Starting phenix.real_space_refine on Wed Mar 20 07:49:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5g06_3366/03_2024/5g06_3366.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5g06_3366/03_2024/5g06_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_3366/03_2024/5g06_3366.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5g06_3366/03_2024/5g06_3366.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5g06_3366/03_2024/5g06_3366.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5g06_3366/03_2024/5g06_3366.pdb" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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-dev-5265/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: 14.06, per 1000 atoms: 0.52 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: 9.46 Conformation dependent library (CDL) restraints added in 5.3 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: 3.35 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: 11.01 Time building geometry restraints manager: 10.41 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: 0.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.130 Check model and map are aligned: 0.340 Set scattering table: 0.270 Process input model: 70.720 Find NCS groups from input model: 0.920 Set up NCS constraints: 0.090 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:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.410 ------------------------------------------------------------------------------- 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 % Allowed : 8.31 % Favored : 88.68 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.232 0.050 TRP J 180 HIS 0.056 0.018 HIS C 161 PHE 0.165 0.038 PHE E 40 TYR 0.245 0.045 TYR I 21 ARG 0.077 0.012 ARG J 531 *********************** 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 : 3.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 136 MET cc_start: 0.6028 (tpt) cc_final: 0.5783 (tpp) REVERT: B 165 LEU cc_start: 0.6725 (tp) cc_final: 0.6476 (tp) REVERT: B 201 VAL cc_start: 0.7133 (t) cc_final: 0.6744 (t) REVERT: B 228 MET cc_start: 0.4334 (mtp) cc_final: 0.4029 (mtm) REVERT: C 153 GLN cc_start: 0.6389 (tm-30) cc_final: 0.6077 (tm-30) REVERT: D 1 MET cc_start: 0.3335 (ppp) cc_final: 0.2529 (ppp) REVERT: D 9 ILE cc_start: 0.6568 (OUTLIER) cc_final: 0.6164 (mt) REVERT: D 52 VAL cc_start: 0.7493 (t) cc_final: 0.7026 (t) REVERT: E 182 ILE cc_start: 0.6597 (tt) cc_final: 0.6181 (tt) REVERT: F 53 ILE cc_start: 0.5186 (pt) cc_final: 0.4708 (pt) REVERT: F 245 LEU cc_start: 0.7627 (mt) cc_final: 0.7249 (mt) REVERT: G 96 SER cc_start: 0.4557 (OUTLIER) cc_final: 0.3516 (t) REVERT: H 329 TYR cc_start: 0.5148 (m-80) cc_final: 0.4853 (m-10) REVERT: I 53 LEU cc_start: 0.1199 (OUTLIER) cc_final: 0.0959 (tm) REVERT: I 161 LYS cc_start: 0.1978 (OUTLIER) cc_final: 0.1236 (pptt) REVERT: J 231 ILE cc_start: 0.3336 (mt) cc_final: 0.3094 (mp) REVERT: J 326 TRP cc_start: 0.3527 (m-10) cc_final: 0.3252 (m-10) REVERT: J 341 VAL cc_start: 0.6063 (m) cc_final: 0.5535 (p) REVERT: J 411 SER cc_start: 0.5963 (m) cc_final: 0.5323 (t) REVERT: J 870 THR cc_start: 0.6236 (OUTLIER) cc_final: 0.5898 (p) outliers start: 91 outliers final: 13 residues processed: 1056 average time/residue: 0.4345 time to fit residues: 689.0462 Evaluate side-chains 466 residues out of total 3020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 448 time to evaluate : 3.233 ------------------------------------------------------------------------------- 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: 0.7980 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: 5.1588 ------------------------------------------------------------------------------- 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 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 ** D 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 114 ASN D 208 ASN E 85 GLN E 150 ASN E 173 HIS E 195 ASN E 196 ASN E 204 ASN F 99 ASN F 235 ASN G 53 GLN H 53 GLN H 92 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 Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5371 moved from start: 0.4860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 27233 Z= 0.335 Angle : 0.804 9.847 36846 Z= 0.434 Chirality : 0.048 0.216 4271 Planarity : 0.007 0.082 4773 Dihedral : 6.303 55.169 3690 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.32 % Favored : 96.51 % Rotamer: Outliers : 0.26 % Allowed : 4.64 % Favored : 95.10 % 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: -0.94 (0.13), residues: 3378 helix: 0.90 (0.16), residues: 955 sheet: 0.01 (0.18), residues: 706 loop : -1.85 (0.13), residues: 1717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.005 TRP J 628 HIS 0.010 0.002 HIS I 48 PHE 0.031 0.003 PHE G 91 TYR 0.033 0.003 TYR C 272 ARG 0.015 0.001 ARG C 269 *********************** 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 536 residues out of total 3020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 528 time to evaluate : 3.050 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: A 226 LYS cc_start: 0.4938 (ptpt) cc_final: 0.4668 (mttt) REVERT: D 82 CYS cc_start: 0.5533 (t) cc_final: 0.4968 (t) REVERT: G 162 PHE cc_start: 0.5988 (t80) cc_final: 0.5699 (t80) REVERT: H 54 ILE cc_start: 0.5574 (tp) cc_final: 0.5281 (tp) REVERT: I 146 LEU cc_start: 0.8403 (tp) cc_final: 0.7644 (mt) REVERT: I 156 LEU cc_start: 0.6269 (pp) cc_final: 0.5651 (tp) REVERT: J 238 MET cc_start: 0.0676 (tpt) cc_final: -0.0844 (mmm) REVERT: J 411 SER cc_start: 0.6283 (m) cc_final: 0.5870 (t) REVERT: J 552 ASP cc_start: 0.6798 (p0) cc_final: 0.6268 (p0) REVERT: J 853 VAL cc_start: 0.5084 (t) cc_final: 0.4473 (t) outliers start: 8 outliers final: 1 residues processed: 535 average time/residue: 0.4187 time to fit residues: 341.0319 Evaluate side-chains 330 residues out of total 3020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 329 time to evaluate : 2.841 ------------------------------------------------------------------------------- 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: 7.9990 chunk 95 optimal weight: 4.9990 chunk 255 optimal weight: 30.0000 chunk 209 optimal weight: 0.6980 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: 0.7980 chunk 246 optimal weight: 6.9990 overall best weight: 4.2986 ------------------------------------------------------------------------------- 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** ** B 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 GLN ** C 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 ASN D 45 GLN D 81 HIS D 86 GLN D 208 ASN D 216 ASN ** E 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 211 ASN ** 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 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 213 HIS I 45 GLN ** I 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 361 ASN J 466 HIS ** J 755 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 85 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5504 moved from start: 0.5820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 27233 Z= 0.271 Angle : 0.686 13.116 36846 Z= 0.369 Chirality : 0.045 0.252 4271 Planarity : 0.005 0.058 4773 Dihedral : 5.598 50.524 3690 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 16.41 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.43 % Favored : 96.42 % Rotamer: Outliers : 0.03 % Allowed : 3.58 % Favored : 96.39 % 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: -0.58 (0.14), residues: 3378 helix: 1.09 (0.16), residues: 976 sheet: 0.19 (0.19), residues: 681 loop : -1.56 (0.13), residues: 1721 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP J 628 HIS 0.009 0.001 HIS B 34 PHE 0.021 0.002 PHE G 4 TYR 0.024 0.002 TYR G 84 ARG 0.013 0.001 ARG B 3 *********************** 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 457 residues out of total 3020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 456 time to evaluate : 3.026 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: B 140 ILE cc_start: 0.7618 (mt) cc_final: 0.7225 (mt) REVERT: C 146 ASP cc_start: 0.5595 (p0) cc_final: 0.4735 (p0) REVERT: C 362 LEU cc_start: 0.6444 (tp) cc_final: 0.5934 (tp) REVERT: F 110 LEU cc_start: 0.8160 (mt) cc_final: 0.7759 (mt) REVERT: F 128 SER cc_start: 0.7523 (m) cc_final: 0.7265 (p) REVERT: H 113 VAL cc_start: 0.6734 (p) cc_final: 0.6533 (p) REVERT: I 146 LEU cc_start: 0.8260 (tp) cc_final: 0.7770 (mt) REVERT: J 238 MET cc_start: 0.0840 (tpt) cc_final: 0.0194 (mmm) REVERT: J 713 ASN cc_start: 0.7039 (t0) cc_final: 0.6677 (t0) outliers start: 1 outliers final: 0 residues processed: 456 average time/residue: 0.4059 time to fit residues: 288.3083 Evaluate side-chains 320 residues out of total 3020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 320 time to evaluate : 3.179 ------------------------------------------------------------------------------- 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: 7.9990 chunk 231 optimal weight: 2.9990 chunk 159 optimal weight: 4.9990 chunk 34 optimal weight: 9.9990 chunk 146 optimal weight: 6.9990 chunk 206 optimal weight: 3.9990 chunk 308 optimal weight: 7.9990 chunk 326 optimal weight: 5.9990 chunk 161 optimal weight: 20.0000 chunk 292 optimal weight: 0.0270 chunk 88 optimal weight: 6.9990 overall best weight: 3.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 GLN A 177 HIS A 242 ASN ** B 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 GLN C 56 ASN ** E 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 210 ASN ** E 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 53 GLN ** H 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 213 HIS H 295 GLN I 130 ASN J 149 HIS ** J 755 HIS ** 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: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5544 moved from start: 0.6339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 27233 Z= 0.235 Angle : 0.628 13.027 36846 Z= 0.336 Chirality : 0.044 0.196 4271 Planarity : 0.005 0.068 4773 Dihedral : 5.253 48.058 3690 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 16.00 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.14 % Favored : 96.71 % Rotamer: Outliers : 0.07 % Allowed : 3.18 % Favored : 96.75 % 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: -0.38 (0.14), residues: 3378 helix: 1.18 (0.16), residues: 985 sheet: 0.26 (0.19), residues: 682 loop : -1.37 (0.14), residues: 1711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP H 124 HIS 0.008 0.001 HIS J 149 PHE 0.027 0.002 PHE I 256 TYR 0.016 0.001 TYR I 46 ARG 0.007 0.001 ARG D 210 *********************** 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 435 residues out of total 3020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 433 time to evaluate : 3.330 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: B 136 MET cc_start: 0.5554 (tpp) cc_final: 0.5251 (tpp) REVERT: B 140 ILE cc_start: 0.7998 (mt) cc_final: 0.7595 (mt) REVERT: C 146 ASP cc_start: 0.5404 (p0) cc_final: 0.4566 (p0) REVERT: E 1 MET cc_start: 0.2520 (pmm) cc_final: 0.2016 (ppp) REVERT: F 108 ASN cc_start: 0.6274 (m-40) cc_final: 0.6021 (m110) REVERT: F 110 LEU cc_start: 0.8145 (mt) cc_final: 0.7840 (mp) REVERT: G 88 LEU cc_start: 0.6793 (tp) cc_final: 0.6380 (tp) REVERT: I 146 LEU cc_start: 0.8647 (tp) cc_final: 0.8060 (mt) REVERT: J 238 MET cc_start: 0.1047 (tpt) cc_final: 0.0224 (mmm) REVERT: J 674 MET cc_start: 0.3951 (ptp) cc_final: 0.3435 (ptp) outliers start: 2 outliers final: 0 residues processed: 433 average time/residue: 0.4080 time to fit residues: 278.2776 Evaluate side-chains 315 residues out of total 3020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 315 time to evaluate : 3.102 ------------------------------------------------------------------------------- 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: 0.0040 chunk 185 optimal weight: 2.9990 chunk 4 optimal weight: 6.9990 chunk 243 optimal weight: 6.9990 chunk 134 optimal weight: 0.8980 chunk 278 optimal weight: 0.0770 chunk 225 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 166 optimal weight: 0.0570 chunk 293 optimal weight: 20.0000 chunk 82 optimal weight: 9.9990 overall best weight: 0.8070 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 210 ASN ** F 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 53 GLN ** G 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 196 ASN H 213 HIS J 97 GLN ** J 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 171 ASN J 201 ASN ** J 755 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 888 HIS ** P 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5424 moved from start: 0.6545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 27233 Z= 0.161 Angle : 0.586 9.914 36846 Z= 0.307 Chirality : 0.044 0.234 4271 Planarity : 0.004 0.055 4773 Dihedral : 4.836 43.936 3690 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.96 % Favored : 96.89 % Rotamer: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % 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: -0.15 (0.14), residues: 3378 helix: 1.33 (0.17), residues: 971 sheet: 0.23 (0.19), residues: 719 loop : -1.12 (0.14), residues: 1688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP H 124 HIS 0.004 0.001 HIS B 235 PHE 0.024 0.001 PHE D 117 TYR 0.016 0.001 TYR C 189 ARG 0.012 0.000 ARG J 28 *********************** 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 458 residues out of total 3020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 458 time to evaluate : 3.357 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: A 225 LEU cc_start: 0.6862 (pp) cc_final: 0.6651 (pp) REVERT: B 107 MET cc_start: 0.5012 (tpp) cc_final: 0.4719 (tpp) REVERT: B 136 MET cc_start: 0.5405 (tpp) cc_final: 0.5019 (tpp) REVERT: B 140 ILE cc_start: 0.7645 (mt) cc_final: 0.7277 (mt) REVERT: D 82 CYS cc_start: 0.5348 (t) cc_final: 0.4667 (t) REVERT: E 1 MET cc_start: 0.1756 (pmm) cc_final: 0.1080 (tmm) REVERT: E 185 PRO cc_start: 0.6935 (Cg_exo) cc_final: 0.6660 (Cg_endo) REVERT: F 108 ASN cc_start: 0.5643 (m-40) cc_final: 0.5314 (m-40) REVERT: F 110 LEU cc_start: 0.8244 (mt) cc_final: 0.8025 (mp) REVERT: F 174 THR cc_start: 0.8184 (p) cc_final: 0.7781 (p) REVERT: I 146 LEU cc_start: 0.8574 (tp) cc_final: 0.7984 (mt) REVERT: I 156 LEU cc_start: 0.6104 (pp) cc_final: 0.5579 (tp) REVERT: J 238 MET cc_start: 0.0923 (tpt) cc_final: 0.0246 (mmm) REVERT: J 411 SER cc_start: 0.7072 (m) cc_final: 0.5987 (t) REVERT: J 674 MET cc_start: 0.3798 (ptp) cc_final: 0.3467 (ptp) REVERT: J 853 VAL cc_start: 0.5283 (t) cc_final: 0.4474 (t) REVERT: P 12 LYS cc_start: 0.2060 (mmmt) cc_final: 0.1772 (mmtm) outliers start: 0 outliers final: 0 residues processed: 458 average time/residue: 0.3972 time to fit residues: 287.4095 Evaluate side-chains 310 residues out of total 3020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 310 time to evaluate : 3.287 ------------------------------------------------------------------------------- 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: 9.9990 chunk 64 optimal weight: 8.9990 chunk 191 optimal weight: 20.0000 chunk 80 optimal weight: 0.7980 chunk 327 optimal weight: 20.0000 chunk 271 optimal weight: 9.9990 chunk 151 optimal weight: 5.9990 chunk 27 optimal weight: 5.9990 chunk 108 optimal weight: 4.9990 chunk 171 optimal weight: 8.9990 overall best weight: 4.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN A 240 ASN A 242 ASN ** 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** C 56 ASN ** C 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 359 GLN D 114 ASN ** E 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 210 ASN ** F 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 69 HIS F 206 ASN G 53 GLN ** G 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 203 ASN ** H 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 285 ASN ** H 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 149 HIS J 170 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 ** 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: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5658 moved from start: 0.7154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 27233 Z= 0.277 Angle : 0.657 8.790 36846 Z= 0.348 Chirality : 0.044 0.236 4271 Planarity : 0.005 0.051 4773 Dihedral : 5.056 41.598 3690 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 20.13 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.97 % Favored : 95.89 % Rotamer: Outliers : 0.10 % Allowed : 2.15 % Favored : 97.75 % 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: -0.31 (0.14), residues: 3378 helix: 1.07 (0.16), residues: 994 sheet: 0.08 (0.18), residues: 744 loop : -1.14 (0.15), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP J 456 HIS 0.007 0.002 HIS J 338 PHE 0.020 0.002 PHE D 117 TYR 0.016 0.002 TYR J 839 ARG 0.007 0.001 ARG B 119 *********************** 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 397 residues out of total 3020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 394 time to evaluate : 3.588 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: A 225 LEU cc_start: 0.7006 (pp) cc_final: 0.6770 (pp) REVERT: C 25 ILE cc_start: 0.6720 (pt) cc_final: 0.6454 (pt) REVERT: D 52 VAL cc_start: 0.7816 (p) cc_final: 0.7533 (p) REVERT: D 82 CYS cc_start: 0.6028 (t) cc_final: 0.4939 (t) REVERT: D 141 ASP cc_start: 0.5168 (p0) cc_final: 0.4899 (p0) REVERT: F 110 LEU cc_start: 0.8064 (mt) cc_final: 0.7690 (mp) REVERT: F 174 THR cc_start: 0.8179 (p) cc_final: 0.7685 (p) REVERT: G 100 MET cc_start: 0.6638 (ppp) cc_final: 0.6157 (ppp) REVERT: H 54 ILE cc_start: 0.6197 (tp) cc_final: 0.5954 (tp) REVERT: I 146 LEU cc_start: 0.8477 (tp) cc_final: 0.7893 (mp) REVERT: J 238 MET cc_start: 0.0983 (tpt) cc_final: 0.0247 (mmm) REVERT: J 674 MET cc_start: 0.4364 (ptp) cc_final: 0.4045 (ptp) REVERT: J 713 ASN cc_start: 0.7079 (OUTLIER) cc_final: 0.6397 (t0) REVERT: J 899 ILE cc_start: 0.7327 (pt) cc_final: 0.6961 (pt) outliers start: 3 outliers final: 0 residues processed: 397 average time/residue: 0.4169 time to fit residues: 267.8507 Evaluate side-chains 274 residues out of total 3020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 273 time to evaluate : 2.590 ------------------------------------------------------------------------------- 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: 0.8980 chunk 36 optimal weight: 0.7980 chunk 186 optimal weight: 0.7980 chunk 238 optimal weight: 9.9990 chunk 185 optimal weight: 5.9990 chunk 275 optimal weight: 0.3980 chunk 182 optimal weight: 7.9990 chunk 325 optimal weight: 8.9990 chunk 203 optimal weight: 0.9980 chunk 198 optimal weight: 0.0980 chunk 150 optimal weight: 10.0000 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 30 ASN B 34 HIS B 44 GLN ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 GLN D 114 ASN E 210 ASN ** F 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 53 GLN ** G 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 312 ASN ** 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: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5467 moved from start: 0.7229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 27233 Z= 0.157 Angle : 0.593 9.688 36846 Z= 0.307 Chirality : 0.044 0.191 4271 Planarity : 0.004 0.050 4773 Dihedral : 4.639 37.861 3690 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.87 % Favored : 96.98 % Rotamer: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % 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: -0.14 (0.14), residues: 3378 helix: 1.22 (0.17), residues: 986 sheet: 0.28 (0.18), residues: 719 loop : -1.06 (0.15), residues: 1673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP J 456 HIS 0.007 0.001 HIS B 235 PHE 0.027 0.001 PHE D 117 TYR 0.019 0.001 TYR J 974 ARG 0.015 0.001 ARG J 773 *********************** 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 431 residues out of total 3020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 431 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 25 ILE cc_start: 0.6484 (pt) cc_final: 0.6149 (pt) REVERT: D 82 CYS cc_start: 0.5719 (t) cc_final: 0.4775 (t) REVERT: D 141 ASP cc_start: 0.5180 (p0) cc_final: 0.4943 (p0) REVERT: E 130 VAL cc_start: 0.6783 (t) cc_final: 0.6531 (t) REVERT: E 185 PRO cc_start: 0.6901 (Cg_exo) cc_final: 0.6688 (Cg_endo) REVERT: F 110 LEU cc_start: 0.8086 (mt) cc_final: 0.7706 (mp) REVERT: F 201 VAL cc_start: 0.5937 (p) cc_final: 0.5549 (p) REVERT: G 100 MET cc_start: 0.6326 (ppp) cc_final: 0.5845 (ppp) REVERT: I 146 LEU cc_start: 0.8006 (tp) cc_final: 0.7658 (mp) REVERT: J 238 MET cc_start: 0.0907 (tpt) cc_final: 0.0148 (mmm) REVERT: J 411 SER cc_start: 0.7219 (m) cc_final: 0.6271 (t) REVERT: J 674 MET cc_start: 0.3802 (ptp) cc_final: 0.3484 (ptp) outliers start: 0 outliers final: 0 residues processed: 431 average time/residue: 0.3811 time to fit residues: 262.9738 Evaluate side-chains 304 residues out of total 3020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 304 time to evaluate : 2.914 ------------------------------------------------------------------------------- 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: 20.0000 chunk 130 optimal weight: 0.7980 chunk 194 optimal weight: 10.0000 chunk 98 optimal weight: 0.9990 chunk 64 optimal weight: 5.9990 chunk 63 optimal weight: 8.9990 chunk 207 optimal weight: 10.0000 chunk 221 optimal weight: 20.0000 chunk 161 optimal weight: 20.0000 chunk 30 optimal weight: 5.9990 chunk 256 optimal weight: 20.0000 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 GLN ** B 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 4 GLN D 114 ASN ** E 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 210 ASN ** F 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 171 HIS ** 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 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 185 HIS ** H 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 302 ASN ** H 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 115 GLN ** J 771 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5685 moved from start: 0.7655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 27233 Z= 0.261 Angle : 0.651 7.823 36846 Z= 0.342 Chirality : 0.045 0.279 4271 Planarity : 0.005 0.046 4773 Dihedral : 4.908 35.355 3690 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 19.29 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.14 % Favored : 95.71 % Rotamer: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % 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: -0.25 (0.14), residues: 3378 helix: 1.14 (0.17), residues: 981 sheet: 0.13 (0.18), residues: 729 loop : -1.10 (0.15), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 209 HIS 0.006 0.001 HIS D 81 PHE 0.023 0.002 PHE C 247 TYR 0.016 0.002 TYR J 839 ARG 0.009 0.001 ARG J 773 *********************** 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 391 residues out of total 3020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 391 time to evaluate : 3.487 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: C 25 ILE cc_start: 0.7194 (pt) cc_final: 0.6812 (pt) REVERT: D 52 VAL cc_start: 0.7701 (p) cc_final: 0.7486 (p) REVERT: D 82 CYS cc_start: 0.5891 (t) cc_final: 0.5434 (t) REVERT: D 141 ASP cc_start: 0.5234 (p0) cc_final: 0.4940 (p0) REVERT: E 96 THR cc_start: 0.7117 (p) cc_final: 0.6793 (p) REVERT: E 130 VAL cc_start: 0.7824 (t) cc_final: 0.7241 (t) REVERT: F 110 LEU cc_start: 0.8194 (mt) cc_final: 0.7758 (mt) REVERT: G 100 MET cc_start: 0.6688 (ppp) cc_final: 0.6069 (ppp) REVERT: H 54 ILE cc_start: 0.6108 (tp) cc_final: 0.5883 (tp) REVERT: I 146 LEU cc_start: 0.8022 (tp) cc_final: 0.7591 (mm) REVERT: J 238 MET cc_start: 0.1282 (tpt) cc_final: 0.0519 (mmm) REVERT: J 674 MET cc_start: 0.4425 (ptp) cc_final: 0.4128 (ptp) outliers start: 0 outliers final: 0 residues processed: 391 average time/residue: 0.3885 time to fit residues: 240.4488 Evaluate side-chains 287 residues out of total 3020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 287 time to evaluate : 2.664 ------------------------------------------------------------------------------- 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: 5.9990 chunk 312 optimal weight: 30.0000 chunk 284 optimal weight: 30.0000 chunk 303 optimal weight: 0.7980 chunk 182 optimal weight: 20.0000 chunk 132 optimal weight: 20.0000 chunk 238 optimal weight: 7.9990 chunk 93 optimal weight: 5.9990 chunk 274 optimal weight: 2.9990 chunk 287 optimal weight: 9.9990 chunk 302 optimal weight: 2.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 247 GLN ** 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 210 ASN ** F 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 108 ASN G 53 GLN ** G 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 111 HIS ** H 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 771 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5670 moved from start: 0.7841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 27233 Z= 0.225 Angle : 0.621 8.797 36846 Z= 0.327 Chirality : 0.044 0.215 4271 Planarity : 0.004 0.048 4773 Dihedral : 4.919 35.067 3690 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 17.96 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.00 % Favored : 95.89 % Rotamer: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % 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: -0.40 (0.14), residues: 3378 helix: 1.01 (0.17), residues: 973 sheet: 0.03 (0.18), residues: 740 loop : -1.18 (0.15), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP C 209 HIS 0.006 0.001 HIS B 34 PHE 0.024 0.002 PHE D 117 TYR 0.014 0.001 TYR G 120 ARG 0.015 0.001 ARG J 896 *********************** 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 383 residues out of total 3020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 383 time to evaluate : 3.159 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: A 225 LEU cc_start: 0.7005 (pp) cc_final: 0.6794 (pp) REVERT: C 25 ILE cc_start: 0.7174 (pt) cc_final: 0.6867 (pt) REVERT: D 82 CYS cc_start: 0.6028 (t) cc_final: 0.5637 (t) REVERT: D 141 ASP cc_start: 0.5272 (p0) cc_final: 0.5023 (p0) REVERT: E 1 MET cc_start: 0.2824 (ppp) cc_final: 0.1608 (ppp) REVERT: G 100 MET cc_start: 0.6961 (ppp) cc_final: 0.6263 (ppp) REVERT: I 146 LEU cc_start: 0.7977 (tp) cc_final: 0.7395 (mp) REVERT: J 238 MET cc_start: 0.1462 (tpt) cc_final: 0.0658 (mmm) REVERT: J 674 MET cc_start: 0.4057 (ptp) cc_final: 0.3726 (ptp) outliers start: 0 outliers final: 0 residues processed: 383 average time/residue: 0.3800 time to fit residues: 232.6200 Evaluate side-chains 273 residues out of total 3020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 273 time to evaluate : 3.041 ------------------------------------------------------------------------------- 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: 4.9990 chunk 321 optimal weight: 7.9990 chunk 195 optimal weight: 5.9990 chunk 152 optimal weight: 0.8980 chunk 223 optimal weight: 0.0470 chunk 336 optimal weight: 0.8980 chunk 309 optimal weight: 8.9990 chunk 268 optimal weight: 8.9990 chunk 27 optimal weight: 3.9990 chunk 207 optimal weight: 10.0000 chunk 164 optimal weight: 0.9990 overall best weight: 1.3682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 ASN ** B 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 210 ASN ** F 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 53 GLN ** G 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 115 GLN ** J 771 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5580 moved from start: 0.7887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 27233 Z= 0.172 Angle : 0.597 9.123 36846 Z= 0.309 Chirality : 0.044 0.188 4271 Planarity : 0.004 0.049 4773 Dihedral : 4.700 31.605 3690 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 15.48 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.46 % Favored : 96.42 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % 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: -0.32 (0.14), residues: 3378 helix: 1.08 (0.17), residues: 976 sheet: 0.13 (0.19), residues: 731 loop : -1.16 (0.15), residues: 1671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 209 HIS 0.006 0.001 HIS B 235 PHE 0.026 0.001 PHE D 117 TYR 0.011 0.001 TYR J 181 ARG 0.007 0.000 ARG B 3 ********************** 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 394 residues out of total 3020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 394 time to evaluate : 3.218 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: A 225 LEU cc_start: 0.7084 (pp) cc_final: 0.6874 (pp) REVERT: C 25 ILE cc_start: 0.7115 (pt) cc_final: 0.6781 (pt) REVERT: D 82 CYS cc_start: 0.5964 (t) cc_final: 0.5563 (t) REVERT: D 141 ASP cc_start: 0.5267 (p0) cc_final: 0.5002 (p0) REVERT: E 1 MET cc_start: 0.3005 (ppp) cc_final: 0.1838 (ppp) REVERT: E 185 PRO cc_start: 0.6992 (Cg_exo) cc_final: 0.6747 (Cg_endo) REVERT: F 174 THR cc_start: 0.7830 (p) cc_final: 0.7629 (p) REVERT: G 100 MET cc_start: 0.6844 (ppp) cc_final: 0.6154 (ppp) REVERT: H 329 TYR cc_start: 0.4736 (m-80) cc_final: 0.4513 (m-80) REVERT: J 238 MET cc_start: 0.1393 (tpt) cc_final: 0.0269 (tpt) REVERT: J 674 MET cc_start: 0.3572 (ptp) cc_final: 0.3305 (ptp) REVERT: J 987 MET cc_start: 0.5157 (tpp) cc_final: 0.4827 (mmm) outliers start: 0 outliers final: 0 residues processed: 394 average time/residue: 0.3936 time to fit residues: 247.7464 Evaluate side-chains 286 residues out of total 3020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 286 time to evaluate : 3.274 ------------------------------------------------------------------------------- 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: 9.9990 chunk 285 optimal weight: 20.0000 chunk 82 optimal weight: 0.0170 chunk 247 optimal weight: 7.9990 chunk 39 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 chunk 268 optimal weight: 7.9990 chunk 112 optimal weight: 3.9990 chunk 275 optimal weight: 6.9990 chunk 34 optimal weight: 8.9990 chunk 49 optimal weight: 0.3980 overall best weight: 1.8824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 GLN ** E 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 210 ASN ** F 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 108 ASN G 53 GLN ** G 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 181 HIS H 174 GLN ** H 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 771 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.078856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.060701 restraints weight = 141680.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.062956 restraints weight = 87665.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.064559 restraints weight = 61736.829| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.7998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 27233 Z= 0.173 Angle : 0.594 9.465 36846 Z= 0.308 Chirality : 0.044 0.197 4271 Planarity : 0.004 0.049 4773 Dihedral : 4.637 27.984 3690 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 15.95 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.52 % Favored : 96.36 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % 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: -0.28 (0.14), residues: 3378 helix: 1.12 (0.17), residues: 979 sheet: 0.13 (0.19), residues: 711 loop : -1.11 (0.15), residues: 1688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 209 HIS 0.004 0.001 HIS J 855 PHE 0.026 0.002 PHE D 117 TYR 0.032 0.001 TYR B 41 ARG 0.007 0.000 ARG I 206 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6085.64 seconds wall clock time: 110 minutes 55.97 seconds (6655.97 seconds total)