Starting phenix.real_space_refine (version: 1.21rc1) on Sun Oct 8 00:22:14 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7niv_12366/10_2023/7niv_12366_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7niv_12366/10_2023/7niv_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_12366/10_2023/7niv_12366.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7niv_12366/10_2023/7niv_12366.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7niv_12366/10_2023/7niv_12366_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7niv_12366/10_2023/7niv_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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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: 9.85, per 1000 atoms: 0.63 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: 6.79 Conformation dependent library (CDL) restraints added in 3.0 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: 3.35 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: 5.26 Time building geometry restraints manager: 7.22 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: 8846 23.80 - 47.59: 601 47.59 - 71.38: 57 71.38 - 95.18: 13 95.18 - 118.97: 1 Dihedral angle restraints: 9518 sinusoidal: 3687 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 9515 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: 6.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 19.910 Check model and map are aligned: 0.230 Set scattering table: 0.140 Process input model: 45.440 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.080 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:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.080 ------------------------------------------------------------------------------- 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 : 15.416 118.974 5762 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 *********************** 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 : 1.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 7 residues processed: 193 average time/residue: 0.3300 time to fit residues: 90.2408 Evaluate side-chains 139 residues out of total 1675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 132 time to evaluate : 1.578 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1769 time to fit residues: 4.3199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0970 chunk 94 optimal weight: 0.0670 chunk 116 optimal weight: 0.7980 chunk 180 optimal weight: 9.9990 overall best weight: 0.5516 ------------------------------------------------------------------------------- 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 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: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5800 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16064 Z= 0.166 Angle : 0.628 8.550 21806 Z= 0.323 Chirality : 0.043 0.171 2499 Planarity : 0.005 0.078 2727 Dihedral : 8.342 111.803 2271 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 1.43 % Allowed : 12.18 % Favored : 86.39 % 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: -3.06 (0.17), residues: 2010 helix: -1.60 (0.18), residues: 695 sheet: -1.79 (0.24), residues: 417 loop : -2.42 (0.20), residues: 898 *********************** 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 180 residues out of total 1675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 156 time to evaluate : 1.767 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 11 residues processed: 173 average time/residue: 0.3320 time to fit residues: 86.0139 Evaluate side-chains 135 residues out of total 1675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 124 time to evaluate : 1.874 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1511 time to fit residues: 5.4627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 150 optimal weight: 6.9990 chunk 123 optimal weight: 0.8980 chunk 49 optimal weight: 5.9990 chunk 181 optimal weight: 4.9990 chunk 195 optimal weight: 50.0000 chunk 161 optimal weight: 20.0000 chunk 179 optimal weight: 10.0000 chunk 61 optimal weight: 5.9990 chunk 145 optimal weight: 0.6980 overall best weight: 3.1186 ------------------------------------------------------------------------------- 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 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 841 ASN ** A1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1238 ASN ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 161 GLN ** 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: 0.6012 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 16064 Z= 0.344 Angle : 0.711 9.875 21806 Z= 0.364 Chirality : 0.046 0.328 2499 Planarity : 0.005 0.062 2727 Dihedral : 8.613 117.861 2271 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 15.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.98 % Favored : 92.02 % Rotamer: Outliers : 2.32 % Allowed : 16.16 % Favored : 81.52 % 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: -2.82 (0.18), residues: 2010 helix: -1.55 (0.18), residues: 689 sheet: -1.41 (0.25), residues: 408 loop : -2.26 (0.20), residues: 913 *********************** 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 167 residues out of total 1675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 128 time to evaluate : 1.703 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 20 residues processed: 155 average time/residue: 0.2701 time to fit residues: 64.4819 Evaluate side-chains 137 residues out of total 1675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 117 time to evaluate : 1.759 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.1477 time to fit residues: 8.0339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 93 optimal weight: 10.0000 chunk 20 optimal weight: 0.0470 chunk 86 optimal weight: 7.9990 chunk 121 optimal weight: 2.9990 chunk 181 optimal weight: 6.9990 chunk 192 optimal weight: 8.9990 chunk 94 optimal weight: 6.9990 chunk 172 optimal weight: 50.0000 chunk 51 optimal weight: 0.5980 overall best weight: 2.3282 ------------------------------------------------------------------------------- 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 902 ASN ** A1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1214 GLN A1238 ASN B 90 GLN C 106 ASN ** C 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5964 moved from start: 0.2335 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= 0.273 Angle : 0.646 9.923 21806 Z= 0.330 Chirality : 0.044 0.209 2499 Planarity : 0.005 0.050 2727 Dihedral : 8.352 115.423 2271 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 2.02 % Allowed : 18.78 % Favored : 79.20 % 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: -2.44 (0.18), residues: 2010 helix: -1.17 (0.19), residues: 689 sheet: -1.40 (0.24), residues: 453 loop : -1.99 (0.21), residues: 868 *********************** 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 164 residues out of total 1675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 130 time to evaluate : 1.787 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 11 residues processed: 157 average time/residue: 0.2695 time to fit residues: 65.4611 Evaluate side-chains 128 residues out of total 1675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 117 time to evaluate : 1.804 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1480 time to fit residues: 5.5633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 2 optimal weight: 40.0000 chunk 143 optimal weight: 3.9990 chunk 79 optimal weight: 5.9990 chunk 164 optimal weight: 0.0060 chunk 132 optimal weight: 0.7980 chunk 0 optimal weight: 30.0000 chunk 98 optimal weight: 7.9990 chunk 172 optimal weight: 50.0000 chunk 48 optimal weight: 3.9990 overall best weight: 2.1602 ------------------------------------------------------------------------------- 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 841 ASN ** A1129 ASN ** 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: 0.5954 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 16064 Z= 0.257 Angle : 0.635 10.307 21806 Z= 0.322 Chirality : 0.044 0.207 2499 Planarity : 0.004 0.051 2727 Dihedral : 8.244 115.981 2271 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 2.14 % Allowed : 19.49 % Favored : 78.37 % 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: -2.08 (0.18), residues: 2010 helix: -0.89 (0.19), residues: 684 sheet: -1.11 (0.24), residues: 434 loop : -1.81 (0.21), residues: 892 *********************** 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 160 residues out of total 1675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 124 time to evaluate : 1.730 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 15 residues processed: 148 average time/residue: 0.2651 time to fit residues: 61.4121 Evaluate side-chains 131 residues out of total 1675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 116 time to evaluate : 1.758 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1466 time to fit residues: 6.5959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 64 optimal weight: 1.9990 chunk 173 optimal weight: 8.9990 chunk 38 optimal weight: 20.0000 chunk 112 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 192 optimal weight: 10.0000 chunk 159 optimal weight: 4.9990 chunk 89 optimal weight: 0.0070 chunk 16 optimal weight: 40.0000 chunk 63 optimal weight: 0.9990 chunk 101 optimal weight: 0.7980 overall best weight: 1.5604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 106 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5905 moved from start: 0.2852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 16064 Z= 0.215 Angle : 0.608 10.059 21806 Z= 0.307 Chirality : 0.043 0.199 2499 Planarity : 0.004 0.052 2727 Dihedral : 8.042 115.439 2271 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 1.66 % Allowed : 20.44 % Favored : 77.90 % 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: -1.77 (0.19), residues: 2010 helix: -0.61 (0.19), residues: 684 sheet: -1.02 (0.24), residues: 439 loop : -1.61 (0.21), residues: 887 *********************** 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 158 residues out of total 1675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 130 time to evaluate : 1.835 Fit side-chains revert: symmetry clash outliers start: 28 outliers final: 9 residues processed: 151 average time/residue: 0.2698 time to fit residues: 63.2704 Evaluate side-chains 128 residues out of total 1675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 119 time to evaluate : 1.641 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1527 time to fit residues: 5.0254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 185 optimal weight: 8.9990 chunk 21 optimal weight: 0.4980 chunk 109 optimal weight: 1.9990 chunk 140 optimal weight: 10.0000 chunk 108 optimal weight: 0.7980 chunk 162 optimal weight: 20.0000 chunk 107 optimal weight: 0.9980 chunk 191 optimal weight: 50.0000 chunk 120 optimal weight: 0.1980 chunk 116 optimal weight: 2.9990 chunk 88 optimal weight: 8.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 168 ASN ** A 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 106 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5835 moved from start: 0.3203 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= 0.169 Angle : 0.576 10.148 21806 Z= 0.289 Chirality : 0.041 0.181 2499 Planarity : 0.004 0.050 2727 Dihedral : 7.712 114.593 2271 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 1.72 % Allowed : 20.32 % Favored : 77.96 % 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: -1.41 (0.19), residues: 2010 helix: -0.14 (0.20), residues: 675 sheet: -0.94 (0.24), residues: 454 loop : -1.47 (0.22), residues: 881 *********************** 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 159 residues out of total 1675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 130 time to evaluate : 1.736 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 10 residues processed: 151 average time/residue: 0.2711 time to fit residues: 64.2381 Evaluate side-chains 133 residues out of total 1675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 123 time to evaluate : 1.863 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1543 time to fit residues: 5.2885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 9.9990 chunk 114 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 37 optimal weight: 6.9990 chunk 121 optimal weight: 5.9990 chunk 130 optimal weight: 1.9990 chunk 94 optimal weight: 0.9990 chunk 17 optimal weight: 50.0000 chunk 150 optimal weight: 10.0000 chunk 174 optimal weight: 7.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 168 ASN A 174 ASN ** 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 C 106 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5962 moved from start: 0.3043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 16064 Z= 0.294 Angle : 0.659 10.155 21806 Z= 0.332 Chirality : 0.045 0.217 2499 Planarity : 0.004 0.047 2727 Dihedral : 8.131 117.050 2271 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 0.89 % Allowed : 21.15 % Favored : 77.96 % 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: -1.59 (0.19), residues: 2010 helix: -0.60 (0.19), residues: 677 sheet: -0.81 (0.25), residues: 438 loop : -1.44 (0.22), residues: 895 *********************** 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 133 residues out of total 1675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 118 time to evaluate : 1.828 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 6 residues processed: 127 average time/residue: 0.2781 time to fit residues: 54.6808 Evaluate side-chains 120 residues out of total 1675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 114 time to evaluate : 1.646 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2127 time to fit residues: 4.5485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 183 optimal weight: 10.0000 chunk 167 optimal weight: 50.0000 chunk 178 optimal weight: 20.0000 chunk 107 optimal weight: 0.7980 chunk 77 optimal weight: 5.9990 chunk 140 optimal weight: 0.0370 chunk 54 optimal weight: 0.8980 chunk 161 optimal weight: 20.0000 chunk 169 optimal weight: 6.9990 chunk 117 optimal weight: 3.9990 chunk 189 optimal weight: 0.2980 overall best weight: 1.2060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 837 GLN ** A1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 106 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5856 moved from start: 0.3386 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= 0.190 Angle : 0.603 10.302 21806 Z= 0.302 Chirality : 0.042 0.189 2499 Planarity : 0.004 0.048 2727 Dihedral : 7.675 114.217 2271 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 0.65 % Allowed : 21.39 % Favored : 77.96 % 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: -1.34 (0.19), residues: 2010 helix: -0.29 (0.20), residues: 690 sheet: -0.76 (0.24), residues: 443 loop : -1.34 (0.22), residues: 877 *********************** 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 131 residues out of total 1675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 120 time to evaluate : 1.761 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 5 residues processed: 125 average time/residue: 0.2761 time to fit residues: 54.5204 Evaluate side-chains 115 residues out of total 1675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 110 time to evaluate : 1.582 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1512 time to fit residues: 3.8264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 115 optimal weight: 0.9990 chunk 89 optimal weight: 10.0000 chunk 131 optimal weight: 0.6980 chunk 198 optimal weight: 20.0000 chunk 182 optimal weight: 10.0000 chunk 157 optimal weight: 9.9990 chunk 16 optimal weight: 30.0000 chunk 121 optimal weight: 0.0670 chunk 96 optimal weight: 20.0000 chunk 125 optimal weight: 0.8980 chunk 168 optimal weight: 6.9990 overall best weight: 1.9322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 174 ASN ** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 837 GLN ** A 881 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5915 moved from start: 0.3348 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= 0.246 Angle : 0.627 10.960 21806 Z= 0.315 Chirality : 0.043 0.204 2499 Planarity : 0.004 0.050 2727 Dihedral : 7.863 116.316 2271 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 0.30 % Allowed : 21.75 % Favored : 77.96 % 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: -1.32 (0.19), residues: 2010 helix: -0.36 (0.20), residues: 684 sheet: -0.68 (0.25), residues: 442 loop : -1.29 (0.22), residues: 884 ********************** 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 117 residues out of total 1675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 112 time to evaluate : 1.799 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 115 average time/residue: 0.2830 time to fit residues: 50.8580 Evaluate side-chains 108 residues out of total 1675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 106 time to evaluate : 1.802 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1656 time to fit residues: 3.1644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 48 optimal weight: 0.7980 chunk 145 optimal weight: 5.9990 chunk 23 optimal weight: 8.9990 chunk 43 optimal weight: 0.8980 chunk 158 optimal weight: 7.9990 chunk 66 optimal weight: 0.8980 chunk 162 optimal weight: 0.0870 chunk 20 optimal weight: 6.9990 chunk 29 optimal weight: 5.9990 chunk 138 optimal weight: 9.9990 chunk 9 optimal weight: 10.0000 overall best weight: 1.7360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 837 GLN A 881 ASN ** A1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 106 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4962 r_free = 0.4962 target = 0.253745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4799 r_free = 0.4799 target = 0.234658 restraints weight = 35999.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4764 r_free = 0.4764 target = 0.231285 restraints weight = 48377.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4751 r_free = 0.4751 target = 0.229754 restraints weight = 46610.050| |-----------------------------------------------------------------------------| r_work (final): 0.4802 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4802 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4802 r_free = 0.4802 target_work(ls_wunit_k1) = 0.234 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4801 r_free = 0.4801 target_work(ls_wunit_k1) = 0.234 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| r_final: 0.4801 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5704 moved from start: 0.3455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 16064 Z= 0.228 Angle : 0.619 11.277 21806 Z= 0.310 Chirality : 0.043 0.200 2499 Planarity : 0.004 0.049 2727 Dihedral : 7.817 115.580 2271 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 0.59 % Allowed : 21.81 % Favored : 77.60 % 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: -1.30 (0.19), residues: 2010 helix: -0.38 (0.20), residues: 691 sheet: -0.62 (0.25), residues: 441 loop : -1.27 (0.22), residues: 878 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3389.74 seconds wall clock time: 62 minutes 50.18 seconds (3770.18 seconds total)