Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 28 01:19:35 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5g06_3366/04_2023/5g06_3366.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5g06_3366/04_2023/5g06_3366.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5g06_3366/04_2023/5g06_3366.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5g06_3366/04_2023/5g06_3366.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5g06_3366/04_2023/5g06_3366.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5g06_3366/04_2023/5g06_3366.pdb" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.001 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 130 5.16 5 C 16865 2.51 5 N 4641 2.21 5 O 5158 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C GLU 339": "OE1" <-> "OE2" Residue "E PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 263": "OE1" <-> "OE2" Residue "F ASP 219": "OD1" <-> "OD2" Residue "G GLU 135": "OE1" <-> "OE2" Residue "H ASP 64": "OD1" <-> "OD2" Residue "I TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 216": "OD1" <-> "OD2" Residue "I PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 189": "OD1" <-> "OD2" Residue "J PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 668": "OD1" <-> "OD2" Residue "J TYR 832": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 933": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 26794 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 2350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2350 Classifications: {'peptide': 302} Link IDs: {'PTRANS': 10, 'TRANS': 291} Chain: "B" Number of atoms: 1890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1890 Classifications: {'peptide': 240} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 232} Chain: "C" Number of atoms: 2622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2622 Classifications: {'peptide': 335} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 14, 'TRANS': 319} Chain breaks: 3 Chain: "D" Number of atoms: 1707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1707 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 213} Chain: "E" Number of atoms: 2048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2048 Classifications: {'peptide': 265} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 250} Chain: "F" Number of atoms: 1627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1627 Classifications: {'peptide': 211} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 205} Chain breaks: 2 Chain: "G" Number of atoms: 1831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1831 Classifications: {'peptide': 236} Link IDs: {'PTRANS': 11, 'TRANS': 224} Chain: "H" Number of atoms: 2277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2277 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 8, 'TRANS': 284} Chain breaks: 2 Chain: "I" Number of atoms: 1750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1750 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 10, 'TRANS': 216} Chain breaks: 3 Chain: "J" Number of atoms: 7942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 993, 7942 Classifications: {'peptide': 993} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 50, 'TRANS': 941} Chain: "P" Number of atoms: 750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 750 Classifications: {'peptide': 95} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 87} Time building chain proxies: 12.87, per 1000 atoms: 0.48 Number of scatterers: 26794 At special positions: 0 Unit cell: (155.478, 142.413, 138.493, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 130 16.00 O 5158 8.00 N 4641 7.00 C 16865 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS I 3 " - pdb=" SG CYS I 66 " distance=2.04 Simple disulfide: pdb=" SG CYS J 52 " - pdb=" SG CYS J 55 " distance=2.02 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: 10.25 Conformation dependent library (CDL) restraints added in 4.3 seconds 6756 Ramachandran restraints generated. 3378 Oldfield, 0 Emsley, 3378 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6472 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 44 sheets defined 31.5% alpha, 27.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.66 Creating SS restraints... Processing helix chain 'A' and resid 8 through 21 removed outlier: 3.590A pdb=" N LEU A 16 " --> pdb=" O SER A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 113 Processing helix chain 'A' and resid 120 through 122 No H-bonds generated for 'chain 'A' and resid 120 through 122' Processing helix chain 'A' and resid 146 through 162 Processing helix chain 'A' and resid 205 through 211 removed outlier: 4.182A pdb=" N LYS A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 231 Processing helix chain 'A' and resid 257 through 291 removed outlier: 3.553A pdb=" N GLU A 273 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS A 274 " --> pdb=" O SER A 270 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LYS A 289 " --> pdb=" O GLU A 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 65 removed outlier: 3.583A pdb=" N GLN B 64 " --> pdb=" O LEU B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 112 removed outlier: 3.506A pdb=" N ARG B 106 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS B 110 " --> pdb=" O ARG B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 151 removed outlier: 4.189A pdb=" N ILE B 140 " --> pdb=" O MET B 136 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASN B 141 " --> pdb=" O GLY B 137 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE B 143 " --> pdb=" O LEU B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 180 Processing helix chain 'B' and resid 209 through 239 removed outlier: 3.605A pdb=" N VAL B 213 " --> pdb=" O ARG B 209 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE B 216 " --> pdb=" O ASN B 212 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N HIS B 222 " --> pdb=" O ILE B 218 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG B 223 " --> pdb=" O ALA B 219 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL B 224 " --> pdb=" O GLY B 220 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LEU B 227 " --> pdb=" O ARG B 223 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N MET B 228 " --> pdb=" O VAL B 224 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS B 238 " --> pdb=" O LYS B 234 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG B 239 " --> pdb=" O HIS B 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 26 Processing helix chain 'C' and resid 26 through 37 removed outlier: 4.245A pdb=" N LEU C 37 " --> pdb=" O ARG C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 64 removed outlier: 4.347A pdb=" N ASP C 64 " --> pdb=" O ARG C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 126 Processing helix chain 'C' and resid 145 through 163 removed outlier: 3.511A pdb=" N ILE C 151 " --> pdb=" O GLU C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 170 Processing helix chain 'C' and resid 226 through 239 removed outlier: 3.831A pdb=" N TYR C 236 " --> pdb=" O ASN C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 254 removed outlier: 3.530A pdb=" N ASP C 254 " --> pdb=" O ARG C 251 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 251 through 254' Processing helix chain 'C' and resid 336 through 343 removed outlier: 3.522A pdb=" N SER C 342 " --> pdb=" O ALA C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 392 removed outlier: 4.150A pdb=" N ILE C 374 " --> pdb=" O THR C 370 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU C 379 " --> pdb=" O LYS C 375 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG C 382 " --> pdb=" O LEU C 378 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 41 removed outlier: 3.583A pdb=" N GLU D 41 " --> pdb=" O ALA D 38 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 78 removed outlier: 3.503A pdb=" N VAL D 65 " --> pdb=" O THR D 61 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL D 73 " --> pdb=" O LYS D 69 " (cutoff:3.500A) Proline residue: D 76 - end of helix Processing helix chain 'D' and resid 79 through 83 removed outlier: 3.822A pdb=" N TYR D 83 " --> pdb=" O ARG D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 124 Processing helix chain 'D' and resid 150 through 156 removed outlier: 3.578A pdb=" N ILE D 156 " --> pdb=" O GLU D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 218 removed outlier: 3.555A pdb=" N SER D 193 " --> pdb=" O ASP D 189 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLN D 200 " --> pdb=" O GLU D 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 17 removed outlier: 3.527A pdb=" N SER E 17 " --> pdb=" O ASP E 13 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 103 removed outlier: 3.507A pdb=" N GLU E 93 " --> pdb=" O ALA E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 150 Processing helix chain 'E' and resid 202 through 207 Processing helix chain 'E' and resid 240 through 264 removed outlier: 3.530A pdb=" N LEU E 244 " --> pdb=" O LYS E 240 " (cutoff:3.500A) Proline residue: E 256 - end of helix removed outlier: 3.814A pdb=" N ASN E 264 " --> pdb=" O ARG E 260 " (cutoff:3.500A) Processing helix chain 'F' and resid 106 through 125 removed outlier: 3.746A pdb=" N SER F 123 " --> pdb=" O GLY F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 165 through 167 No H-bonds generated for 'chain 'F' and resid 165 through 167' Processing helix chain 'F' and resid 168 through 184 Processing helix chain 'F' and resid 222 through 245 removed outlier: 3.684A pdb=" N GLU F 232 " --> pdb=" O ASP F 228 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ASP F 239 " --> pdb=" O ASN F 235 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LEU F 240 " --> pdb=" O ARG F 236 " (cutoff:3.500A) Processing helix chain 'G' and resid 159 through 169 Processing helix chain 'G' and resid 173 through 182 removed outlier: 3.869A pdb=" N ALA G 180 " --> pdb=" O LYS G 176 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N HIS G 181 " --> pdb=" O VAL G 177 " (cutoff:3.500A) Processing helix chain 'G' and resid 200 through 218 removed outlier: 3.503A pdb=" N LYS G 217 " --> pdb=" O GLU G 213 " (cutoff:3.500A) Processing helix chain 'G' and resid 221 through 234 removed outlier: 4.057A pdb=" N ASP G 225 " --> pdb=" O ALA G 221 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS G 228 " --> pdb=" O LYS G 224 " (cutoff:3.500A) Processing helix chain 'H' and resid 139 through 141 No H-bonds generated for 'chain 'H' and resid 139 through 141' Processing helix chain 'H' and resid 155 through 163 removed outlier: 3.850A pdb=" N PHE H 162 " --> pdb=" O GLN H 158 " (cutoff:3.500A) Processing helix chain 'H' and resid 237 through 241 Processing helix chain 'H' and resid 290 through 310 Processing helix chain 'H' and resid 315 through 326 removed outlier: 3.586A pdb=" N ILE H 319 " --> pdb=" O THR H 315 " (cutoff:3.500A) Processing helix chain 'H' and resid 327 through 329 No H-bonds generated for 'chain 'H' and resid 327 through 329' Processing helix chain 'H' and resid 331 through 335 Processing helix chain 'H' and resid 337 through 356 Processing helix chain 'I' and resid 208 through 210 No H-bonds generated for 'chain 'I' and resid 208 through 210' Processing helix chain 'I' and resid 219 through 223 Processing helix chain 'I' and resid 259 through 263 Processing helix chain 'J' and resid 54 through 59 removed outlier: 3.658A pdb=" N ILE J 58 " --> pdb=" O LYS J 54 " (cutoff:3.500A) Processing helix chain 'J' and resid 91 through 98 removed outlier: 3.536A pdb=" N VAL J 95 " --> pdb=" O ASP J 91 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU J 96 " --> pdb=" O THR J 92 " (cutoff:3.500A) Processing helix chain 'J' and resid 98 through 104 Processing helix chain 'J' and resid 115 through 125 removed outlier: 3.646A pdb=" N GLU J 120 " --> pdb=" O ILE J 116 " (cutoff:3.500A) Processing helix chain 'J' and resid 125 through 138 removed outlier: 3.515A pdb=" N TYR J 129 " --> pdb=" O SER J 125 " (cutoff:3.500A) Processing helix chain 'J' and resid 165 through 185 removed outlier: 3.858A pdb=" N ARG J 169 " --> pdb=" O THR J 165 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ILE J 174 " --> pdb=" O ASN J 170 " (cutoff:3.500A) Processing helix chain 'J' and resid 186 through 189 Processing helix chain 'J' and resid 198 through 208 Processing helix chain 'J' and resid 218 through 225 removed outlier: 3.614A pdb=" N LEU J 224 " --> pdb=" O GLN J 220 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU J 225 " --> pdb=" O TYR J 221 " (cutoff:3.500A) Processing helix chain 'J' and resid 260 through 270 Processing helix chain 'J' and resid 303 through 308 removed outlier: 3.936A pdb=" N ASN J 308 " --> pdb=" O GLN J 304 " (cutoff:3.500A) Processing helix chain 'J' and resid 366 through 381 Processing helix chain 'J' and resid 440 through 446 removed outlier: 4.409A pdb=" N ASP J 446 " --> pdb=" O ALA J 442 " (cutoff:3.500A) Processing helix chain 'J' and resid 476 through 488 Processing helix chain 'J' and resid 496 through 502 removed outlier: 3.840A pdb=" N GLU J 501 " --> pdb=" O LYS J 497 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N CYS J 502 " --> pdb=" O LYS J 498 " (cutoff:3.500A) Processing helix chain 'J' and resid 520 through 525 Processing helix chain 'J' and resid 526 through 531 removed outlier: 4.411A pdb=" N THR J 529 " --> pdb=" O PRO J 526 " (cutoff:3.500A) Processing helix chain 'J' and resid 581 through 591 Processing helix chain 'J' and resid 605 through 611 Processing helix chain 'J' and resid 654 through 663 Processing helix chain 'J' and resid 668 through 693 removed outlier: 3.899A pdb=" N VAL J 682 " --> pdb=" O LEU J 678 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N LYS J 683 " --> pdb=" O LYS J 679 " (cutoff:3.500A) Processing helix chain 'J' and resid 698 through 703 Processing helix chain 'J' and resid 721 through 746 removed outlier: 3.523A pdb=" N VAL J 727 " --> pdb=" O THR J 723 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLU J 728 " --> pdb=" O ASN J 724 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLU J 729 " --> pdb=" O SER J 725 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N PHE J 730 " --> pdb=" O LEU J 726 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N MET J 731 " --> pdb=" O VAL J 727 " (cutoff:3.500A) Processing helix chain 'J' and resid 759 through 775 Processing helix chain 'J' and resid 782 through 792 Processing helix chain 'J' and resid 800 through 813 Processing helix chain 'J' and resid 825 through 829 removed outlier: 3.503A pdb=" N PHE J 829 " --> pdb=" O TYR J 826 " (cutoff:3.500A) Processing helix chain 'J' and resid 848 through 862 removed outlier: 3.624A pdb=" N VAL J 852 " --> pdb=" O ARG J 848 " (cutoff:3.500A) Processing helix chain 'J' and resid 868 through 872 Processing helix chain 'J' and resid 873 through 911 removed outlier: 3.632A pdb=" N MET J 877 " --> pdb=" O ASP J 873 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ILE J 880 " --> pdb=" O LYS J 876 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE J 899 " --> pdb=" O GLY J 895 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N TYR J 902 " --> pdb=" O SER J 898 " (cutoff:3.500A) Processing helix chain 'J' and resid 940 through 944 Processing helix chain 'P' and resid 2 through 20 removed outlier: 3.766A pdb=" N SER P 19 " --> pdb=" O LYS P 15 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N THR P 20 " --> pdb=" O ASN P 16 " (cutoff:3.500A) Processing helix chain 'P' and resid 31 through 37 removed outlier: 3.784A pdb=" N LYS P 35 " --> pdb=" O PHE P 31 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N HIS P 37 " --> pdb=" O SER P 33 " (cutoff:3.500A) Processing helix chain 'P' and resid 53 through 64 removed outlier: 3.821A pdb=" N VAL P 57 " --> pdb=" O THR P 53 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ALA P 58 " --> pdb=" O THR P 54 " (cutoff:3.500A) Processing helix chain 'P' and resid 64 through 72 removed outlier: 4.589A pdb=" N ASP P 68 " --> pdb=" O ARG P 64 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE P 71 " --> pdb=" O PRO P 67 " (cutoff:3.500A) Processing helix chain 'P' and resid 76 through 95 removed outlier: 3.515A pdb=" N ASN P 85 " --> pdb=" O GLU P 81 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LYS P 89 " --> pdb=" O ASN P 85 " (cutoff:3.500A) Proline residue: P 92 - end of helix Processing sheet with id= AA, first strand: chain 'A' and resid 36 through 40 removed outlier: 6.231A pdb=" N LYS A 55 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 8.295A pdb=" N TRP A 132 " --> pdb=" O ILE A 125 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'A' and resid 36 through 40 removed outlier: 6.231A pdb=" N LYS A 55 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU A 76 " --> pdb=" O TRP A 132 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'A' and resid 124 through 126 removed outlier: 7.460A pdb=" N LYS A 130 " --> pdb=" O CYS A 124 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N TRP A 132 " --> pdb=" O VAL A 126 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'A' and resid 163 through 164 Processing sheet with id= AE, first strand: chain 'A' and resid 167 through 170 Processing sheet with id= AF, first strand: chain 'A' and resid 218 through 221 removed outlier: 3.520A pdb=" N LEU A 239 " --> pdb=" O ILE A 194 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N THR A 236 " --> pdb=" O VAL A 248 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N VAL A 248 " --> pdb=" O THR A 236 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N THR A 238 " --> pdb=" O VAL A 246 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'A' and resid 301 through 302 Processing sheet with id= BA, first strand: chain 'B' and resid 25 through 29 removed outlier: 7.365A pdb=" N ILE B 49 " --> pdb=" O LEU B 129 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N LEU B 129 " --> pdb=" O ILE B 49 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N THR B 51 " --> pdb=" O HIS B 127 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N HIS B 127 " --> pdb=" O THR B 51 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N VAL B 53 " --> pdb=" O GLU B 125 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N GLU B 125 " --> pdb=" O VAL B 53 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N GLY B 55 " --> pdb=" O ASP B 123 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N ASP B 123 " --> pdb=" O GLY B 55 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'B' and resid 169 through 172 removed outlier: 8.374A pdb=" N THR B 184 " --> pdb=" O VAL B 201 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N VAL B 201 " --> pdb=" O THR B 184 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N THR B 186 " --> pdb=" O LEU B 199 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N LEU B 199 " --> pdb=" O THR B 186 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N GLY B 188 " --> pdb=" O SER B 197 " (cutoff:3.500A) Processing sheet with id= CA, first strand: chain 'C' and resid 53 through 56 removed outlier: 3.663A pdb=" N GLY C 76 " --> pdb=" O ILE C 91 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE C 86 " --> pdb=" O LEU C 220 " (cutoff:3.500A) Processing sheet with id= CB, first strand: chain 'C' and resid 96 through 97 Processing sheet with id= CC, first strand: chain 'C' and resid 185 through 188 removed outlier: 3.575A pdb=" N GLY C 175 " --> pdb=" O ALA C 246 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE C 248 " --> pdb=" O GLY C 175 " (cutoff:3.500A) removed outlier: 11.012A pdb=" N LEU C 243 " --> pdb=" O THR C 279 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N THR C 279 " --> pdb=" O LEU C 243 " (cutoff:3.500A) Processing sheet with id= CD, first strand: chain 'C' and resid 255 through 257 removed outlier: 3.901A pdb=" N LEU C 255 " --> pdb=" O THR C 271 " (cutoff:3.500A) Processing sheet with id= CE, first strand: chain 'C' and resid 329 through 332 removed outlier: 3.812A pdb=" N ILE C 349 " --> pdb=" O SER C 295 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ILE C 347 " --> pdb=" O TYR C 297 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N SER C 345 " --> pdb=" O ILE C 299 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N THR C 346 " --> pdb=" O LEU C 362 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N LEU C 362 " --> pdb=" O THR C 346 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N SER C 348 " --> pdb=" O LEU C 360 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N LEU C 360 " --> pdb=" O SER C 348 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N LEU C 350 " --> pdb=" O LYS C 358 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N LYS C 358 " --> pdb=" O GLY D 184 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLY D 184 " --> pdb=" O LYS C 358 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N LEU D 178 " --> pdb=" O GLY C 364 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N LYS D 175 " --> pdb=" O VAL D 168 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N VAL D 168 " --> pdb=" O LYS D 175 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N VAL D 177 " --> pdb=" O GLU D 166 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N GLU D 166 " --> pdb=" O VAL D 177 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N ASP D 185 " --> pdb=" O LEU D 158 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N LEU D 158 " --> pdb=" O ASP D 185 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER D 159 " --> pdb=" O ILE D 138 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU D 163 " --> pdb=" O ILE D 134 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE D 134 " --> pdb=" O LEU D 163 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU D 165 " --> pdb=" O ALA D 132 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ALA D 132 " --> pdb=" O LEU D 165 " (cutoff:3.500A) Processing sheet with id= DA, first strand: chain 'D' and resid 3 through 7 removed outlier: 7.051A pdb=" N VAL D 26 " --> pdb=" O LEU D 95 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N LEU D 95 " --> pdb=" O VAL D 26 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N CYS D 28 " --> pdb=" O GLN D 93 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N GLN D 93 " --> pdb=" O CYS D 28 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N VAL D 30 " --> pdb=" O THR D 91 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N THR D 91 " --> pdb=" O VAL D 30 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N GLY D 32 " --> pdb=" O GLN D 89 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N GLN D 89 " --> pdb=" O GLY D 32 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU D 49 " --> pdb=" O CYS D 88 " (cutoff:3.500A) Processing sheet with id= EA, first strand: chain 'E' and resid 76 through 82 Processing sheet with id= EB, first strand: chain 'E' and resid 115 through 117 removed outlier: 9.337A pdb=" N PHE E 122 " --> pdb=" O LEU E 116 " (cutoff:3.500A) Processing sheet with id= HA, first strand: chain 'H' and resid 7 through 9 removed outlier: 3.665A pdb=" N ILE E 36 " --> pdb=" O THR H 8 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N GLU E 57 " --> pdb=" O ILE E 131 " (cutoff:3.500A) removed outlier: 9.337A pdb=" N PHE E 122 " --> pdb=" O LEU E 116 " (cutoff:3.500A) Processing sheet with id= HB, first strand: chain 'H' and resid 7 through 9 removed outlier: 3.665A pdb=" N ILE E 36 " --> pdb=" O THR H 8 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N GLU E 57 " --> pdb=" O ILE E 131 " (cutoff:3.500A) Processing sheet with id= EC, first strand: chain 'E' and resid 153 through 157 removed outlier: 8.698A pdb=" N LEU E 154 " --> pdb=" O TYR E 175 " (cutoff:3.500A) removed outlier: 9.024A pdb=" N TYR E 175 " --> pdb=" O LEU E 154 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N LYS E 156 " --> pdb=" O HIS E 173 " (cutoff:3.500A) Processing sheet with id= ED, first strand: chain 'E' and resid 196 through 199 removed outlier: 3.707A pdb=" N ASN E 211 " --> pdb=" O VAL E 192 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N GLY E 212 " --> pdb=" O ARG E 227 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N ARG E 227 " --> pdb=" O GLY E 212 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N ILE E 214 " --> pdb=" O PRO E 225 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N SER E 216 " --> pdb=" O THR E 223 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N PHE F 213 " --> pdb=" O SER E 228 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N ILE F 210 " --> pdb=" O ILE F 204 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N ILE F 204 " --> pdb=" O ILE F 210 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY F 212 " --> pdb=" O SER F 202 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY F 192 " --> pdb=" O PHE F 203 " (cutoff:3.500A) Processing sheet with id= FA, first strand: chain 'F' and resid 45 through 50 removed outlier: 3.798A pdb=" N GLY F 58 " --> pdb=" O VAL F 77 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N HIS F 69 " --> pdb=" O ASP F 146 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ASP F 146 " --> pdb=" O HIS F 69 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N THR F 71 " --> pdb=" O ASP F 144 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ASP F 144 " --> pdb=" O THR F 71 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N LEU F 73 " --> pdb=" O THR F 142 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N THR F 142 " --> pdb=" O LEU F 73 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N SER F 75 " --> pdb=" O TYR F 140 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N TYR F 140 " --> pdb=" O SER F 75 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N VAL F 77 " --> pdb=" O PHE F 138 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N PHE F 138 " --> pdb=" O VAL F 77 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N GLY F 79 " --> pdb=" O ASP F 136 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N ASP F 136 " --> pdb=" O GLY F 79 " (cutoff:3.500A) Processing sheet with id= GA, first strand: chain 'G' and resid 2 through 5 Processing sheet with id= GB, first strand: chain 'G' and resid 25 through 27 Processing sheet with id= GC, first strand: chain 'G' and resid 71 through 79 removed outlier: 6.773A pdb=" N GLU G 133 " --> pdb=" O CYS G 124 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N SER G 98 " --> pdb=" O ILE G 134 " (cutoff:3.500A) Processing sheet with id= GD, first strand: chain 'G' and resid 154 through 157 removed outlier: 3.540A pdb=" N VAL G 196 " --> pdb=" O MET G 154 " (cutoff:3.500A) Processing sheet with id= HC, first strand: chain 'H' and resid 75 through 76 Processing sheet with id= HD, first strand: chain 'H' and resid 86 through 91 Processing sheet with id= HE, first strand: chain 'H' and resid 111 through 119 removed outlier: 7.586A pdb=" N SER H 183 " --> pdb=" O VAL H 173 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N HIS H 185 " --> pdb=" O SER H 175 " (cutoff:3.500A) removed outlier: 12.618A pdb=" N ALA H 182 " --> pdb=" O MET H 137 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N MET H 137 " --> pdb=" O ALA H 182 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N VAL H 135 " --> pdb=" O LEU H 184 " (cutoff:3.500A) Processing sheet with id= HF, first strand: chain 'H' and resid 197 through 201 removed outlier: 3.700A pdb=" N ILE H 221 " --> pdb=" O LEU H 217 " (cutoff:3.500A) Processing sheet with id= IA, first strand: chain 'I' and resid 10 through 11 removed outlier: 3.555A pdb=" N THR I 63 " --> pdb=" O LEU I 111 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU I 111 " --> pdb=" O THR I 63 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER I 109 " --> pdb=" O ARG I 65 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLU I 67 " --> pdb=" O LEU I 107 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LYS I 104 " --> pdb=" O ILE I 32 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASN I 34 " --> pdb=" O LYS I 104 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE I 106 " --> pdb=" O ASN I 34 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL I 36 " --> pdb=" O ILE I 106 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU I 24 " --> pdb=" O ILE I 31 " (cutoff:3.500A) Processing sheet with id= IB, first strand: chain 'I' and resid 16 through 19 removed outlier: 7.035A pdb=" N ILE I 56 " --> pdb=" O ILE I 17 " (cutoff:3.500A) removed outlier: 8.653A pdb=" N GLU I 54 " --> pdb=" O PRO I 19 " (cutoff:3.500A) Processing sheet with id= IC, first strand: chain 'I' and resid 138 through 146 removed outlier: 6.879A pdb=" N TYR I 244 " --> pdb=" O GLN I 233 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N THR I 246 " --> pdb=" O LEU I 235 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N ILE I 204 " --> pdb=" O LEU I 245 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 150 through 158 current: chain 'I' and resid 138 through 146 Processing sheet with id= ID, first strand: chain 'I' and resid 269 through 271 removed outlier: 6.422A pdb=" N MET I 274 " --> pdb=" O THR I 270 " (cutoff:3.500A) Processing sheet with id= JA, first strand: chain 'J' and resid 11 through 14 removed outlier: 7.071A pdb=" N LEU J 17 " --> pdb=" O LEU J 13 " (cutoff:3.500A) Processing sheet with id= JB, first strand: chain 'J' and resid 78 through 79 removed outlier: 6.696A pdb=" N HIS J 86 " --> pdb=" O LEU J 79 " (cutoff:3.500A) Processing sheet with id= JC, first strand: chain 'J' and resid 144 through 148 removed outlier: 5.767A pdb=" N ASP J 110 " --> pdb=" O HIS J 86 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ILE J 214 " --> pdb=" O VAL J 192 " (cutoff:3.500A) Processing sheet with id= JD, first strand: chain 'J' and resid 144 through 148 removed outlier: 5.767A pdb=" N ASP J 110 " --> pdb=" O HIS J 86 " (cutoff:3.500A) Processing sheet with id= JE, first strand: chain 'J' and resid 274 through 280 removed outlier: 7.211A pdb=" N GLN J 315 " --> pdb=" O ILE J 395 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N ILE J 395 " --> pdb=" O GLN J 315 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ILE J 317 " --> pdb=" O VAL J 393 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N VAL J 302 " --> pdb=" O ALA J 390 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N VAL J 392 " --> pdb=" O VAL J 302 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER J 291 " --> pdb=" O ASN J 277 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ASN J 277 " --> pdb=" O SER J 291 " (cutoff:3.500A) Processing sheet with id= JF, first strand: chain 'J' and resid 403 through 407 removed outlier: 4.849A pdb=" N LEU J 407 " --> pdb=" O LYS J 447 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N LYS J 447 " --> pdb=" O LEU J 407 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N ARG J 448 " --> pdb=" O ASP J 470 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N ASP J 470 " --> pdb=" O ARG J 448 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N VAL J 450 " --> pdb=" O VAL J 468 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N LEU J 464 " --> pdb=" O ASP J 454 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N ARG J 437 " --> pdb=" O GLY J 465 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N PHE J 467 " --> pdb=" O ARG J 437 " (cutoff:3.500A) Processing sheet with id= JG, first strand: chain 'J' and resid 532 through 533 removed outlier: 3.968A pdb=" N ASN J 638 " --> pdb=" O GLU J 629 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N SER J 648 " --> pdb=" O VAL J 619 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N VAL J 619 " --> pdb=" O SER J 648 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N ASP J 552 " --> pdb=" O ILE J 542 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ILE J 542 " --> pdb=" O ASP J 552 " (cutoff:3.500A) Processing sheet with id= JH, first strand: chain 'J' and resid 751 through 754 Processing sheet with id= JI, first strand: chain 'J' and resid 936 through 939 removed outlier: 6.766A pdb=" N VAL J 927 " --> pdb=" O ILE J 919 " (cutoff:3.500A) Processing sheet with id= JJ, first strand: chain 'J' and resid 952 through 954 1154 hydrogen bonds defined for protein. 3216 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.86 Time building geometry restraints manager: 10.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.31: 4834 1.31 - 1.46: 9304 1.46 - 1.61: 12755 1.61 - 1.77: 164 1.77 - 1.92: 176 Bond restraints: 27233 Sorted by residual: bond pdb=" CA GLY I 265 " pdb=" C GLY I 265 " ideal model delta sigma weight residual 1.516 1.418 0.099 8.90e-03 1.26e+04 1.23e+02 bond pdb=" N VAL J 113 " pdb=" CA VAL J 113 " ideal model delta sigma weight residual 1.460 1.378 0.082 7.60e-03 1.73e+04 1.18e+02 bond pdb=" CA LYS A 130 " pdb=" C LYS A 130 " ideal model delta sigma weight residual 1.520 1.391 0.129 1.22e-02 6.72e+03 1.12e+02 bond pdb=" CA GLY B 188 " pdb=" C GLY B 188 " ideal model delta sigma weight residual 1.513 1.404 0.108 1.03e-02 9.43e+03 1.11e+02 bond pdb=" CA GLY C 298 " pdb=" C GLY C 298 " ideal model delta sigma weight residual 1.510 1.394 0.116 1.11e-02 8.12e+03 1.10e+02 ... (remaining 27228 not shown) Histogram of bond angle deviations from ideal: 83.49 - 94.35: 18 94.35 - 105.21: 2007 105.21 - 116.07: 16219 116.07 - 126.93: 17474 126.93 - 137.79: 1128 Bond angle restraints: 36846 Sorted by residual: angle pdb=" CA PHE J 641 " pdb=" CB PHE J 641 " pdb=" CG PHE J 641 " ideal model delta sigma weight residual 113.80 99.54 14.26 1.00e+00 1.00e+00 2.03e+02 angle pdb=" CA LEU J 225 " pdb=" C LEU J 225 " pdb=" O LEU J 225 " ideal model delta sigma weight residual 119.75 108.32 11.43 9.40e-01 1.13e+00 1.48e+02 angle pdb=" N ASP B 132 " pdb=" CA ASP B 132 " pdb=" C ASP B 132 " ideal model delta sigma weight residual 112.03 96.52 15.51 1.31e+00 5.83e-01 1.40e+02 angle pdb=" CA LEU A 254 " pdb=" C LEU A 254 " pdb=" N PRO A 255 " ideal model delta sigma weight residual 118.85 129.76 -10.91 9.50e-01 1.11e+00 1.32e+02 angle pdb=" CA LEU J 225 " pdb=" C LEU J 225 " pdb=" N PRO J 226 " ideal model delta sigma weight residual 118.87 129.20 -10.33 9.00e-01 1.23e+00 1.32e+02 ... (remaining 36841 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.29: 15231 19.29 - 38.58: 1102 38.58 - 57.87: 241 57.87 - 77.16: 114 77.16 - 96.45: 69 Dihedral angle restraints: 16757 sinusoidal: 6794 harmonic: 9963 Sorted by residual: dihedral pdb=" C ILE C 12 " pdb=" N ILE C 12 " pdb=" CA ILE C 12 " pdb=" CB ILE C 12 " ideal model delta harmonic sigma weight residual -122.00 -151.11 29.11 0 2.50e+00 1.60e-01 1.36e+02 dihedral pdb=" N ILE C 12 " pdb=" C ILE C 12 " pdb=" CA ILE C 12 " pdb=" CB ILE C 12 " ideal model delta harmonic sigma weight residual 123.40 147.06 -23.66 0 2.50e+00 1.60e-01 8.96e+01 dihedral pdb=" N ALA J 634 " pdb=" C ALA J 634 " pdb=" CA ALA J 634 " pdb=" CB ALA J 634 " ideal model delta harmonic sigma weight residual 122.90 145.13 -22.23 0 2.50e+00 1.60e-01 7.91e+01 ... (remaining 16754 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.213: 3004 0.213 - 0.426: 1107 0.426 - 0.638: 143 0.638 - 0.851: 16 0.851 - 1.064: 1 Chirality restraints: 4271 Sorted by residual: chirality pdb=" CA ILE C 12 " pdb=" N ILE C 12 " pdb=" C ILE C 12 " pdb=" CB ILE C 12 " both_signs ideal model delta sigma weight residual False 2.43 1.37 1.06 2.00e-01 2.50e+01 2.83e+01 chirality pdb=" CA ALA J 634 " pdb=" N ALA J 634 " pdb=" C ALA J 634 " pdb=" CB ALA J 634 " both_signs ideal model delta sigma weight residual False 2.48 1.64 0.84 2.00e-01 2.50e+01 1.77e+01 chirality pdb=" CA LEU J 48 " pdb=" N LEU J 48 " pdb=" C LEU J 48 " pdb=" CB LEU J 48 " both_signs ideal model delta sigma weight residual False 2.51 1.71 0.80 2.00e-01 2.50e+01 1.62e+01 ... (remaining 4268 not shown) Planarity restraints: 4773 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR I 21 " 0.168 2.00e-02 2.50e+03 1.30e-01 3.35e+02 pdb=" CG TYR I 21 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 TYR I 21 " -0.062 2.00e-02 2.50e+03 pdb=" CD2 TYR I 21 " -0.099 2.00e-02 2.50e+03 pdb=" CE1 TYR I 21 " -0.140 2.00e-02 2.50e+03 pdb=" CE2 TYR I 21 " -0.083 2.00e-02 2.50e+03 pdb=" CZ TYR I 21 " -0.065 2.00e-02 2.50e+03 pdb=" OH TYR I 21 " 0.245 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP J 180 " -0.232 2.00e-02 2.50e+03 1.15e-01 3.33e+02 pdb=" CG TRP J 180 " 0.077 2.00e-02 2.50e+03 pdb=" CD1 TRP J 180 " 0.083 2.00e-02 2.50e+03 pdb=" CD2 TRP J 180 " 0.080 2.00e-02 2.50e+03 pdb=" NE1 TRP J 180 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP J 180 " 0.051 2.00e-02 2.50e+03 pdb=" CE3 TRP J 180 " 0.134 2.00e-02 2.50e+03 pdb=" CZ2 TRP J 180 " -0.095 2.00e-02 2.50e+03 pdb=" CZ3 TRP J 180 " 0.068 2.00e-02 2.50e+03 pdb=" CH2 TRP J 180 " -0.161 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR J 221 " 0.141 2.00e-02 2.50e+03 1.08e-01 2.34e+02 pdb=" CG TYR J 221 " 0.006 2.00e-02 2.50e+03 pdb=" CD1 TYR J 221 " -0.044 2.00e-02 2.50e+03 pdb=" CD2 TYR J 221 " -0.041 2.00e-02 2.50e+03 pdb=" CE1 TYR J 221 " -0.090 2.00e-02 2.50e+03 pdb=" CE2 TYR J 221 " -0.129 2.00e-02 2.50e+03 pdb=" CZ TYR J 221 " -0.050 2.00e-02 2.50e+03 pdb=" OH TYR J 221 " 0.207 2.00e-02 2.50e+03 ... (remaining 4770 not shown) Histogram of nonbonded interaction distances: 1.19 - 1.93: 11 1.93 - 2.67: 1398 2.67 - 3.42: 32699 3.42 - 4.16: 64893 4.16 - 4.90: 113998 Nonbonded interactions: 212999 Sorted by model distance: nonbonded pdb=" OE2 GLU C 48 " pdb=" CB ASN P 49 " model vdw 1.189 3.440 nonbonded pdb=" CD2 TRP I 272 " pdb=" NZ LYS P 82 " model vdw 1.318 3.340 nonbonded pdb=" CD GLU C 48 " pdb=" CB ASN P 49 " model vdw 1.410 3.670 nonbonded pdb=" CD LYS C 81 " pdb=" CD LYS P 35 " model vdw 1.485 3.840 nonbonded pdb=" N LEU I 16 " pdb=" NZ LYS P 15 " model vdw 1.542 3.200 ... (remaining 212994 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.280 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: 0.020 Extract box with map and model: 3.910 Check model and map are aligned: 0.420 Set scattering table: 0.260 Process input model: 66.750 Find NCS groups from input model: 0.900 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: 0.010 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4815 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 : 0.036 0.151 27233 Z= 2.347 Angle : 3.534 17.412 36846 Z= 2.392 Chirality : 0.208 1.064 4271 Planarity : 0.029 0.366 4773 Dihedral : 17.027 96.449 10279 Min Nonbonded Distance : 1.189 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 1.87 % Allowed : 5.86 % Favored : 92.27 % Rotamer Outliers : 3.01 % Cbeta Deviations : 7.60 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.06 % Twisted Proline : 0.69 % Twisted General : 0.12 % 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: -2.39 (0.12), residues: 3378 helix: -0.80 (0.15), residues: 927 sheet: -0.35 (0.19), residues: 656 loop : -2.59 (0.12), residues: 1795 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6756 Ramachandran restraints generated. 3378 Oldfield, 0 Emsley, 3378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6756 Ramachandran restraints generated. 3378 Oldfield, 0 Emsley, 3378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1074 residues out of total 3020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 983 time to evaluate : 3.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 91 outliers final: 13 residues processed: 1056 average time/residue: 0.4467 time to fit residues: 707.7626 Evaluate side-chains 459 residues out of total 3020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 446 time to evaluate : 3.124 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.3909 time to fit residues: 12.1156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 285 optimal weight: 5.9990 chunk 256 optimal weight: 9.9990 chunk 142 optimal weight: 10.0000 chunk 87 optimal weight: 5.9990 chunk 172 optimal weight: 5.9990 chunk 136 optimal weight: 7.9990 chunk 264 optimal weight: 6.9990 chunk 102 optimal weight: 5.9990 chunk 161 optimal weight: 6.9990 chunk 197 optimal weight: 9.9990 chunk 306 optimal weight: 10.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 215 ASN ** A 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 247 GLN A 291 ASN B 20 ASN ** B 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 ASN ** C 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 114 ASN D 208 ASN ** E 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 GLN E 150 ASN E 173 HIS E 195 ASN E 196 ASN E 204 ASN E 210 ASN F 99 ASN F 235 ASN G 53 GLN H 53 GLN H 92 ASN ** H 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 285 ASN H 302 ASN ** H 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 6 GLN ** I 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 277 ASN J 279 GLN J 284 ASN J 406 GLN J 420 GLN J 460 HIS J 478 GLN J 555 HIS J 569 HIS J 667 ASN ** J 755 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 771 ASN J 923 ASN ** P 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 16 ASN P 49 ASN P 85 ASN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5441 moved from start: 0.4995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.081 27233 Z= 0.373 Angle : 0.837 9.903 36846 Z= 0.451 Chirality : 0.048 0.224 4271 Planarity : 0.007 0.095 4773 Dihedral : 6.382 55.135 3690 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 16.45 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.52 % Favored : 96.27 % Rotamer Outliers : 0.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.06 % 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: -1.00 (0.13), residues: 3378 helix: 0.76 (0.16), residues: 973 sheet: 0.12 (0.19), residues: 688 loop : -1.91 (0.13), residues: 1717 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6756 Ramachandran restraints generated. 3378 Oldfield, 0 Emsley, 3378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6756 Ramachandran restraints generated. 3378 Oldfield, 0 Emsley, 3378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 3020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 512 time to evaluate : 3.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 2 residues processed: 520 average time/residue: 0.4394 time to fit residues: 348.0269 Evaluate side-chains 328 residues out of total 3020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 326 time to evaluate : 3.270 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2516 time to fit residues: 5.4937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 170 optimal weight: 20.0000 chunk 95 optimal weight: 8.9990 chunk 255 optimal weight: 30.0000 chunk 209 optimal weight: 4.9990 chunk 84 optimal weight: 10.0000 chunk 307 optimal weight: 20.0000 chunk 332 optimal weight: 20.0000 chunk 273 optimal weight: 20.0000 chunk 304 optimal weight: 7.9990 chunk 104 optimal weight: 6.9990 chunk 246 optimal weight: 9.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 GLN ** A 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 247 GLN ** B 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 GLN ** C 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 ASN C 359 GLN D 4 GLN D 45 GLN D 81 HIS D 86 GLN ** D 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 216 ASN ** E 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 69 HIS ** F 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 174 GLN H 213 HIS H 295 GLN ** I 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 130 ASN J 97 GLN J 323 GLN J 466 HIS ** J 755 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 767 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 771 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 841 HIS ** P 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5752 moved from start: 0.6540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.123 27233 Z= 0.402 Angle : 0.828 14.207 36846 Z= 0.444 Chirality : 0.048 0.219 4271 Planarity : 0.006 0.087 4773 Dihedral : 6.218 52.073 3690 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 24.11 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.26 % Favored : 95.59 % Rotamer Outliers : 0.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.06 % 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: -0.98 (0.14), residues: 3378 helix: 0.45 (0.16), residues: 981 sheet: -0.09 (0.18), residues: 710 loop : -1.60 (0.14), residues: 1687 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6756 Ramachandran restraints generated. 3378 Oldfield, 0 Emsley, 3378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6756 Ramachandran restraints generated. 3378 Oldfield, 0 Emsley, 3378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 3020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 433 time to evaluate : 3.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 1 residues processed: 441 average time/residue: 0.4263 time to fit residues: 289.7542 Evaluate side-chains 307 residues out of total 3020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 306 time to evaluate : 3.543 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2992 time to fit residues: 5.2866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 303 optimal weight: 9.9990 chunk 231 optimal weight: 8.9990 chunk 159 optimal weight: 7.9990 chunk 34 optimal weight: 10.0000 chunk 146 optimal weight: 6.9990 chunk 206 optimal weight: 6.9990 chunk 308 optimal weight: 0.7980 chunk 326 optimal weight: 7.9990 chunk 161 optimal weight: 3.9990 chunk 292 optimal weight: 7.9990 chunk 88 optimal weight: 6.9990 overall best weight: 5.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 247 GLN ** B 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 208 ASN ** E 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 171 HIS ** G 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 185 HIS ** H 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 213 HIS J 21 GLN J 149 HIS J 170 ASN J 771 ASN J 888 HIS ** P 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5723 moved from start: 0.7001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.067 27233 Z= 0.294 Angle : 0.691 10.130 36846 Z= 0.369 Chirality : 0.045 0.197 4271 Planarity : 0.005 0.055 4773 Dihedral : 5.695 51.197 3690 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 20.63 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.79 % Favored : 96.06 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.06 % 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: -0.74 (0.14), residues: 3378 helix: 0.73 (0.16), residues: 987 sheet: -0.07 (0.19), residues: 669 loop : -1.42 (0.14), residues: 1722 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6756 Ramachandran restraints generated. 3378 Oldfield, 0 Emsley, 3378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6756 Ramachandran restraints generated. 3378 Oldfield, 0 Emsley, 3378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 3020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 424 time to evaluate : 3.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 424 average time/residue: 0.4165 time to fit residues: 276.4484 Evaluate side-chains 294 residues out of total 3020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 294 time to evaluate : 3.200 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.4001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 272 optimal weight: 6.9990 chunk 185 optimal weight: 4.9990 chunk 4 optimal weight: 5.9990 chunk 243 optimal weight: 8.9990 chunk 134 optimal weight: 5.9990 chunk 278 optimal weight: 7.9990 chunk 225 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 166 optimal weight: 0.0670 chunk 293 optimal weight: 5.9990 chunk 82 optimal weight: 9.9990 overall best weight: 4.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN ** A 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 GLN ** C 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 197 ASN G 53 GLN ** G 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 203 ASN ** G 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 174 GLN ** H 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 213 HIS J 149 HIS J 191 ASN ** J 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 713 ASN ** J 755 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 771 ASN ** P 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5738 moved from start: 0.7406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.069 27233 Z= 0.267 Angle : 0.654 9.939 36846 Z= 0.349 Chirality : 0.045 0.187 4271 Planarity : 0.005 0.043 4773 Dihedral : 5.479 48.911 3690 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 20.63 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.38 % Favored : 95.47 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.06 % 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: -0.65 (0.14), residues: 3378 helix: 0.83 (0.16), residues: 982 sheet: -0.06 (0.19), residues: 691 loop : -1.36 (0.14), residues: 1705 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6756 Ramachandran restraints generated. 3378 Oldfield, 0 Emsley, 3378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6756 Ramachandran restraints generated. 3378 Oldfield, 0 Emsley, 3378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 3020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 413 time to evaluate : 3.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 415 average time/residue: 0.4326 time to fit residues: 280.0392 Evaluate side-chains 300 residues out of total 3020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 299 time to evaluate : 3.313 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2497 time to fit residues: 4.9596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 109 optimal weight: 5.9990 chunk 294 optimal weight: 30.0000 chunk 64 optimal weight: 2.9990 chunk 191 optimal weight: 1.9990 chunk 80 optimal weight: 0.3980 chunk 327 optimal weight: 30.0000 chunk 271 optimal weight: 0.0570 chunk 151 optimal weight: 9.9990 chunk 27 optimal weight: 5.9990 chunk 108 optimal weight: 0.9990 chunk 171 optimal weight: 5.9990 overall best weight: 1.2904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 HIS A 247 GLN ** B 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 77 ASN ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 57 ASN D 4 GLN ** E 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 197 ASN G 53 GLN ** G 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 111 HIS H 196 ASN H 213 HIS H 279 GLN J 171 ASN J 201 ASN J 338 HIS J 841 HIS ** P 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5603 moved from start: 0.7464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 27233 Z= 0.168 Angle : 0.605 9.860 36846 Z= 0.316 Chirality : 0.045 0.200 4271 Planarity : 0.004 0.037 4773 Dihedral : 5.061 45.525 3690 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.20 % Favored : 96.65 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.06 % 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: -0.42 (0.14), residues: 3378 helix: 1.14 (0.17), residues: 969 sheet: -0.00 (0.19), residues: 679 loop : -1.23 (0.14), residues: 1730 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6756 Ramachandran restraints generated. 3378 Oldfield, 0 Emsley, 3378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6756 Ramachandran restraints generated. 3378 Oldfield, 0 Emsley, 3378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 3020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 416 time to evaluate : 3.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 417 average time/residue: 0.3943 time to fit residues: 261.6804 Evaluate side-chains 283 residues out of total 3020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 283 time to evaluate : 3.323 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.5193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 315 optimal weight: 0.0470 chunk 36 optimal weight: 6.9990 chunk 186 optimal weight: 10.0000 chunk 238 optimal weight: 3.9990 chunk 185 optimal weight: 10.0000 chunk 275 optimal weight: 20.0000 chunk 182 optimal weight: 2.9990 chunk 325 optimal weight: 3.9990 chunk 203 optimal weight: 2.9990 chunk 198 optimal weight: 9.9990 chunk 150 optimal weight: 0.5980 overall best weight: 2.1284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 GLN ** B 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 53 GLN ** G 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 48 HIS J 638 ASN ** P 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5628 moved from start: 0.7673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 27233 Z= 0.181 Angle : 0.599 12.670 36846 Z= 0.314 Chirality : 0.044 0.222 4271 Planarity : 0.004 0.069 4773 Dihedral : 4.883 40.994 3690 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 16.15 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.64 % Favored : 96.18 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.06 % 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: -0.36 (0.14), residues: 3378 helix: 1.19 (0.17), residues: 980 sheet: -0.05 (0.19), residues: 689 loop : -1.17 (0.15), residues: 1709 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6756 Ramachandran restraints generated. 3378 Oldfield, 0 Emsley, 3378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6756 Ramachandran restraints generated. 3378 Oldfield, 0 Emsley, 3378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 3020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 406 time to evaluate : 3.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 406 average time/residue: 0.4096 time to fit residues: 264.0511 Evaluate side-chains 290 residues out of total 3020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 290 time to evaluate : 3.341 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.6411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 201 optimal weight: 4.9990 chunk 130 optimal weight: 6.9990 chunk 194 optimal weight: 10.0000 chunk 98 optimal weight: 6.9990 chunk 64 optimal weight: 9.9990 chunk 63 optimal weight: 1.9990 chunk 207 optimal weight: 10.0000 chunk 221 optimal weight: 2.9990 chunk 161 optimal weight: 30.0000 chunk 30 optimal weight: 0.0570 chunk 256 optimal weight: 8.9990 overall best weight: 3.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 240 ASN ** A 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 32 GLN ** D 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 53 GLN ** G 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 174 GLN ** H 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 361 ASN J 402 GLN ** J 771 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5684 moved from start: 0.7891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.079 27233 Z= 0.220 Angle : 0.614 12.641 36846 Z= 0.323 Chirality : 0.044 0.208 4271 Planarity : 0.004 0.047 4773 Dihedral : 4.980 38.415 3690 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 17.97 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.79 % Favored : 96.09 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.06 % 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: -0.37 (0.14), residues: 3378 helix: 1.20 (0.17), residues: 986 sheet: -0.11 (0.19), residues: 695 loop : -1.18 (0.15), residues: 1697 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6756 Ramachandran restraints generated. 3378 Oldfield, 0 Emsley, 3378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6756 Ramachandran restraints generated. 3378 Oldfield, 0 Emsley, 3378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 3020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 393 time to evaluate : 3.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 394 average time/residue: 0.4158 time to fit residues: 265.4450 Evaluate side-chains 283 residues out of total 3020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 283 time to evaluate : 4.446 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.5125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 296 optimal weight: 6.9990 chunk 312 optimal weight: 20.0000 chunk 284 optimal weight: 7.9990 chunk 303 optimal weight: 5.9990 chunk 182 optimal weight: 10.0000 chunk 132 optimal weight: 8.9990 chunk 238 optimal weight: 5.9990 chunk 93 optimal weight: 0.9990 chunk 274 optimal weight: 7.9990 chunk 287 optimal weight: 9.9990 chunk 302 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 ASN ** D 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 134 HIS ** E 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 53 GLN ** G 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 57 GLN J 284 ASN ** J 767 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 771 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 775 ASN ** J 855 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5795 moved from start: 0.8252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.085 27233 Z= 0.282 Angle : 0.665 12.384 36846 Z= 0.351 Chirality : 0.045 0.264 4271 Planarity : 0.005 0.053 4773 Dihedral : 5.242 37.755 3690 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 21.91 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.97 % Favored : 94.91 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.06 % 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: -0.56 (0.14), residues: 3378 helix: 1.01 (0.17), residues: 986 sheet: -0.32 (0.18), residues: 733 loop : -1.24 (0.15), residues: 1659 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6756 Ramachandran restraints generated. 3378 Oldfield, 0 Emsley, 3378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6756 Ramachandran restraints generated. 3378 Oldfield, 0 Emsley, 3378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 3020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 378 time to evaluate : 3.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 379 average time/residue: 0.4091 time to fit residues: 247.7514 Evaluate side-chains 271 residues out of total 3020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 271 time to evaluate : 3.595 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.7394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 199 optimal weight: 0.2980 chunk 321 optimal weight: 6.9990 chunk 195 optimal weight: 5.9990 chunk 152 optimal weight: 10.0000 chunk 223 optimal weight: 10.0000 chunk 336 optimal weight: 0.1980 chunk 309 optimal weight: 8.9990 chunk 268 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 207 optimal weight: 9.9990 chunk 164 optimal weight: 10.0000 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 247 GLN ** B 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 923 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 924 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5686 moved from start: 0.8303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 27233 Z= 0.195 Angle : 0.621 11.712 36846 Z= 0.324 Chirality : 0.045 0.221 4271 Planarity : 0.004 0.043 4773 Dihedral : 5.003 35.526 3690 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 17.42 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.61 % Favored : 96.27 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.06 % 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: -0.47 (0.14), residues: 3378 helix: 1.09 (0.17), residues: 980 sheet: -0.26 (0.19), residues: 688 loop : -1.16 (0.15), residues: 1710 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6756 Ramachandran restraints generated. 3378 Oldfield, 0 Emsley, 3378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6756 Ramachandran restraints generated. 3378 Oldfield, 0 Emsley, 3378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 3020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 392 time to evaluate : 3.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 392 average time/residue: 0.4167 time to fit residues: 260.1246 Evaluate side-chains 283 residues out of total 3020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 283 time to evaluate : 3.257 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.4464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 212 optimal weight: 30.0000 chunk 285 optimal weight: 6.9990 chunk 82 optimal weight: 5.9990 chunk 247 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 268 optimal weight: 6.9990 chunk 112 optimal weight: 0.9990 chunk 275 optimal weight: 7.9990 chunk 34 optimal weight: 7.9990 chunk 49 optimal weight: 6.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 53 GLN ** G 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 387 GLN ** J 755 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.077422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.059988 restraints weight = 148921.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.062127 restraints weight = 91957.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.063680 restraints weight = 65100.772| |-----------------------------------------------------------------------------| r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.8419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 27233 Z= 0.200 Angle : 0.615 11.513 36846 Z= 0.323 Chirality : 0.045 0.316 4271 Planarity : 0.004 0.044 4773 Dihedral : 4.932 32.529 3690 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 17.88 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.23 % Favored : 95.65 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.06 % 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: -0.47 (0.14), residues: 3378 helix: 1.11 (0.17), residues: 976 sheet: -0.34 (0.19), residues: 701 loop : -1.14 (0.15), residues: 1701 =============================================================================== Job complete usr+sys time: 5809.11 seconds wall clock time: 107 minutes 13.01 seconds (6433.01 seconds total)