=" O VAL D 134 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N VAL D 134 " --> pdb=" O PHE D 119 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N TYR D 174 " --> pdb=" O ASN D 139 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 146 through 151 Processing sheet with id= E, first strand: chain 'E' and resid 21 through 25 removed outlier: 3.556A pdb=" N CYS E 25 " --> pdb=" O ALA E 82 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA E 82 " --> pdb=" O CYS E 25 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'E' and resid 133 through 137 removed outlier: 3.854A pdb=" N GLY E 152 " --> pdb=" O LEU E 137 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N CYS E 153 " --> pdb=" O SER E 193 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N SER E 193 " --> pdb=" O CYS E 153 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N VAL E 155 " --> pdb=" O LEU E 191 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N LEU E 191 " --> pdb=" O VAL E 155 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'E' and resid 164 through 167 removed outlier: 3.761A pdb=" N TYR E 207 " --> pdb=" O VAL E 224 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LYS E 222 " --> pdb=" O CYS E 209 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'E' and resid 38 through 42 removed outlier: 3.553A pdb=" N TRP E 39 " --> pdb=" O ALA E 52 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA E 52 " --> pdb=" O TRP E 39 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N ARG E 41 " --> pdb=" O TRP E 50 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N TRP E 50 " --> pdb=" O ARG E 41 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'A' and resid 452 through 455 Processing sheet with id= J, first strand: chain 'A' and resid 472 through 475 removed outlier: 6.760A pdb=" N ILE A 553 " --> pdb=" O GLY A 473 " (cutoff:3.500A) removed outlier: 8.874A pdb=" N VAL A 475 " --> pdb=" O ILE A 553 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N LEU A 555 " --> pdb=" O VAL A 475 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N THR A 583 " --> pdb=" O LEU A 554 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N LEU A 556 " --> pdb=" O THR A 583 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ILE A 585 " --> pdb=" O LEU A 556 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'A' and resid 1034 through 1036 Processing sheet with id= L, first strand: chain 'A' and resid 1195 through 1197 removed outlier: 7.562A pdb=" N THR A1225 " --> pdb=" O LEU A1196 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'B' and resid 20 through 23 Processing sheet with id= N, first strand: chain 'B' and resid 34 through 39 removed outlier: 3.777A pdb=" N ALA B 35 " --> pdb=" O GLN B 90 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLN B 90 " --> pdb=" O ALA B 35 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 115 through 119 Processing sheet with id= P, first strand: chain 'B' and resid 146 through 151 removed outlier: 4.201A pdb=" N CYS B 195 " --> pdb=" O LYS B 208 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LYS B 208 " --> pdb=" O CYS B 195 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL B 197 " --> pdb=" O VAL B 206 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL B 206 " --> pdb=" O VAL B 197 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 6 through 10 removed outlier: 3.657A pdb=" N SER C 24 " --> pdb=" O SER C 10 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 96 through 101 removed outlier: 4.063A pdb=" N ILE C 37 " --> pdb=" O ILE C 54 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE C 54 " --> pdb=" O ILE C 37 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA C 52 " --> pdb=" O TRP C 39 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N ARG C 41 " --> pdb=" O TRP C 50 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N TRP C 50 " --> pdb=" O ARG C 41 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N ALA C 43 " --> pdb=" O LEU C 48 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N LEU C 48 " --> pdb=" O ALA C 43 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 140 through 142 removed outlier: 5.904A pdb=" N TYR C 196 " --> pdb=" O ASP C 164 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 170 through 174 573 hydrogen bonds defined for protein. 1608 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: 5.23 Time building geometry restraints manager: 7.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2524 1.31 - 1.44: 4312 1.44 - 1.57: 9121 1.57 - 1.69: 26 1.69 - 1.82: 81 Bond restraints: 16064 Sorted by residual: bond pdb=" C11 DLP A1301 " pdb=" O3 DLP A1301 " ideal model delta sigma weight residual 1.327 1.422 -0.095 2.00e-02 2.50e+03 2.26e+01 bond pdb=" C31 DLP A1301 " pdb=" O2 DLP A1301 " ideal model delta sigma weight residual 1.331 1.426 -0.095 2.00e-02 2.50e+03 2.25e+01 bond pdb=" N DLP A1301 " pdb=" C7 DLP A1301 " ideal model delta sigma weight residual 1.491 1.427 0.064 2.00e-02 2.50e+03 1.02e+01 bond pdb=" N VAL E 124 " pdb=" CA VAL E 124 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.19e-02 7.06e+03 8.58e+00 bond pdb=" C23 CLR A1307 " pdb=" C24 CLR A1307 " ideal model delta sigma weight residual 1.525 1.578 -0.053 2.00e-02 2.50e+03 7.07e+00 ... (remaining 16059 not shown) Histogram of bond angle deviations from ideal: 98.08 - 105.28: 277 105.28 - 112.48: 8337 112.48 - 119.68: 5352 119.68 - 126.87: 7679 126.87 - 134.07: 161 Bond angle restraints: 21806 Sorted by residual: angle pdb=" N TYR E 107 " pdb=" CA TYR E 107 " pdb=" C TYR E 107 " ideal model delta sigma weight residual 111.71 118.65 -6.94 1.15e+00 7.56e-01 3.65e+01 angle pdb=" O3P DLP A1301 " pdb=" P DLP A1301 " pdb=" O4P DLP A1301 " ideal model delta sigma weight residual 93.58 108.62 -15.04 3.00e+00 1.11e-01 2.51e+01 angle pdb=" C ALA E 112 " pdb=" CA ALA E 112 " pdb=" CB ALA E 112 " ideal model delta sigma weight residual 116.54 110.79 5.75 1.15e+00 7.56e-01 2.50e+01 angle pdb=" CA VAL A 609 " pdb=" C VAL A 609 " pdb=" N GLU A 610 " ideal model delta sigma weight residual 117.15 120.86 -3.71 7.80e-01 1.64e+00 2.26e+01 angle pdb=" CA ALA E 112 " pdb=" C ALA E 112 " pdb=" N MET E 113 " ideal model delta sigma weight residual 119.52 115.97 3.55 7.90e-01 1.60e+00 2.02e+01 ... (remaining 21801 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.80: 9208 23.80 - 47.59: 624 47.59 - 71.38: 71 71.38 - 95.18: 15 95.18 - 118.97: 2 Dihedral angle restraints: 9920 sinusoidal: 4089 harmonic: 5831 Sorted by residual: dihedral pdb=" CA PHE A 732 " pdb=" C PHE A 732 " pdb=" N SER A 733 " pdb=" CA SER A 733 " ideal model delta harmonic sigma weight residual 180.00 151.12 28.88 0 5.00e+00 4.00e-02 3.34e+01 dihedral pdb=" CB CYS B 135 " pdb=" SG CYS B 135 " pdb=" SG CYS B 195 " pdb=" CB CYS B 195 " ideal model delta sinusoidal sigma weight residual 93.00 45.35 47.65 1 1.00e+01 1.00e-02 3.13e+01 dihedral pdb=" CA PHE A 982 " pdb=" C PHE A 982 " pdb=" N GLY A 983 " pdb=" CA GLY A 983 " ideal model delta harmonic sigma weight residual 180.00 153.21 26.79 0 5.00e+00 4.00e-02 2.87e+01 ... (remaining 9917 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 2169 0.077 - 0.155: 285 0.155 - 0.232: 27 0.232 - 0.309: 14 0.309 - 0.386: 4 Chirality restraints: 2499 Sorted by residual: chirality pdb=" C17 CLR A1303 " pdb=" C13 CLR A1303 " pdb=" C16 CLR A1303 " pdb=" C20 CLR A1303 " both_signs ideal model delta sigma weight residual False 2.55 2.94 -0.39 2.00e-01 2.50e+01 3.73e+00 chirality pdb=" C17 CLR A1302 " pdb=" C13 CLR A1302 " pdb=" C16 CLR A1302 " pdb=" C20 CLR A1302 " both_signs ideal model delta sigma weight residual False 2.55 2.91 -0.36 2.00e-01 2.50e+01 3.17e+00 chirality pdb=" C17 CLR A1304 " pdb=" C13 CLR A1304 " pdb=" C16 CLR A1304 " pdb=" C20 CLR A1304 " both_signs ideal model delta sigma weight residual False 2.55 2.91 -0.35 2.00e-01 2.50e+01 3.13e+00 ... (remaining 2496 not shown) Planarity restraints: 2727 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 305 " -0.021 2.00e-02 2.50e+03 2.62e-02 1.20e+01 pdb=" CG PHE A 305 " 0.059 2.00e-02 2.50e+03 pdb=" CD1 PHE A 305 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 PHE A 305 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE A 305 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE A 305 " -0.010 2.00e-02 2.50e+03 pdb=" CZ PHE A 305 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 175 " 0.011 2.00e-02 2.50e+03 2.30e-02 5.31e+00 pdb=" C THR A 175 " -0.040 2.00e-02 2.50e+03 pdb=" O THR A 175 " 0.015 2.00e-02 2.50e+03 pdb=" N ARG A 176 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 958 " 0.016 2.00e-02 2.50e+03 1.62e-02 4.61e+00 pdb=" CG PHE A 958 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 PHE A 958 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE A 958 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE A 958 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 958 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE A 958 " 0.002 2.00e-02 2.50e+03 ... (remaining 2724 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1680 2.74 - 3.28: 16303 3.28 - 3.82: 25260 3.82 - 4.36: 30884 4.36 - 4.90: 51395 Nonbonded interactions: 125522 Sorted by model distance: nonbonded pdb=" N ASP A 243 " pdb=" OD1 ASP A 243 " model vdw 2.197 2.520 nonbonded pdb=" OE1 GLN A 443 " pdb=" OG SER A 908 " model vdw 2.200 2.440 nonbonded pdb=" NE2 GLN B 39 " pdb=" O LYS B 43 " model vdw 2.210 2.520 nonbonded pdb=" OD1 ASP A 166 " pdb=" OH TYR A 446 " model vdw 2.215 2.440 nonbonded pdb=" O GLY A 845 " pdb=" OG SER A 849 " model vdw 2.216 2.440 ... (remaining 125517 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'B' and (resid 6 through 91 or resid 94 or resid 96 through 114 or resid \ 116 through 156 or resid 158 through 203 or resid 205 through 213)) selection = (chain 'D' and (resid 6 through 91 or resid 94 or resid 96 through 114 or resid \ 116 through 156 or resid 158 through 203 or resid 205 through 213)) } ncs_group { reference = (chain 'C' and (resid 3 through 31 or resid 34 through 35 or resid 37 through 52 \ or resid 54 through 56 or resid 59 through 101 or resid 109 or resid 111 throug \ h 112 or resid 115 or resid 121 through 236)) selection = (chain 'E' and (resid 3 through 31 or resid 34 through 35 or resid 37 through 52 \ or resid 54 through 56 or resid 59 through 101 or resid 103 or resid 105 throug \ h 106 or resid 108 or resid 114 through 229)) } 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=0.30 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: 4.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 19.150 Check model and map are aligned: 0.260 Set scattering table: 0.140 Process input model: 48.570 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.100 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:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6054 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 : 0.008 0.095 16064 Z= 0.484 Angle : 1.042 15.045 21806 Z= 0.568 Chirality : 0.058 0.386 2499 Planarity : 0.006 0.047 2727 Dihedral : 15.580 118.974 6164 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 22.51 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.62 % Favored : 90.33 % Rotamer: Outliers : 0.89 % Allowed : 7.72 % Favored : 91.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.19 (0.15), residues: 2010 helix: -3.96 (0.12), residues: 688 sheet: -2.34 (0.24), residues: 406 loop : -3.48 (0.17), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 112 HIS 0.008 0.001 HIS C 38 PHE 0.059 0.003 PHE A 305 TYR 0.031 0.003 TYR A 710 ARG 0.010 0.001 ARG A 831 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 180 time to evaluate : 1.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 88 TYR cc_start: 0.5676 (m-80) cc_final: 0.5361 (m-80) REVERT: A 206 PHE cc_start: 0.6256 (t80) cc_final: 0.5800 (t80) REVERT: A 246 LEU cc_start: 0.1126 (OUTLIER) cc_final: 0.0761 (mt) REVERT: A 738 ILE cc_start: 0.8134 (OUTLIER) cc_final: 0.7744 (pt) REVERT: B 95 LYS cc_start: 0.5449 (mmmt) cc_final: 0.4585 (mtmt) outliers start: 15 outliers final: 7 residues processed: 193 average time/residue: 0.3257 time to fit residues: 89.0125 Evaluate side-chains 142 residues out of total 1675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 133 time to evaluate : 1.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 192 SER Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 738 ILE Chi-restraints excluded: chain A residue 739 PHE Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 747 LYS Chi-restraints excluded: chain A residue 1019 SER Chi-restraints excluded: chain A residue 1065 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 168 optimal weight: 20.0000 chunk 150 optimal weight: 9.9990 chunk 83 optimal weight: 9.9990 chunk 51 optimal weight: 0.9980 chunk 101 optimal weight: 0.7980 chunk 80 optimal weight: 3.9990 chunk 155 optimal weight: 7.9990 chunk 60 optimal weight: 0.7980 chunk 94 optimal weight: 0.0670 chunk 116 optimal weight: 0.7980 chunk 180 optimal weight: 9.9990 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 85 GLN E 108 GLN A 151 GLN A 280 GLN A 332 ASN A 400 HIS A 537 GLN A 748 GLN A 837 GLN A 838 ASN A 841 ASN A 935 HIS A1033 ASN A1111 GLN ** A1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1152 ASN A1238 ASN B 4 GLN ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 GLN ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 42 GLN C 80 ASN C 87 ASN C 106 ASN C 175 ASN ** C 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5846 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16064 Z= 0.176 Angle : 0.638 8.531 21806 Z= 0.329 Chirality : 0.043 0.170 2499 Planarity : 0.005 0.078 2727 Dihedral : 8.880 83.176 2690 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 1.78 % Allowed : 12.12 % Favored : 86.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.29 (0.17), residues: 2010 helix: -1.85 (0.17), residues: 701 sheet: -1.82 (0.24), residues: 415 loop : -2.55 (0.19), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP E 106 HIS 0.003 0.001 HIS C 38 PHE 0.026 0.002 PHE A 732 TYR 0.017 0.002 TYR A 119 ARG 0.005 0.001 ARG A 494 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 153 time to evaluate : 1.726 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 154 PHE cc_start: 0.6464 (t80) cc_final: 0.6242 (t80) REVERT: A 206 PHE cc_start: 0.5781 (t80) cc_final: 0.5382 (t80) REVERT: A 552 LYS cc_start: 0.6728 (tppt) cc_final: 0.6348 (mmtm) REVERT: A 738 ILE cc_start: 0.7952 (OUTLIER) cc_final: 0.7742 (pt) REVERT: B 95 LYS cc_start: 0.5479 (mmmt) cc_final: 0.4614 (mtmt) REVERT: C 86 MET cc_start: 0.4389 (ptp) cc_final: 0.3958 (ptm) outliers start: 30 outliers final: 15 residues processed: 175 average time/residue: 0.3152 time to fit residues: 82.8299 Evaluate side-chains 139 residues out of total 1675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 123 time to evaluate : 1.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 192 SER Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 203 PHE Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 738 ILE Chi-restraints excluded: chain A residue 739 PHE Chi-restraints excluded: chain A residue 885 ASP Chi-restraints excluded: chain A residue 996 ASP Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 87 TYR Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain C residue 106 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 100 optimal weight: 5.9990 chunk 56 optimal weight: 4.9990 chunk 150 optimal weight: 5.9990 chunk 123 optimal weight: 4.9990 chunk 49 optimal weight: 5.9990 chunk 181 optimal weight: 4.9990 chunk 195 optimal weight: 20.0000 chunk 161 optimal weight: 20.0000 chunk 179 optimal weight: 9.9990 chunk 61 optimal weight: 8.9990 chunk 145 optimal weight: 0.2980 overall best weight: 4.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 7 GLN A 67 HIS A 134 GLN A 272 GLN ** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 332 ASN A 841 ASN ** A 881 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1238 ASN B 90 GLN ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6077 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.080 16064 Z= 0.439 Angle : 0.779 11.137 21806 Z= 0.401 Chirality : 0.049 0.384 2499 Planarity : 0.006 0.084 2727 Dihedral : 9.241 89.300 2682 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 17.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.17 % Favored : 90.83 % Rotamer: Outliers : 3.39 % Allowed : 15.98 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.26 (0.17), residues: 2010 helix: -2.03 (0.17), residues: 701 sheet: -1.51 (0.25), residues: 415 loop : -2.50 (0.19), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP E 106 HIS 0.007 0.001 HIS C 38 PHE 0.032 0.003 PHE A 305 TYR 0.021 0.002 TYR A 249 ARG 0.007 0.001 ARG A 957 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 132 time to evaluate : 1.744 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 71 PHE cc_start: 0.5588 (OUTLIER) cc_final: 0.5193 (m-80) REVERT: A 206 PHE cc_start: 0.6116 (t80) cc_final: 0.5835 (t80) REVERT: A 872 ILE cc_start: 0.8266 (OUTLIER) cc_final: 0.7550 (mt) REVERT: A 895 ILE cc_start: 0.7542 (OUTLIER) cc_final: 0.7100 (mp) REVERT: A 927 TYR cc_start: 0.7382 (t80) cc_final: 0.7114 (t80) REVERT: A 947 PHE cc_start: 0.7575 (OUTLIER) cc_final: 0.6810 (m-80) REVERT: A 1002 LEU cc_start: 0.7861 (OUTLIER) cc_final: 0.7391 (tp) REVERT: B 95 LYS cc_start: 0.5546 (mmmt) cc_final: 0.4636 (mtmt) outliers start: 57 outliers final: 33 residues processed: 176 average time/residue: 0.2589 time to fit residues: 69.8196 Evaluate side-chains 157 residues out of total 1675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 119 time to evaluate : 1.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 71 PHE Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 192 SER Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 203 PHE Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 739 PHE Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 810 THR Chi-restraints excluded: chain A residue 849 SER Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 872 ILE Chi-restraints excluded: chain A residue 885 ASP Chi-restraints excluded: chain A residue 889 LEU Chi-restraints excluded: chain A residue 895 ILE Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 947 PHE Chi-restraints excluded: chain A residue 996 ASP Chi-restraints excluded: chain A residue 1002 LEU Chi-restraints excluded: chain A residue 1043 TYR Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1126 ILE Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 87 TYR Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 162 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 178 optimal weight: 20.0000 chunk 136 optimal weight: 10.0000 chunk 93 optimal weight: 7.9990 chunk 20 optimal weight: 4.9990 chunk 86 optimal weight: 8.9990 chunk 121 optimal weight: 0.7980 chunk 181 optimal weight: 5.9990 chunk 192 optimal weight: 20.0000 chunk 94 optimal weight: 7.9990 chunk 172 optimal weight: 9.9990 chunk 51 optimal weight: 1.9990 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 332 ASN ** A 881 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1214 GLN A1238 ASN C 106 ASN ** C 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6090 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.077 16064 Z= 0.443 Angle : 0.772 10.593 21806 Z= 0.397 Chirality : 0.049 0.242 2499 Planarity : 0.006 0.092 2727 Dihedral : 9.206 87.515 2680 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 17.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.17 % Favored : 90.83 % Rotamer: Outliers : 4.52 % Allowed : 17.83 % Favored : 77.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.13 (0.17), residues: 2010 helix: -2.02 (0.17), residues: 705 sheet: -1.31 (0.25), residues: 399 loop : -2.39 (0.20), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 167 HIS 0.007 0.001 HIS C 38 PHE 0.034 0.003 PHE A 982 TYR 0.021 0.002 TYR A 710 ARG 0.007 0.001 ARG A 957 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 128 time to evaluate : 1.899 Fit side-chains revert: symmetry clash REVERT: E 71 PHE cc_start: 0.5487 (OUTLIER) cc_final: 0.5146 (m-80) REVERT: A 552 LYS cc_start: 0.6780 (tppt) cc_final: 0.6356 (mmtm) REVERT: A 698 LEU cc_start: 0.8375 (OUTLIER) cc_final: 0.8164 (mp) REVERT: A 800 MET cc_start: 0.6805 (ttt) cc_final: 0.6575 (ttt) REVERT: A 872 ILE cc_start: 0.8235 (OUTLIER) cc_final: 0.7523 (mt) REVERT: A 895 ILE cc_start: 0.7551 (OUTLIER) cc_final: 0.7161 (mp) REVERT: A 927 TYR cc_start: 0.7435 (t80) cc_final: 0.7195 (t80) REVERT: A 947 PHE cc_start: 0.7638 (OUTLIER) cc_final: 0.6914 (m-80) REVERT: A 1002 LEU cc_start: 0.7889 (OUTLIER) cc_final: 0.7443 (tp) REVERT: A 1238 ASN cc_start: 0.1188 (OUTLIER) cc_final: -0.0208 (t0) REVERT: B 95 LYS cc_start: 0.5508 (mmmt) cc_final: 0.4666 (mtmt) REVERT: C 86 MET cc_start: 0.3848 (ptp) cc_final: 0.3338 (ptm) outliers start: 76 outliers final: 52 residues processed: 190 average time/residue: 0.2517 time to fit residues: 73.7145 Evaluate side-chains 175 residues out of total 1675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 116 time to evaluate : 1.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 71 PHE Chi-restraints excluded: chain E residue 89 LEU Chi-restraints excluded: chain E residue 109 MET Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 192 SER Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 194 MET Chi-restraints excluded: chain A residue 203 PHE Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 355 ASP Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 623 VAL Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 730 VAL Chi-restraints excluded: chain A residue 738 ILE Chi-restraints excluded: chain A residue 739 PHE Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 799 ASP Chi-restraints excluded: chain A residue 810 THR Chi-restraints excluded: chain A residue 849 SER Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 872 ILE Chi-restraints excluded: chain A residue 885 ASP Chi-restraints excluded: chain A residue 895 ILE Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 917 SER Chi-restraints excluded: chain A residue 947 PHE Chi-restraints excluded: chain A residue 1002 LEU Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1126 ILE Chi-restraints excluded: chain A residue 1138 VAL Chi-restraints excluded: chain A residue 1238 ASN Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 87 TYR Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 106 ASN Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 202 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 160 optimal weight: 20.0000 chunk 109 optimal weight: 0.6980 chunk 2 optimal weight: 40.0000 chunk 143 optimal weight: 0.9990 chunk 79 optimal weight: 10.0000 chunk 164 optimal weight: 5.9990 chunk 132 optimal weight: 3.9990 chunk 0 optimal weight: 30.0000 chunk 98 optimal weight: 0.0270 chunk 172 optimal weight: 8.9990 chunk 48 optimal weight: 0.7980 overall best weight: 1.3042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 332 ASN A 841 ASN ** A1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 161 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5919 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 0.045 16064 Z= 0.201 Angle : 0.609 9.612 21806 Z= 0.312 Chirality : 0.043 0.192 2499 Planarity : 0.004 0.069 2727 Dihedral : 8.292 88.095 2680 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 2.97 % Allowed : 20.14 % Favored : 76.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.26 (0.18), residues: 2010 helix: -0.98 (0.19), residues: 686 sheet: -1.25 (0.25), residues: 424 loop : -1.96 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 167 HIS 0.004 0.001 HIS C 38 PHE 0.034 0.002 PHE A 206 TYR 0.013 0.001 TYR A 919 ARG 0.005 0.000 ARG A 957 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 136 time to evaluate : 1.834 Fit side-chains revert: symmetry clash REVERT: A 552 LYS cc_start: 0.6624 (tppt) cc_final: 0.6221 (mmtm) REVERT: A 563 LEU cc_start: 0.0557 (OUTLIER) cc_final: 0.0319 (tp) REVERT: A 872 ILE cc_start: 0.8183 (pt) cc_final: 0.7511 (mt) REVERT: A 1002 LEU cc_start: 0.7638 (OUTLIER) cc_final: 0.7292 (tp) REVERT: A 1211 LYS cc_start: 0.3466 (mmmt) cc_final: 0.2979 (mmmt) REVERT: B 95 LYS cc_start: 0.5564 (mmmt) cc_final: 0.4717 (mtmt) REVERT: C 86 MET cc_start: 0.3621 (ptp) cc_final: 0.3167 (ptm) outliers start: 50 outliers final: 27 residues processed: 175 average time/residue: 0.2911 time to fit residues: 78.5667 Evaluate side-chains 148 residues out of total 1675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 119 time to evaluate : 1.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 192 SER Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 203 PHE Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 623 VAL Chi-restraints excluded: chain A residue 739 PHE Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 885 ASP Chi-restraints excluded: chain A residue 996 ASP Chi-restraints excluded: chain A residue 1002 LEU Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1126 ILE Chi-restraints excluded: chain A residue 1157 ILE Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 87 TYR Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 202 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 64 optimal weight: 0.8980 chunk 173 optimal weight: 2.9990 chunk 38 optimal weight: 20.0000 chunk 112 optimal weight: 5.9990 chunk 47 optimal weight: 0.8980 chunk 192 optimal weight: 20.0000 chunk 159 optimal weight: 6.9990 chunk 89 optimal weight: 6.9990 chunk 16 optimal weight: 40.0000 chunk 63 optimal weight: 0.9990 chunk 101 optimal weight: 0.9980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 38 GLN ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5906 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 16064 Z= 0.202 Angle : 0.599 9.730 21806 Z= 0.305 Chirality : 0.042 0.192 2499 Planarity : 0.004 0.074 2727 Dihedral : 8.011 89.985 2680 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 3.92 % Allowed : 19.96 % Favored : 76.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.19), residues: 2010 helix: -0.66 (0.19), residues: 693 sheet: -1.02 (0.25), residues: 427 loop : -1.72 (0.21), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 167 HIS 0.004 0.001 HIS C 38 PHE 0.034 0.002 PHE A 206 TYR 0.011 0.001 TYR A 119 ARG 0.005 0.000 ARG A1187 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 130 time to evaluate : 1.788 Fit side-chains revert: symmetry clash REVERT: E 192 SER cc_start: -0.1393 (OUTLIER) cc_final: -0.1853 (t) REVERT: A 552 LYS cc_start: 0.6702 (tppt) cc_final: 0.6383 (mmtm) REVERT: A 563 LEU cc_start: 0.0619 (OUTLIER) cc_final: 0.0368 (tp) REVERT: A 872 ILE cc_start: 0.8182 (OUTLIER) cc_final: 0.7627 (mt) REVERT: A 876 LYS cc_start: 0.4241 (tmmt) cc_final: 0.3390 (mmtt) REVERT: A 895 ILE cc_start: 0.7509 (OUTLIER) cc_final: 0.6973 (mt) REVERT: A 1002 LEU cc_start: 0.7644 (OUTLIER) cc_final: 0.7337 (tp) REVERT: B 95 LYS cc_start: 0.5541 (mmmt) cc_final: 0.4744 (mtmt) outliers start: 66 outliers final: 40 residues processed: 182 average time/residue: 0.2490 time to fit residues: 70.6058 Evaluate side-chains 165 residues out of total 1675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 120 time to evaluate : 1.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 109 MET Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 192 SER Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 203 PHE Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 355 ASP Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain A residue 623 VAL Chi-restraints excluded: chain A residue 707 GLU Chi-restraints excluded: chain A residue 739 PHE Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 810 THR Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 872 ILE Chi-restraints excluded: chain A residue 885 ASP Chi-restraints excluded: chain A residue 895 ILE Chi-restraints excluded: chain A residue 903 ILE Chi-restraints excluded: chain A residue 1002 LEU Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1126 ILE Chi-restraints excluded: chain A residue 1138 VAL Chi-restraints excluded: chain A residue 1157 ILE Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 87 TYR Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 202 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 185 optimal weight: 10.0000 chunk 21 optimal weight: 9.9990 chunk 109 optimal weight: 2.9990 chunk 140 optimal weight: 0.2980 chunk 108 optimal weight: 0.5980 chunk 162 optimal weight: 4.9990 chunk 107 optimal weight: 0.6980 chunk 191 optimal weight: 50.0000 chunk 120 optimal weight: 0.9980 chunk 116 optimal weight: 1.9990 chunk 88 optimal weight: 9.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 168 ASN ** A1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 38 GLN B 90 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5841 moved from start: 0.3113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16064 Z= 0.170 Angle : 0.573 9.978 21806 Z= 0.290 Chirality : 0.041 0.189 2499 Planarity : 0.004 0.065 2727 Dihedral : 7.608 88.797 2680 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 4.04 % Allowed : 20.08 % Favored : 75.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.19), residues: 2010 helix: -0.26 (0.20), residues: 678 sheet: -0.82 (0.25), residues: 425 loop : -1.58 (0.21), residues: 907 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 167 HIS 0.003 0.001 HIS C 38 PHE 0.034 0.001 PHE A 206 TYR 0.014 0.001 TYR D 87 ARG 0.004 0.000 ARG E 110 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 132 time to evaluate : 1.894 Fit side-chains REVERT: D 47 LEU cc_start: 0.5367 (tp) cc_final: 0.5003 (tp) REVERT: E 172 LEU cc_start: 0.1913 (pt) cc_final: 0.1420 (tp) REVERT: E 192 SER cc_start: -0.1367 (OUTLIER) cc_final: -0.1862 (t) REVERT: A 563 LEU cc_start: 0.0649 (OUTLIER) cc_final: 0.0398 (tp) REVERT: A 698 LEU cc_start: 0.8250 (OUTLIER) cc_final: 0.8019 (mp) REVERT: A 872 ILE cc_start: 0.8179 (OUTLIER) cc_final: 0.7634 (mt) REVERT: A 876 LYS cc_start: 0.4148 (tmmt) cc_final: 0.3574 (mmtt) REVERT: A 895 ILE cc_start: 0.7561 (OUTLIER) cc_final: 0.7164 (mp) REVERT: A 947 PHE cc_start: 0.7378 (OUTLIER) cc_final: 0.6489 (m-80) REVERT: A 1002 LEU cc_start: 0.7514 (OUTLIER) cc_final: 0.7283 (tp) REVERT: A 1249 ARG cc_start: 0.2999 (OUTLIER) cc_final: 0.2399 (mmt-90) REVERT: B 95 LYS cc_start: 0.5487 (mmmt) cc_final: 0.4700 (mtmt) outliers start: 68 outliers final: 36 residues processed: 187 average time/residue: 0.2725 time to fit residues: 78.4517 Evaluate side-chains 164 residues out of total 1675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 120 time to evaluate : 1.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 87 TYR Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 109 MET Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 192 SER Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 203 PHE Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 355 ASP Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain A residue 623 VAL Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 707 GLU Chi-restraints excluded: chain A residue 739 PHE Chi-restraints excluded: chain A residue 810 THR Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 872 ILE Chi-restraints excluded: chain A residue 895 ILE Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 947 PHE Chi-restraints excluded: chain A residue 1002 LEU Chi-restraints excluded: chain A residue 1009 MET Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1126 ILE Chi-restraints excluded: chain A residue 1138 VAL Chi-restraints excluded: chain A residue 1157 ILE Chi-restraints excluded: chain A residue 1249 ARG Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 87 TYR Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 202 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 118 optimal weight: 0.9990 chunk 76 optimal weight: 20.0000 chunk 114 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 37 optimal weight: 40.0000 chunk 121 optimal weight: 3.9990 chunk 130 optimal weight: 5.9990 chunk 94 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 150 optimal weight: 20.0000 chunk 174 optimal weight: 9.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 837 GLN A 841 ASN ** A 881 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1179 GLN B 38 GLN C 106 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5983 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 16064 Z= 0.317 Angle : 0.669 10.429 21806 Z= 0.340 Chirality : 0.045 0.220 2499 Planarity : 0.005 0.066 2727 Dihedral : 8.264 86.809 2680 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 15.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 3.57 % Allowed : 20.86 % Favored : 75.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.19), residues: 2010 helix: -0.77 (0.19), residues: 691 sheet: -0.76 (0.25), residues: 418 loop : -1.58 (0.21), residues: 901 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP E 106 HIS 0.005 0.001 HIS C 38 PHE 0.032 0.002 PHE A 154 TYR 0.014 0.002 TYR A1086 ARG 0.010 0.001 ARG A 957 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 128 time to evaluate : 2.476 Fit side-chains REVERT: E 172 LEU cc_start: 0.1640 (pt) cc_final: 0.1139 (tp) REVERT: E 192 SER cc_start: -0.1299 (OUTLIER) cc_final: -0.1803 (t) REVERT: A 552 LYS cc_start: 0.6628 (tppt) cc_final: 0.6340 (mmtm) REVERT: A 563 LEU cc_start: 0.0725 (OUTLIER) cc_final: 0.0462 (tp) REVERT: A 698 LEU cc_start: 0.8322 (OUTLIER) cc_final: 0.8067 (mp) REVERT: A 872 ILE cc_start: 0.8279 (OUTLIER) cc_final: 0.7631 (mt) REVERT: A 876 LYS cc_start: 0.4246 (tmmt) cc_final: 0.3447 (mmtt) REVERT: A 895 ILE cc_start: 0.7516 (OUTLIER) cc_final: 0.6981 (mt) REVERT: A 947 PHE cc_start: 0.7497 (OUTLIER) cc_final: 0.6736 (m-80) REVERT: A 1002 LEU cc_start: 0.7769 (OUTLIER) cc_final: 0.7375 (tp) REVERT: A 1137 ARG cc_start: 0.6500 (ptm-80) cc_final: 0.6196 (ttp80) REVERT: A 1249 ARG cc_start: 0.2983 (OUTLIER) cc_final: 0.2764 (mmt-90) REVERT: B 95 LYS cc_start: 0.5589 (mmmt) cc_final: 0.4718 (mtmt) REVERT: C 86 MET cc_start: 0.3864 (ptp) cc_final: 0.3033 (ptm) outliers start: 60 outliers final: 42 residues processed: 175 average time/residue: 0.2807 time to fit residues: 74.6549 Evaluate side-chains 165 residues out of total 1675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 115 time to evaluate : 1.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 87 TYR Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 109 MET Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 192 SER Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 203 PHE Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 707 GLU Chi-restraints excluded: chain A residue 810 THR Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 872 ILE Chi-restraints excluded: chain A residue 895 ILE Chi-restraints excluded: chain A residue 903 ILE Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 947 PHE Chi-restraints excluded: chain A residue 1002 LEU Chi-restraints excluded: chain A residue 1009 MET Chi-restraints excluded: chain A residue 1043 TYR Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1126 ILE Chi-restraints excluded: chain A residue 1138 VAL Chi-restraints excluded: chain A residue 1157 ILE Chi-restraints excluded: chain A residue 1249 ARG Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 87 TYR Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 106 ASN Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 202 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 183 optimal weight: 9.9990 chunk 167 optimal weight: 50.0000 chunk 178 optimal weight: 5.9990 chunk 107 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 140 optimal weight: 4.9990 chunk 54 optimal weight: 0.6980 chunk 161 optimal weight: 20.0000 chunk 169 optimal weight: 9.9990 chunk 117 optimal weight: 3.9990 chunk 189 optimal weight: 0.9980 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 400 HIS A 837 GLN ** A 881 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 902 ASN ** A1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 38 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5936 moved from start: 0.3131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 16064 Z= 0.247 Angle : 0.630 10.519 21806 Z= 0.317 Chirality : 0.043 0.204 2499 Planarity : 0.004 0.055 2727 Dihedral : 8.070 87.867 2678 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 3.68 % Allowed : 21.27 % Favored : 75.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.19), residues: 2010 helix: -0.64 (0.19), residues: 697 sheet: -0.80 (0.25), residues: 436 loop : -1.56 (0.21), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 123 HIS 0.004 0.001 HIS C 38 PHE 0.031 0.002 PHE A 982 TYR 0.012 0.001 TYR A 365 ARG 0.009 0.000 ARG A 957 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 120 time to evaluate : 1.793 Fit side-chains REVERT: E 172 LEU cc_start: 0.1647 (pt) cc_final: 0.1071 (tp) REVERT: E 192 SER cc_start: -0.1333 (OUTLIER) cc_final: -0.1820 (t) REVERT: A 552 LYS cc_start: 0.6636 (tppt) cc_final: 0.6312 (mmtm) REVERT: A 563 LEU cc_start: 0.0685 (OUTLIER) cc_final: 0.0408 (tp) REVERT: A 698 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.8030 (mp) REVERT: A 872 ILE cc_start: 0.8254 (OUTLIER) cc_final: 0.7557 (mt) REVERT: A 876 LYS cc_start: 0.4136 (tmmt) cc_final: 0.3355 (mmtt) REVERT: A 895 ILE cc_start: 0.7582 (OUTLIER) cc_final: 0.7027 (mt) REVERT: A 947 PHE cc_start: 0.7454 (OUTLIER) cc_final: 0.6557 (m-80) REVERT: A 1002 LEU cc_start: 0.7718 (OUTLIER) cc_final: 0.7316 (tp) REVERT: A 1137 ARG cc_start: 0.6543 (ptm-80) cc_final: 0.6255 (ttp80) REVERT: A 1249 ARG cc_start: 0.2948 (OUTLIER) cc_final: 0.2737 (mmt-90) REVERT: B 95 LYS cc_start: 0.5517 (mmmt) cc_final: 0.4661 (mtmt) REVERT: C 89 LEU cc_start: 0.4300 (OUTLIER) cc_final: 0.4092 (tp) outliers start: 62 outliers final: 48 residues processed: 167 average time/residue: 0.2735 time to fit residues: 70.2072 Evaluate side-chains 173 residues out of total 1675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 116 time to evaluate : 1.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 87 TYR Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 106 TRP Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 192 SER Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 203 PHE Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 355 ASP Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain A residue 623 VAL Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 707 GLU Chi-restraints excluded: chain A residue 739 PHE Chi-restraints excluded: chain A residue 810 THR Chi-restraints excluded: chain A residue 849 SER Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 872 ILE Chi-restraints excluded: chain A residue 895 ILE Chi-restraints excluded: chain A residue 903 ILE Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 917 SER Chi-restraints excluded: chain A residue 947 PHE Chi-restraints excluded: chain A residue 1002 LEU Chi-restraints excluded: chain A residue 1009 MET Chi-restraints excluded: chain A residue 1010 LEU Chi-restraints excluded: chain A residue 1043 TYR Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1126 ILE Chi-restraints excluded: chain A residue 1138 VAL Chi-restraints excluded: chain A residue 1157 ILE Chi-restraints excluded: chain A residue 1225 THR Chi-restraints excluded: chain A residue 1249 ARG Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 87 TYR Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 202 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 115 optimal weight: 0.6980 chunk 89 optimal weight: 10.0000 chunk 131 optimal weight: 2.9990 chunk 198 optimal weight: 30.0000 chunk 182 optimal weight: 6.9990 chunk 157 optimal weight: 0.7980 chunk 16 optimal weight: 6.9990 chunk 121 optimal weight: 4.9990 chunk 96 optimal weight: 30.0000 chunk 125 optimal weight: 0.6980 chunk 168 optimal weight: 20.0000 overall best weight: 2.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 400 HIS A 837 GLN ** A 881 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 38 GLN C 106 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5943 moved from start: 0.3206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 16064 Z= 0.255 Angle : 0.638 10.806 21806 Z= 0.320 Chirality : 0.043 0.207 2499 Planarity : 0.004 0.048 2727 Dihedral : 8.125 87.146 2678 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 3.62 % Allowed : 21.39 % Favored : 74.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.19), residues: 2010 helix: -0.64 (0.19), residues: 697 sheet: -0.76 (0.25), residues: 432 loop : -1.55 (0.21), residues: 881 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 123 HIS 0.005 0.001 HIS C 38 PHE 0.040 0.002 PHE A 154 TYR 0.017 0.002 TYR E 115 ARG 0.009 0.000 ARG A 957 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 120 time to evaluate : 1.556 Fit side-chains REVERT: E 172 LEU cc_start: 0.1627 (pt) cc_final: 0.1023 (tp) REVERT: E 192 SER cc_start: -0.1260 (OUTLIER) cc_final: -0.1735 (t) REVERT: A 552 LYS cc_start: 0.6643 (tppt) cc_final: 0.6435 (mmtm) REVERT: A 563 LEU cc_start: 0.0671 (OUTLIER) cc_final: 0.0351 (tp) REVERT: A 698 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.8041 (mp) REVERT: A 872 ILE cc_start: 0.8287 (OUTLIER) cc_final: 0.7549 (mt) REVERT: A 876 LYS cc_start: 0.4124 (tmmt) cc_final: 0.3400 (mmtt) REVERT: A 895 ILE cc_start: 0.7604 (OUTLIER) cc_final: 0.7042 (mt) REVERT: A 947 PHE cc_start: 0.7464 (OUTLIER) cc_final: 0.6589 (m-80) REVERT: A 1002 LEU cc_start: 0.7722 (OUTLIER) cc_final: 0.7317 (tp) REVERT: A 1137 ARG cc_start: 0.6547 (ptm-80) cc_final: 0.6265 (ttp80) REVERT: A 1249 ARG cc_start: 0.2949 (OUTLIER) cc_final: 0.2738 (mmt-90) REVERT: B 95 LYS cc_start: 0.5536 (mmmt) cc_final: 0.4685 (mtmt) REVERT: C 86 MET cc_start: 0.3942 (ptp) cc_final: 0.2984 (ptm) REVERT: C 89 LEU cc_start: 0.4439 (OUTLIER) cc_final: 0.4052 (tp) outliers start: 61 outliers final: 47 residues processed: 168 average time/residue: 0.2604 time to fit residues: 67.8219 Evaluate side-chains 173 residues out of total 1675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 117 time to evaluate : 1.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 87 TYR Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 106 TRP Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 192 SER Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 203 PHE Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain A residue 623 VAL Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 707 GLU Chi-restraints excluded: chain A residue 739 PHE Chi-restraints excluded: chain A residue 810 THR Chi-restraints excluded: chain A residue 849 SER Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 872 ILE Chi-restraints excluded: chain A residue 895 ILE Chi-restraints excluded: chain A residue 903 ILE Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 917 SER Chi-restraints excluded: chain A residue 947 PHE Chi-restraints excluded: chain A residue 1002 LEU Chi-restraints excluded: chain A residue 1009 MET Chi-restraints excluded: chain A residue 1010 LEU Chi-restraints excluded: chain A residue 1043 TYR Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1126 ILE Chi-restraints excluded: chain A residue 1138 VAL Chi-restraints excluded: chain A residue 1157 ILE Chi-restraints excluded: chain A residue 1225 THR Chi-restraints excluded: chain A residue 1249 ARG Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 87 TYR Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 106 ASN Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 202 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 48 optimal weight: 1.9990 chunk 145 optimal weight: 5.9990 chunk 23 optimal weight: 6.9990 chunk 43 optimal weight: 2.9990 chunk 158 optimal weight: 9.9990 chunk 66 optimal weight: 0.9980 chunk 162 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 chunk 29 optimal weight: 7.9990 chunk 138 optimal weight: 0.0470 chunk 9 optimal weight: 4.9990 overall best weight: 2.2084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 400 HIS ** A 881 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 38 GLN ** C 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5016 r_free = 0.5016 target = 0.257884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4870 r_free = 0.4870 target = 0.240764 restraints weight = 36370.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4843 r_free = 0.4843 target = 0.238336 restraints weight = 50189.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4825 r_free = 0.4825 target = 0.236333 restraints weight = 33316.018| |-----------------------------------------------------------------------------| r_work (final): 0.4906 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4906 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4906 r_free = 0.4906 target_work(ls_wunit_k1) = 0.244 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4905 r_free = 0.4905 target_work(ls_wunit_k1) = 0.244 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| r_final: 0.4905 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5714 moved from start: 0.3232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 16064 Z= 0.268 Angle : 0.647 10.752 21806 Z= 0.324 Chirality : 0.044 0.209 2499 Planarity : 0.004 0.046 2727 Dihedral : 8.170 88.388 2678 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 3.62 % Allowed : 21.33 % Favored : 75.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.19), residues: 2010 helix: -0.64 (0.19), residues: 693 sheet: -0.78 (0.25), residues: 438 loop : -1.51 (0.21), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 123 HIS 0.005 0.001 HIS C 38 PHE 0.039 0.002 PHE A 154 TYR 0.014 0.002 TYR E 115 ARG 0.009 0.001 ARG A 957 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3894.91 seconds wall clock time: 71 minutes 23.55 seconds (4283.55 seconds total)