Starting phenix.real_space_refine on Sat Dec 16 10:21:27 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h40_34476/12_2023/8h40_34476.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h40_34476/12_2023/8h40_34476.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h40_34476/12_2023/8h40_34476.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h40_34476/12_2023/8h40_34476.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h40_34476/12_2023/8h40_34476.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h40_34476/12_2023/8h40_34476.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 120 5.49 5 S 109 5.16 5 C 21516 2.51 5 N 6193 2.21 5 O 6895 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 29": "OD1" <-> "OD2" Residue "A PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 118": "OD1" <-> "OD2" Residue "A TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 191": "NH1" <-> "NH2" Residue "A PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 233": "OE1" <-> "OE2" Residue "A TYR 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 316": "OD1" <-> "OD2" Residue "A PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 486": "OD1" <-> "OD2" Residue "A ASP 712": "OD1" <-> "OD2" Residue "A GLU 745": "OE1" <-> "OE2" Residue "A ARG 749": "NH1" <-> "NH2" Residue "A GLU 778": "OE1" <-> "OE2" Residue "A GLU 823": "OE1" <-> "OE2" Residue "A TYR 873": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 921": "OE1" <-> "OE2" Residue "A GLU 925": "OE1" <-> "OE2" Residue "A ASP 969": "OD1" <-> "OD2" Residue "A GLU 1019": "OE1" <-> "OE2" Residue "A ASP 1094": "OD1" <-> "OD2" Residue "B PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 310": "OD1" <-> "OD2" Residue "B GLU 388": "OE1" <-> "OE2" Residue "B ASP 448": "OD1" <-> "OD2" Residue "B GLU 452": "OE1" <-> "OE2" Residue "B PHE 603": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 773": "NH1" <-> "NH2" Residue "B GLU 804": "OE1" <-> "OE2" Residue "B ASP 847": "OD1" <-> "OD2" Residue "B GLU 892": "OE1" <-> "OE2" Residue "B ARG 1001": "NH1" <-> "NH2" Residue "B GLU 1025": "OE1" <-> "OE2" Residue "B GLU 1166": "OE1" <-> "OE2" Residue "B ASP 1205": "OD1" <-> "OD2" Residue "B PHE 1207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1215": "OE1" <-> "OE2" Residue "B ARG 1233": "NH1" <-> "NH2" Residue "C PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 29": "OE1" <-> "OE2" Residue "C GLU 156": "OE1" <-> "OE2" Residue "C ASP 186": "OD1" <-> "OD2" Residue "D PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 14": "OE1" <-> "OE2" Residue "D GLU 26": "OE1" <-> "OE2" Residue "D PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 132": "OE1" <-> "OE2" Residue "E ASP 165": "OD1" <-> "OD2" Residue "E GLU 171": "OE1" <-> "OE2" Residue "E GLU 205": "OE1" <-> "OE2" Residue "E ARG 221": "NH1" <-> "NH2" Residue "E ASP 274": "OD1" <-> "OD2" Residue "E GLU 378": "OE1" <-> "OE2" Residue "E PHE 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 518": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 523": "OE1" <-> "OE2" Residue "E ASP 539": "OD1" <-> "OD2" Residue "E ASP 596": "OD1" <-> "OD2" Residue "G TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 80": "OD1" <-> "OD2" Residue "G GLU 99": "OE1" <-> "OE2" Residue "G TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 303": "OE1" <-> "OE2" Residue "G ASP 305": "OD1" <-> "OD2" Residue "G PHE 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 363": "OE1" <-> "OE2" Residue "G ARG 377": "NH1" <-> "NH2" Residue "G GLU 387": "OE1" <-> "OE2" Residue "X PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 87": "OD1" <-> "OD2" Residue "Y PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 159": "OD1" <-> "OD2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 34833 Number of models: 1 Model: "" Number of chains: 11 Chain: "1" Number of atoms: 1358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 1358 Classifications: {'DNA': 66} Link IDs: {'rna3p': 65} Chain: "2" Number of atoms: 1109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 1109 Classifications: {'DNA': 54} Link IDs: {'rna3p': 53} Chain breaks: 1 Chain: "A" Number of atoms: 8473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1077, 8473 Classifications: {'peptide': 1077} Link IDs: {'PTRANS': 61, 'TRANS': 1015} Chain: "B" Number of atoms: 9292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1217, 9292 Classifications: {'peptide': 1217} Link IDs: {'PTRANS': 52, 'TRANS': 1164} Chain breaks: 3 Chain: "C" Number of atoms: 1762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1762 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 9, 'TRANS': 216} Chain: "D" Number of atoms: 1762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1762 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 9, 'TRANS': 216} Chain: "E" Number of atoms: 4923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 620, 4923 Classifications: {'peptide': 620} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 33, 'TRANS': 586} Chain: "F" Number of atoms: 474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 474 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 1, 'TRANS': 56} Chain: "G" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2600 Classifications: {'peptide': 314} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 303} Chain: "X" Number of atoms: 1540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1540 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 7, 'TRANS': 188} Chain: "Y" Number of atoms: 1540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1540 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 7, 'TRANS': 188} Time building chain proxies: 18.32, per 1000 atoms: 0.53 Number of scatterers: 34833 At special positions: 0 Unit cell: (156.22, 193.67, 146.59, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 109 16.00 P 120 15.00 O 6895 8.00 N 6193 7.00 C 21516 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 214 " - pdb=" SG CYS B 295 " distance=2.03 Simple disulfide: pdb=" SG CYS E 71 " - pdb=" SG CYS E 73 " distance=1.94 Simple disulfide: pdb=" SG CYS E 71 " - pdb=" SG CYS E 86 " distance=2.12 Simple disulfide: pdb=" SG CYS E 73 " - pdb=" SG CYS E 86 " distance=2.05 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: 19.27 Conformation dependent library (CDL) restraints added in 6.2 seconds 8212 Ramachandran restraints generated. 4106 Oldfield, 0 Emsley, 4106 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7636 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 49 sheets defined 31.5% alpha, 7.1% beta 41 base pairs and 66 stacking pairs defined. Time for finding SS restraints: 12.26 Creating SS restraints... Processing helix chain 'A' and resid 31 through 44 removed outlier: 3.823A pdb=" N ARG A 35 " --> pdb=" O ILE A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 54 Processing helix chain 'A' and resid 80 through 87 Processing helix chain 'A' and resid 205 through 210 Processing helix chain 'A' and resid 249 through 263 removed outlier: 3.630A pdb=" N ASP A 263 " --> pdb=" O SER A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 267 Processing helix chain 'A' and resid 270 through 282 Processing helix chain 'A' and resid 293 through 309 removed outlier: 4.171A pdb=" N ILE A 297 " --> pdb=" O THR A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 321 No H-bonds generated for 'chain 'A' and resid 319 through 321' Processing helix chain 'A' and resid 327 through 352 Processing helix chain 'A' and resid 368 through 380 Processing helix chain 'A' and resid 392 through 400 Processing helix chain 'A' and resid 483 through 487 removed outlier: 3.802A pdb=" N ASP A 486 " --> pdb=" O ASP A 483 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ASP A 487 " --> pdb=" O GLU A 484 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 483 through 487' Processing helix chain 'A' and resid 544 through 548 Processing helix chain 'A' and resid 549 through 561 removed outlier: 3.591A pdb=" N ALA A 553 " --> pdb=" O ASP A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 587 removed outlier: 4.147A pdb=" N GLY A 587 " --> pdb=" O ALA A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 613 through 619 Processing helix chain 'A' and resid 706 through 711 Processing helix chain 'A' and resid 782 through 793 Processing helix chain 'A' and resid 867 through 871 removed outlier: 3.771A pdb=" N MET A 871 " --> pdb=" O ILE A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 910 Processing helix chain 'A' and resid 927 through 941 removed outlier: 4.242A pdb=" N ASP A 941 " --> pdb=" O GLN A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 987 through 990 removed outlier: 3.593A pdb=" N ILE A 990 " --> pdb=" O ASP A 987 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 987 through 990' Processing helix chain 'A' and resid 1018 through 1023 Processing helix chain 'A' and resid 1031 through 1039 Processing helix chain 'A' and resid 1044 through 1058 removed outlier: 3.513A pdb=" N GLY A1058 " --> pdb=" O ALA A1054 " (cutoff:3.500A) Processing helix chain 'A' and resid 1067 through 1079 removed outlier: 3.938A pdb=" N LYS A1071 " --> pdb=" O PRO A1067 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 24 Processing helix chain 'B' and resid 27 through 48 Processing helix chain 'B' and resid 61 through 82 Processing helix chain 'B' and resid 86 through 95 removed outlier: 3.809A pdb=" N LYS B 93 " --> pdb=" O GLU B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 115 Processing helix chain 'B' and resid 120 through 125 Processing helix chain 'B' and resid 134 through 142 removed outlier: 3.739A pdb=" N GLN B 139 " --> pdb=" O SER B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 204 removed outlier: 5.267A pdb=" N ALA B 191 " --> pdb=" O ALA B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 239 removed outlier: 3.595A pdb=" N ARG B 238 " --> pdb=" O LYS B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 274 Processing helix chain 'B' and resid 295 through 300 removed outlier: 3.819A pdb=" N GLY B 300 " --> pdb=" O GLN B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 328 Proline residue: B 326 - end of helix Processing helix chain 'B' and resid 697 through 703 Processing helix chain 'B' and resid 1009 through 1020 removed outlier: 3.538A pdb=" N ARG B1013 " --> pdb=" O GLN B1009 " (cutoff:3.500A) Processing helix chain 'B' and resid 1089 through 1100 Processing helix chain 'B' and resid 1105 through 1133 Processing helix chain 'B' and resid 1137 through 1149 removed outlier: 3.562A pdb=" N ILE B1141 " --> pdb=" O ALA B1137 " (cutoff:3.500A) Processing helix chain 'B' and resid 1170 through 1184 Processing helix chain 'B' and resid 1206 through 1214 removed outlier: 3.776A pdb=" N ALA B1210 " --> pdb=" O SER B1206 " (cutoff:3.500A) Processing helix chain 'B' and resid 1217 through 1226 removed outlier: 3.566A pdb=" N GLU B1222 " --> pdb=" O ARG B1218 " (cutoff:3.500A) Processing helix chain 'B' and resid 1237 through 1242 Processing helix chain 'B' and resid 1247 through 1251 Processing helix chain 'C' and resid 31 through 45 removed outlier: 4.000A pdb=" N LEU C 40 " --> pdb=" O VAL C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 84 removed outlier: 4.211A pdb=" N GLU C 84 " --> pdb=" O MET C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 112 Processing helix chain 'C' and resid 205 through 222 Processing helix chain 'C' and resid 223 through 225 No H-bonds generated for 'chain 'C' and resid 223 through 225' Processing helix chain 'D' and resid 35 through 45 Processing helix chain 'D' and resid 74 through 84 removed outlier: 4.212A pdb=" N GLU D 84 " --> pdb=" O MET D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 155 Processing helix chain 'D' and resid 205 through 222 Processing helix chain 'E' and resid 18 through 24 Processing helix chain 'E' and resid 115 through 118 Processing helix chain 'E' and resid 123 through 130 Processing helix chain 'E' and resid 164 through 172 Processing helix chain 'E' and resid 189 through 200 removed outlier: 3.606A pdb=" N LEU E 193 " --> pdb=" O GLY E 189 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ARG E 195 " --> pdb=" O GLU E 191 " (cutoff:3.500A) Processing helix chain 'E' and resid 209 through 215 removed outlier: 3.977A pdb=" N ILE E 213 " --> pdb=" O LEU E 209 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY E 214 " --> pdb=" O ARG E 210 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER E 215 " --> pdb=" O GLU E 211 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 209 through 215' Processing helix chain 'E' and resid 221 through 237 Processing helix chain 'E' and resid 240 through 243 Processing helix chain 'E' and resid 253 through 257 Processing helix chain 'E' and resid 270 through 292 Processing helix chain 'E' and resid 295 through 315 removed outlier: 3.561A pdb=" N VAL E 299 " --> pdb=" O PRO E 295 " (cutoff:3.500A) Processing helix chain 'E' and resid 343 through 349 Processing helix chain 'E' and resid 376 through 396 removed outlier: 3.728A pdb=" N GLU E 382 " --> pdb=" O GLU E 378 " (cutoff:3.500A) Proline residue: E 386 - end of helix Processing helix chain 'E' and resid 400 through 411 Processing helix chain 'E' and resid 412 through 417 Processing helix chain 'E' and resid 418 through 424 removed outlier: 4.355A pdb=" N GLU E 424 " --> pdb=" O GLU E 420 " (cutoff:3.500A) Processing helix chain 'E' and resid 460 through 465 Processing helix chain 'E' and resid 480 through 492 removed outlier: 3.710A pdb=" N LEU E 492 " --> pdb=" O ARG E 488 " (cutoff:3.500A) Processing helix chain 'E' and resid 493 through 496 removed outlier: 3.969A pdb=" N ASN E 496 " --> pdb=" O ALA E 493 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 493 through 496' Processing helix chain 'E' and resid 512 through 522 Processing helix chain 'E' and resid 539 through 547 Processing helix chain 'E' and resid 609 through 624 removed outlier: 3.711A pdb=" N ILE E 614 " --> pdb=" O PRO E 610 " (cutoff:3.500A) Processing helix chain 'F' and resid 14 through 24 Processing helix chain 'F' and resid 27 through 45 Processing helix chain 'F' and resid 56 through 67 Processing helix chain 'G' and resid 81 through 91 removed outlier: 4.170A pdb=" N GLU G 88 " --> pdb=" O LEU G 84 " (cutoff:3.500A) Processing helix chain 'G' and resid 98 through 124 removed outlier: 3.997A pdb=" N LEU G 103 " --> pdb=" O GLU G 99 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU G 113 " --> pdb=" O ASP G 109 " (cutoff:3.500A) Processing helix chain 'G' and resid 140 through 163 removed outlier: 3.529A pdb=" N ARG G 145 " --> pdb=" O LEU G 141 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N LYS G 155 " --> pdb=" O GLY G 151 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N SER G 161 " --> pdb=" O LYS G 157 " (cutoff:3.500A) Processing helix chain 'G' and resid 165 through 177 removed outlier: 3.880A pdb=" N LYS G 172 " --> pdb=" O SER G 168 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N TYR G 173 " --> pdb=" O ILE G 169 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASN G 175 " --> pdb=" O LYS G 171 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ARG G 176 " --> pdb=" O LYS G 172 " (cutoff:3.500A) Processing helix chain 'G' and resid 179 through 197 Processing helix chain 'G' and resid 205 through 208 Processing helix chain 'G' and resid 209 through 223 removed outlier: 4.217A pdb=" N ALA G 221 " --> pdb=" O ALA G 217 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ILE G 222 " --> pdb=" O ILE G 218 " (cutoff:3.500A) Processing helix chain 'G' and resid 232 through 253 removed outlier: 3.704A pdb=" N GLU G 237 " --> pdb=" O VAL G 233 " (cutoff:3.500A) Processing helix chain 'G' and resid 259 through 264 Processing helix chain 'G' and resid 269 through 280 removed outlier: 3.564A pdb=" N LEU G 273 " --> pdb=" O THR G 269 " (cutoff:3.500A) Processing helix chain 'G' and resid 308 through 327 Processing helix chain 'G' and resid 330 through 340 removed outlier: 3.595A pdb=" N VAL G 336 " --> pdb=" O ARG G 332 " (cutoff:3.500A) Processing helix chain 'G' and resid 350 through 360 removed outlier: 3.744A pdb=" N GLN G 356 " --> pdb=" O GLU G 352 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASN G 359 " --> pdb=" O GLY G 355 " (cutoff:3.500A) Processing helix chain 'G' and resid 364 through 377 removed outlier: 4.043A pdb=" N ILE G 368 " --> pdb=" O ARG G 364 " (cutoff:3.500A) Processing helix chain 'G' and resid 381 through 385 Processing helix chain 'X' and resid 82 through 86 removed outlier: 3.789A pdb=" N SER X 86 " --> pdb=" O GLY X 83 " (cutoff:3.500A) Processing helix chain 'X' and resid 104 through 108 Processing helix chain 'X' and resid 109 through 114 Processing helix chain 'X' and resid 115 through 140 removed outlier: 3.672A pdb=" N SER X 119 " --> pdb=" O ASN X 115 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N GLU X 138 " --> pdb=" O GLU X 134 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N THR X 139 " --> pdb=" O MET X 135 " (cutoff:3.500A) Processing helix chain 'X' and resid 146 through 152 Processing helix chain 'X' and resid 152 through 158 Processing helix chain 'X' and resid 177 through 184 Processing helix chain 'X' and resid 187 through 198 removed outlier: 3.823A pdb=" N LEU X 193 " --> pdb=" O THR X 189 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N LEU X 194 " --> pdb=" O VAL X 190 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASP X 196 " --> pdb=" O ARG X 192 " (cutoff:3.500A) Processing helix chain 'Y' and resid 104 through 114 Processing helix chain 'Y' and resid 116 through 118 No H-bonds generated for 'chain 'Y' and resid 116 through 118' Processing helix chain 'Y' and resid 119 through 141 removed outlier: 3.514A pdb=" N GLU Y 134 " --> pdb=" O ILE Y 130 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N MET Y 136 " --> pdb=" O GLN Y 132 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N THR Y 139 " --> pdb=" O MET Y 135 " (cutoff:3.500A) Processing helix chain 'Y' and resid 146 through 159 Processing helix chain 'Y' and resid 175 through 180 Processing helix chain 'Y' and resid 187 through 198 removed outlier: 3.815A pdb=" N LEU Y 194 " --> pdb=" O VAL Y 190 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASP Y 196 " --> pdb=" O ARG Y 192 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU Y 197 " --> pdb=" O LEU Y 193 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 56 through 57 Processing sheet with id=AA2, first strand: chain 'A' and resid 95 through 98 removed outlier: 6.607A pdb=" N MET A 95 " --> pdb=" O ILE A 116 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 128 through 130 Processing sheet with id=AA4, first strand: chain 'A' and resid 323 through 326 removed outlier: 4.002A pdb=" N ASN A 139 " --> pdb=" O ARG A 401 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N SER A 446 " --> pdb=" O CYS A 431 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 146 through 148 Processing sheet with id=AA6, first strand: chain 'A' and resid 152 through 153 Processing sheet with id=AA7, first strand: chain 'A' and resid 464 through 465 Processing sheet with id=AA8, first strand: chain 'A' and resid 574 through 575 Processing sheet with id=AA9, first strand: chain 'A' and resid 590 through 591 removed outlier: 6.239A pdb=" N ILE A 590 " --> pdb=" O LEU A 669 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 595 through 597 Processing sheet with id=AB2, first strand: chain 'A' and resid 850 through 853 removed outlier: 4.942A pdb=" N LYS A 851 " --> pdb=" O LEU A 982 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU A 982 " --> pdb=" O LYS A 851 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N THR A 973 " --> pdb=" O TYR A 690 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N TYR A 690 " --> pdb=" O THR A 973 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N LEU A 884 " --> pdb=" O VAL A 687 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ALA A 689 " --> pdb=" O LEU A 884 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 850 through 853 removed outlier: 4.942A pdb=" N LYS A 851 " --> pdb=" O LEU A 982 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU A 982 " --> pdb=" O LYS A 851 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 701 through 704 removed outlier: 8.106A pdb=" N ILE A 704 " --> pdb=" O SER A 863 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ILE A 865 " --> pdb=" O ILE A 704 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 715 through 716 Processing sheet with id=AB6, first strand: chain 'A' and resid 724 through 727 removed outlier: 6.330A pdb=" N ILE A 724 " --> pdb=" O VAL A 835 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N VAL A 835 " --> pdb=" O ILE A 724 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N ALA A 726 " --> pdb=" O ASN A 833 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 768 through 770 removed outlier: 5.980A pdb=" N LEU A 804 " --> pdb=" O LEU A 769 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 774 through 775 Processing sheet with id=AB9, first strand: chain 'B' and resid 3 through 5 Processing sheet with id=AC1, first strand: chain 'B' and resid 301 through 302 Processing sheet with id=AC2, first strand: chain 'B' and resid 438 through 439 Processing sheet with id=AC3, first strand: chain 'B' and resid 502 through 503 Processing sheet with id=AC4, first strand: chain 'B' and resid 538 through 540 Processing sheet with id=AC5, first strand: chain 'B' and resid 572 through 574 removed outlier: 4.557A pdb=" N THR B 793 " --> pdb=" O LEU B 591 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 602 through 603 Processing sheet with id=AC7, first strand: chain 'B' and resid 641 through 642 Processing sheet with id=AC8, first strand: chain 'B' and resid 660 through 661 Processing sheet with id=AC9, first strand: chain 'B' and resid 670 through 673 Processing sheet with id=AD1, first strand: chain 'B' and resid 765 through 766 Processing sheet with id=AD2, first strand: chain 'B' and resid 940 through 942 removed outlier: 6.684A pdb=" N THR B 965 " --> pdb=" O VAL B 941 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1167 through 1169 removed outlier: 3.655A pdb=" N LYS B1151 " --> pdb=" O VAL B1193 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 10 through 11 removed outlier: 4.038A pdb=" N GLU C 10 " --> pdb=" O LYS C 22 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER C 21 " --> pdb=" O VAL C 198 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL C 198 " --> pdb=" O SER C 21 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N GLU C 197 " --> pdb=" O VAL C 176 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N VAL C 176 " --> pdb=" O GLU C 197 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N TRP C 199 " --> pdb=" O ARG C 174 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 10 through 11 removed outlier: 4.038A pdb=" N GLU C 10 " --> pdb=" O LYS C 22 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER C 21 " --> pdb=" O VAL C 198 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL C 198 " --> pdb=" O SER C 21 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 56 through 57 removed outlier: 3.571A pdb=" N GLY C 97 " --> pdb=" O PHE C 140 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 87 through 88 removed outlier: 3.632A pdb=" N LYS C 88 " --> pdb=" O GLU C 119 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 6 through 8 removed outlier: 4.338A pdb=" N LEU D 194 " --> pdb=" O LEU D 25 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N GLU D 197 " --> pdb=" O VAL D 176 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N VAL D 176 " --> pdb=" O GLU D 197 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N TRP D 199 " --> pdb=" O ARG D 174 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 6 through 8 removed outlier: 4.338A pdb=" N LEU D 194 " --> pdb=" O LEU D 25 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 50 through 51 Processing sheet with id=AE2, first strand: chain 'D' and resid 56 through 57 removed outlier: 3.572A pdb=" N GLY D 97 " --> pdb=" O PHE D 140 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 87 through 88 removed outlier: 3.557A pdb=" N LYS D 88 " --> pdb=" O GLU D 119 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 106 through 108 Processing sheet with id=AE5, first strand: chain 'E' and resid 104 through 113 removed outlier: 6.786A pdb=" N THR E 247 " --> pdb=" O LEU E 108 " (cutoff:3.500A) removed outlier: 10.914A pdb=" N ALA E 110 " --> pdb=" O VAL E 245 " (cutoff:3.500A) removed outlier: 9.881A pdb=" N VAL E 245 " --> pdb=" O ALA E 110 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 260 through 261 Processing sheet with id=AE7, first strand: chain 'E' and resid 357 through 360 removed outlier: 3.619A pdb=" N GLN E 442 " --> pdb=" O LEU E 430 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'E' and resid 363 through 364 removed outlier: 6.221A pdb=" N VAL E 363 " --> pdb=" O LEU E 456 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'E' and resid 586 through 587 removed outlier: 3.557A pdb=" N VAL E 586 " --> pdb=" O VAL E 593 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'X' and resid 45 through 46 Processing sheet with id=AF2, first strand: chain 'X' and resid 161 through 163 Processing sheet with id=AF3, first strand: chain 'Y' and resid 53 through 55 Processing sheet with id=AF4, first strand: chain 'Y' and resid 162 through 163 962 hydrogen bonds defined for protein. 2712 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 88 hydrogen bonds 136 hydrogen bond angles 0 basepair planarities 41 basepair parallelities 66 stacking parallelities Total time for adding SS restraints: 14.36 Time building geometry restraints manager: 19.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.97 - 1.16: 90 1.16 - 1.34: 13392 1.34 - 1.53: 18181 1.53 - 1.71: 3826 1.71 - 1.90: 153 Bond restraints: 35642 Sorted by residual: bond pdb=" CA SER A1079 " pdb=" C SER A1079 " ideal model delta sigma weight residual 1.526 1.044 0.482 1.23e-02 6.61e+03 1.53e+03 bond pdb=" CA LEU D 45 " pdb=" C LEU D 45 " ideal model delta sigma weight residual 1.523 0.981 0.542 1.41e-02 5.03e+03 1.47e+03 bond pdb=" CA LEU C 45 " pdb=" C LEU C 45 " ideal model delta sigma weight residual 1.523 0.981 0.541 1.41e-02 5.03e+03 1.47e+03 bond pdb=" CA TYR E 117 " pdb=" C TYR E 117 " ideal model delta sigma weight residual 1.524 0.971 0.554 1.66e-02 3.63e+03 1.11e+03 bond pdb=" CA ARG E 61 " pdb=" C ARG E 61 " ideal model delta sigma weight residual 1.523 1.030 0.493 1.48e-02 4.57e+03 1.11e+03 ... (remaining 35637 not shown) Histogram of bond angle deviations from ideal: 65.49 - 83.51: 16 83.51 - 101.53: 1216 101.53 - 119.55: 33168 119.55 - 137.57: 14321 137.57 - 155.60: 11 Bond angle restraints: 48732 Sorted by residual: angle pdb=" N MET C 80 " pdb=" CA MET C 80 " pdb=" C MET C 80 " ideal model delta sigma weight residual 112.23 86.51 25.72 1.26e+00 6.30e-01 4.17e+02 angle pdb=" N MET D 80 " pdb=" CA MET D 80 " pdb=" C MET D 80 " ideal model delta sigma weight residual 112.23 86.52 25.71 1.26e+00 6.30e-01 4.16e+02 angle pdb=" C LEU E 538 " pdb=" N ASP E 539 " pdb=" CA ASP E 539 " ideal model delta sigma weight residual 121.54 85.16 36.38 1.91e+00 2.74e-01 3.63e+02 angle pdb=" C ASP X 39 " pdb=" N PRO X 40 " pdb=" CA PRO X 40 " ideal model delta sigma weight residual 119.84 142.94 -23.10 1.25e+00 6.40e-01 3.41e+02 angle pdb=" N ASP C 219 " pdb=" CA ASP C 219 " pdb=" C ASP C 219 " ideal model delta sigma weight residual 111.24 87.71 23.53 1.29e+00 6.01e-01 3.33e+02 ... (remaining 48727 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.31: 20355 35.31 - 70.63: 1122 70.63 - 105.94: 110 105.94 - 141.26: 16 141.26 - 176.57: 10 Dihedral angle restraints: 21613 sinusoidal: 9748 harmonic: 11865 Sorted by residual: dihedral pdb=" CA GLN B 854 " pdb=" C GLN B 854 " pdb=" N THR B 855 " pdb=" CA THR B 855 " ideal model delta harmonic sigma weight residual -180.00 -118.98 -61.02 0 5.00e+00 4.00e-02 1.49e+02 dihedral pdb=" C MET Y 120 " pdb=" N MET Y 120 " pdb=" CA MET Y 120 " pdb=" CB MET Y 120 " ideal model delta harmonic sigma weight residual -122.60 -92.99 -29.61 0 2.50e+00 1.60e-01 1.40e+02 dihedral pdb=" CA GLU A 735 " pdb=" C GLU A 735 " pdb=" N ILE A 736 " pdb=" CA ILE A 736 " ideal model delta harmonic sigma weight residual -180.00 -122.71 -57.29 0 5.00e+00 4.00e-02 1.31e+02 ... (remaining 21610 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.224: 4705 0.224 - 0.448: 730 0.448 - 0.672: 121 0.672 - 0.896: 19 0.896 - 1.120: 7 Chirality restraints: 5582 Sorted by residual: chirality pdb=" CB THR A 222 " pdb=" CA THR A 222 " pdb=" OG1 THR A 222 " pdb=" CG2 THR A 222 " both_signs ideal model delta sigma weight residual False 2.55 1.43 1.12 2.00e-01 2.50e+01 3.14e+01 chirality pdb=" CB THR A 616 " pdb=" CA THR A 616 " pdb=" OG1 THR A 616 " pdb=" CG2 THR A 616 " both_signs ideal model delta sigma weight residual False 2.55 1.48 1.07 2.00e-01 2.50e+01 2.85e+01 chirality pdb=" CA TYR E 117 " pdb=" N TYR E 117 " pdb=" C TYR E 117 " pdb=" CB TYR E 117 " both_signs ideal model delta sigma weight residual False 2.51 1.47 1.04 2.00e-01 2.50e+01 2.69e+01 ... (remaining 5579 not shown) Planarity restraints: 5940 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA 1 100 " -0.069 2.00e-02 2.50e+03 6.94e-02 1.32e+02 pdb=" N9 DA 1 100 " -0.065 2.00e-02 2.50e+03 pdb=" C8 DA 1 100 " 0.000 2.00e-02 2.50e+03 pdb=" N7 DA 1 100 " 0.015 2.00e-02 2.50e+03 pdb=" C5 DA 1 100 " -0.007 2.00e-02 2.50e+03 pdb=" C6 DA 1 100 " -0.029 2.00e-02 2.50e+03 pdb=" N6 DA 1 100 " 0.013 2.00e-02 2.50e+03 pdb=" N1 DA 1 100 " -0.069 2.00e-02 2.50e+03 pdb=" C2 DA 1 100 " -0.046 2.00e-02 2.50e+03 pdb=" N3 DA 1 100 " 0.090 2.00e-02 2.50e+03 pdb=" C4 DA 1 100 " 0.167 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA 2 67 " -0.046 2.00e-02 2.50e+03 6.49e-02 1.16e+02 pdb=" N9 DA 2 67 " -0.069 2.00e-02 2.50e+03 pdb=" C8 DA 2 67 " -0.009 2.00e-02 2.50e+03 pdb=" N7 DA 2 67 " 0.031 2.00e-02 2.50e+03 pdb=" C5 DA 2 67 " 0.138 2.00e-02 2.50e+03 pdb=" C6 DA 2 67 " -0.014 2.00e-02 2.50e+03 pdb=" N6 DA 2 67 " -0.089 2.00e-02 2.50e+03 pdb=" N1 DA 2 67 " -0.037 2.00e-02 2.50e+03 pdb=" C2 DA 2 67 " 0.063 2.00e-02 2.50e+03 pdb=" N3 DA 2 67 " -0.037 2.00e-02 2.50e+03 pdb=" C4 DA 2 67 " 0.068 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 653 " 0.031 2.00e-02 2.50e+03 6.70e-02 8.97e+01 pdb=" CG TYR B 653 " 0.001 2.00e-02 2.50e+03 pdb=" CD1 TYR B 653 " -0.111 2.00e-02 2.50e+03 pdb=" CD2 TYR B 653 " 0.019 2.00e-02 2.50e+03 pdb=" CE1 TYR B 653 " 0.119 2.00e-02 2.50e+03 pdb=" CE2 TYR B 653 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR B 653 " -0.085 2.00e-02 2.50e+03 pdb=" OH TYR B 653 " 0.030 2.00e-02 2.50e+03 ... (remaining 5937 not shown) Histogram of nonbonded interaction distances: 0.73 - 1.56: 13 1.56 - 2.40: 2076 2.40 - 3.23: 54793 3.23 - 4.07: 107850 4.07 - 4.90: 171403 Warning: very small nonbonded interaction distances. Nonbonded interactions: 336135 Sorted by model distance: nonbonded pdb=" N6 DA 1 75 " pdb=" O4 DT 2 51 " model vdw 0.727 2.520 nonbonded pdb=" OP2 DA 2 26 " pdb=" N3 DA 2 26 " model vdw 1.064 3.120 nonbonded pdb=" N6 DA 1 79 " pdb=" O4 DT 2 47 " model vdw 1.188 2.520 nonbonded pdb=" O6 DG 1 85 " pdb=" N4 DC 2 41 " model vdw 1.240 2.520 nonbonded pdb=" C6 DA 1 75 " pdb=" O4 DT 2 51 " model vdw 1.293 3.260 ... (remaining 336130 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'X' selection = chain 'Y' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.10 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: 1.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 7.860 Check model and map are aligned: 0.550 Set scattering table: 0.290 Process input model: 106.690 Find NCS groups from input model: 1.210 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 120.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 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 : 0.059 0.554 35642 Z= 3.753 Angle : 3.508 46.482 48732 Z= 1.903 Chirality : 0.179 1.120 5582 Planarity : 0.023 0.356 5940 Dihedral : 20.656 176.570 13965 Min Nonbonded Distance : 0.727 Molprobity Statistics. All-atom Clashscore : 175.67 Ramachandran Plot: Outliers : 3.82 % Allowed : 35.75 % Favored : 60.42 % Rotamer: Outliers : 4.55 % Allowed : 8.91 % Favored : 86.54 % Cbeta Deviations : 4.27 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.17 % Twisted General : 4.02 % 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: -7.43 (0.08), residues: 4106 helix: -4.92 (0.07), residues: 1098 sheet: -4.54 (0.22), residues: 342 loop : -5.38 (0.08), residues: 2666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.108 0.011 TRP A 905 HIS 0.038 0.005 HIS A1087 PHE 0.084 0.007 PHE A 38 TYR 0.139 0.008 TYR F 29 ARG 0.070 0.003 ARG A 662 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8212 Ramachandran restraints generated. 4106 Oldfield, 0 Emsley, 4106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8212 Ramachandran restraints generated. 4106 Oldfield, 0 Emsley, 4106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 623 residues out of total 3537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 462 time to evaluate : 4.282 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 outliers start: 161 outliers final: 34 residues processed: 580 average time/residue: 0.5421 time to fit residues: 491.5799 Evaluate side-chains 246 residues out of total 3537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 212 time to evaluate : 4.014 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 1 residues processed: 34 average time/residue: 0.3244 time to fit residues: 26.5647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 353 optimal weight: 7.9990 chunk 317 optimal weight: 2.9990 chunk 176 optimal weight: 10.0000 chunk 108 optimal weight: 5.9990 chunk 214 optimal weight: 10.0000 chunk 169 optimal weight: 30.0000 chunk 328 optimal weight: 5.9990 chunk 127 optimal weight: 5.9990 chunk 199 optimal weight: 30.0000 chunk 244 optimal weight: 6.9990 chunk 380 optimal weight: 20.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 140 GLN A 196 GLN A 278 ASN ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 500 ASN A 643 GLN ** A 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1004 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 5 ASN ** B 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 382 ASN ** B 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 573 ASN ** B 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 807 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1126 GLN ** B1172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 GLN D 12 ASN D 93 GLN D 111 HIS ** D 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 114 HIS E 152 ASN E 166 GLN E 180 GLN E 442 GLN ** E 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 616 ASN G 181 GLN G 312 GLN G 378 HIS G 380 ASN ** X 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.4922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.138 35642 Z= 0.583 Angle : 1.303 17.024 48732 Z= 0.680 Chirality : 0.064 0.460 5582 Planarity : 0.010 0.132 5940 Dihedral : 22.712 179.783 5906 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 49.40 Ramachandran Plot: Outliers : 1.10 % Allowed : 19.73 % Favored : 79.18 % Rotamer: Outliers : 4.83 % Allowed : 17.56 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.65 % Twisted General : 1.58 % 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: -6.04 (0.10), residues: 4106 helix: -3.60 (0.10), residues: 1228 sheet: -3.67 (0.22), residues: 391 loop : -4.55 (0.09), residues: 2487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP E 416 HIS 0.022 0.003 HIS B 372 PHE 0.039 0.003 PHE C 112 TYR 0.041 0.004 TYR B 488 ARG 0.019 0.001 ARG E 102 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8212 Ramachandran restraints generated. 4106 Oldfield, 0 Emsley, 4106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8212 Ramachandran restraints generated. 4106 Oldfield, 0 Emsley, 4106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 3537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 238 time to evaluate : 3.969 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 outliers start: 171 outliers final: 63 residues processed: 387 average time/residue: 0.4677 time to fit residues: 303.4765 Evaluate side-chains 242 residues out of total 3537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 179 time to evaluate : 4.296 Switching outliers to nearest non-outliers outliers start: 63 outliers final: 0 residues processed: 63 average time/residue: 0.3539 time to fit residues: 45.8019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 211 optimal weight: 30.0000 chunk 118 optimal weight: 0.4980 chunk 316 optimal weight: 0.9980 chunk 259 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 381 optimal weight: 8.9990 chunk 411 optimal weight: 4.9990 chunk 339 optimal weight: 2.9990 chunk 378 optimal weight: 8.9990 chunk 129 optimal weight: 20.0000 chunk 305 optimal weight: 0.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 523 GLN ** A 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 858 ASN A1049 ASN B 12 GLN B 112 HIS ** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 321 GLN ** B 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 794 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 902 HIS B1123 ASN B1238 ASN ** B1252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 177 ASN ** E 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 442 GLN E 549 GLN ** F 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 185 GLN ** G 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 142 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.6352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.130 35642 Z= 0.305 Angle : 1.019 17.496 48732 Z= 0.522 Chirality : 0.054 0.304 5582 Planarity : 0.007 0.100 5940 Dihedral : 22.080 179.172 5906 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 34.46 Ramachandran Plot: Outliers : 0.80 % Allowed : 16.34 % Favored : 82.85 % Rotamer: Outliers : 3.51 % Allowed : 21.85 % Favored : 74.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.53 % Twisted General : 0.51 % 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: -4.70 (0.11), residues: 4106 helix: -2.15 (0.13), residues: 1238 sheet: -3.13 (0.26), residues: 310 loop : -3.87 (0.10), residues: 2558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP E 416 HIS 0.014 0.002 HIS B 372 PHE 0.026 0.002 PHE D 4 TYR 0.030 0.003 TYR B1190 ARG 0.013 0.001 ARG Y 88 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8212 Ramachandran restraints generated. 4106 Oldfield, 0 Emsley, 4106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8212 Ramachandran restraints generated. 4106 Oldfield, 0 Emsley, 4106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 3537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 232 time to evaluate : 4.090 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 outliers start: 124 outliers final: 43 residues processed: 341 average time/residue: 0.4613 time to fit residues: 263.6234 Evaluate side-chains 220 residues out of total 3537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 177 time to evaluate : 4.025 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 0 residues processed: 43 average time/residue: 0.3538 time to fit residues: 32.9514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 376 optimal weight: 0.0070 chunk 286 optimal weight: 7.9990 chunk 197 optimal weight: 20.0000 chunk 42 optimal weight: 0.9990 chunk 181 optimal weight: 5.9990 chunk 255 optimal weight: 5.9990 chunk 382 optimal weight: 4.9990 chunk 405 optimal weight: 5.9990 chunk 199 optimal weight: 3.9990 chunk 362 optimal weight: 6.9990 chunk 109 optimal weight: 1.9990 overall best weight: 2.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 426 HIS ** A 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 718 HIS ** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 794 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1238 ASN ** D 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 476 HIS E 620 GLN ** F 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 34 GLN G 234 HIS G 251 GLN ** G 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.7023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 35642 Z= 0.301 Angle : 0.915 14.360 48732 Z= 0.472 Chirality : 0.050 0.272 5582 Planarity : 0.006 0.101 5940 Dihedral : 21.749 179.812 5906 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 30.80 Ramachandran Plot: Outliers : 0.75 % Allowed : 15.39 % Favored : 83.85 % Rotamer: Outliers : 3.39 % Allowed : 23.32 % Favored : 73.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.33 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.98 (0.12), residues: 4106 helix: -1.37 (0.14), residues: 1254 sheet: -3.03 (0.24), residues: 380 loop : -3.47 (0.11), residues: 2472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP E 416 HIS 0.010 0.002 HIS B 372 PHE 0.037 0.002 PHE C 112 TYR 0.024 0.002 TYR G 85 ARG 0.009 0.001 ARG G 332 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8212 Ramachandran restraints generated. 4106 Oldfield, 0 Emsley, 4106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8212 Ramachandran restraints generated. 4106 Oldfield, 0 Emsley, 4106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 3537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 195 time to evaluate : 3.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 120 outliers final: 45 residues processed: 303 average time/residue: 0.4335 time to fit residues: 226.0382 Evaluate side-chains 215 residues out of total 3537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 170 time to evaluate : 3.886 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 0 residues processed: 45 average time/residue: 0.3351 time to fit residues: 33.8909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 337 optimal weight: 0.6980 chunk 229 optimal weight: 8.9990 chunk 5 optimal weight: 20.0000 chunk 301 optimal weight: 0.2980 chunk 167 optimal weight: 30.0000 chunk 345 optimal weight: 0.9990 chunk 279 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 206 optimal weight: 0.0270 chunk 363 optimal weight: 5.9990 chunk 102 optimal weight: 0.9990 overall best weight: 0.6042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 HIS ** A 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 278 ASN A 319 HIS A 398 HIS ** A 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 205 GLN ** B 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 GLN ** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 794 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 32 GLN ** D 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 93 GLN D 111 HIS E 46 ASN E 152 ASN ** E 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 511 GLN F 27 ASN ** G 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.7673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 35642 Z= 0.220 Angle : 0.854 14.667 48732 Z= 0.435 Chirality : 0.048 0.308 5582 Planarity : 0.006 0.100 5940 Dihedral : 21.486 177.184 5906 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 25.83 Ramachandran Plot: Outliers : 0.73 % Allowed : 13.18 % Favored : 86.09 % Rotamer: Outliers : 2.46 % Allowed : 25.22 % Favored : 72.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.44 (0.12), residues: 4106 helix: -0.84 (0.14), residues: 1256 sheet: -2.65 (0.27), residues: 309 loop : -3.20 (0.11), residues: 2541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP E 416 HIS 0.010 0.001 HIS A 215 PHE 0.034 0.002 PHE C 112 TYR 0.018 0.001 TYR G 85 ARG 0.015 0.000 ARG F 17 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8212 Ramachandran restraints generated. 4106 Oldfield, 0 Emsley, 4106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8212 Ramachandran restraints generated. 4106 Oldfield, 0 Emsley, 4106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 3537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 204 time to evaluate : 4.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 87 outliers final: 27 residues processed: 276 average time/residue: 0.4247 time to fit residues: 207.1360 Evaluate side-chains 203 residues out of total 3537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 176 time to evaluate : 4.189 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.3434 time to fit residues: 22.9317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 136 optimal weight: 10.0000 chunk 364 optimal weight: 8.9990 chunk 80 optimal weight: 0.7980 chunk 237 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 chunk 405 optimal weight: 0.1980 chunk 336 optimal weight: 0.6980 chunk 187 optimal weight: 10.0000 chunk 33 optimal weight: 0.5980 chunk 134 optimal weight: 7.9990 chunk 212 optimal weight: 9.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 HIS A 306 ASN A 398 HIS ** A 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 462 GLN ** B 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 794 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 380 ASN ** X 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.8076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 35642 Z= 0.211 Angle : 0.817 16.084 48732 Z= 0.415 Chirality : 0.047 0.265 5582 Planarity : 0.005 0.097 5940 Dihedral : 21.285 177.825 5906 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 24.70 Ramachandran Plot: Outliers : 0.63 % Allowed : 13.42 % Favored : 85.95 % Rotamer: Outliers : 2.01 % Allowed : 26.77 % Favored : 71.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.16 (0.12), residues: 4106 helix: -0.55 (0.15), residues: 1260 sheet: -2.46 (0.26), residues: 377 loop : -3.05 (0.11), residues: 2469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 416 HIS 0.007 0.001 HIS B 372 PHE 0.030 0.002 PHE C 112 TYR 0.017 0.001 TYR B 177 ARG 0.006 0.000 ARG B 131 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8212 Ramachandran restraints generated. 4106 Oldfield, 0 Emsley, 4106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8212 Ramachandran restraints generated. 4106 Oldfield, 0 Emsley, 4106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 3537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 193 time to evaluate : 4.380 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 outliers start: 71 outliers final: 28 residues processed: 255 average time/residue: 0.4416 time to fit residues: 195.6226 Evaluate side-chains 190 residues out of total 3537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 162 time to evaluate : 3.981 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.3718 time to fit residues: 24.3255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 390 optimal weight: 5.9990 chunk 45 optimal weight: 0.1980 chunk 230 optimal weight: 7.9990 chunk 296 optimal weight: 4.9990 chunk 229 optimal weight: 6.9990 chunk 341 optimal weight: 7.9990 chunk 226 optimal weight: 0.9980 chunk 403 optimal weight: 3.9990 chunk 252 optimal weight: 9.9990 chunk 246 optimal weight: 3.9990 chunk 186 optimal weight: 9.9990 overall best weight: 2.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 802 ASN ** B 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 794 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 GLN ** D 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 201 ASN E 204 GLN ** E 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 549 GLN X 177 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.8279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 35642 Z= 0.283 Angle : 0.829 16.241 48732 Z= 0.420 Chirality : 0.047 0.259 5582 Planarity : 0.005 0.096 5940 Dihedral : 21.175 179.300 5906 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 26.00 Ramachandran Plot: Outliers : 0.66 % Allowed : 13.59 % Favored : 85.75 % Rotamer: Outliers : 1.50 % Allowed : 27.28 % Favored : 71.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.02 (0.12), residues: 4106 helix: -0.39 (0.15), residues: 1249 sheet: -2.31 (0.26), residues: 382 loop : -3.00 (0.11), residues: 2475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 416 HIS 0.006 0.001 HIS B 305 PHE 0.025 0.002 PHE D 163 TYR 0.016 0.002 TYR A 637 ARG 0.008 0.000 ARG X 158 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8212 Ramachandran restraints generated. 4106 Oldfield, 0 Emsley, 4106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8212 Ramachandran restraints generated. 4106 Oldfield, 0 Emsley, 4106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 3537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 170 time to evaluate : 3.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 53 outliers final: 22 residues processed: 218 average time/residue: 0.4394 time to fit residues: 167.4360 Evaluate side-chains 178 residues out of total 3537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 156 time to evaluate : 3.992 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.3905 time to fit residues: 20.3751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 249 optimal weight: 0.4980 chunk 161 optimal weight: 9.9990 chunk 241 optimal weight: 7.9990 chunk 121 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 chunk 78 optimal weight: 0.8980 chunk 256 optimal weight: 3.9990 chunk 275 optimal weight: 5.9990 chunk 199 optimal weight: 20.0000 chunk 37 optimal weight: 10.0000 chunk 317 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 112 HIS ** B 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 794 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 390 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.8631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 35642 Z= 0.213 Angle : 0.805 15.025 48732 Z= 0.405 Chirality : 0.046 0.253 5582 Planarity : 0.005 0.094 5940 Dihedral : 21.059 176.133 5906 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 23.38 Ramachandran Plot: Outliers : 0.63 % Allowed : 12.52 % Favored : 86.85 % Rotamer: Outliers : 0.71 % Allowed : 27.88 % Favored : 71.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.90 (0.13), residues: 4106 helix: -0.30 (0.15), residues: 1257 sheet: -2.13 (0.27), residues: 361 loop : -2.95 (0.11), residues: 2488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 199 HIS 0.005 0.001 HIS B 372 PHE 0.024 0.001 PHE D 163 TYR 0.018 0.001 TYR G 85 ARG 0.007 0.000 ARG C 57 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8212 Ramachandran restraints generated. 4106 Oldfield, 0 Emsley, 4106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8212 Ramachandran restraints generated. 4106 Oldfield, 0 Emsley, 4106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 3537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 166 time to evaluate : 3.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 6 residues processed: 189 average time/residue: 0.4369 time to fit residues: 145.0495 Evaluate side-chains 165 residues out of total 3537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 159 time to evaluate : 3.775 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.3432 time to fit residues: 8.8816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 367 optimal weight: 5.9990 chunk 386 optimal weight: 20.0000 chunk 352 optimal weight: 4.9990 chunk 376 optimal weight: 9.9990 chunk 226 optimal weight: 1.9990 chunk 163 optimal weight: 30.0000 chunk 295 optimal weight: 8.9990 chunk 115 optimal weight: 0.9990 chunk 340 optimal weight: 9.9990 chunk 355 optimal weight: 6.9990 chunk 375 optimal weight: 0.9980 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 794 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 390 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.8713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 35642 Z= 0.283 Angle : 0.829 15.434 48732 Z= 0.417 Chirality : 0.047 0.358 5582 Planarity : 0.005 0.094 5940 Dihedral : 21.006 179.857 5906 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 25.43 Ramachandran Plot: Outliers : 0.63 % Allowed : 14.03 % Favored : 85.34 % Rotamer: Outliers : 0.57 % Allowed : 28.13 % Favored : 71.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.87 (0.12), residues: 4106 helix: -0.24 (0.15), residues: 1252 sheet: -2.01 (0.28), residues: 356 loop : -2.96 (0.11), residues: 2498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 199 HIS 0.006 0.001 HIS B 305 PHE 0.027 0.001 PHE D 163 TYR 0.021 0.002 TYR A 873 ARG 0.006 0.000 ARG D 174 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8212 Ramachandran restraints generated. 4106 Oldfield, 0 Emsley, 4106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8212 Ramachandran restraints generated. 4106 Oldfield, 0 Emsley, 4106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 3537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 155 time to evaluate : 4.060 Fit side-chains revert: symmetry clash outliers start: 20 outliers final: 6 residues processed: 166 average time/residue: 0.4516 time to fit residues: 132.6565 Evaluate side-chains 154 residues out of total 3537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 148 time to evaluate : 3.967 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.3496 time to fit residues: 9.2864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 247 optimal weight: 7.9990 chunk 397 optimal weight: 6.9990 chunk 242 optimal weight: 0.9980 chunk 188 optimal weight: 0.8980 chunk 276 optimal weight: 0.4980 chunk 417 optimal weight: 7.9990 chunk 384 optimal weight: 7.9990 chunk 332 optimal weight: 0.9980 chunk 34 optimal weight: 5.9990 chunk 256 optimal weight: 4.9990 chunk 203 optimal weight: 0.0470 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 348 GLN B 557 GLN ** B 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 794 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 GLN ** E 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 181 GLN G 316 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.9099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 35642 Z= 0.199 Angle : 0.807 16.009 48732 Z= 0.403 Chirality : 0.046 0.421 5582 Planarity : 0.005 0.093 5940 Dihedral : 20.794 175.476 5906 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 22.05 Ramachandran Plot: Outliers : 0.61 % Allowed : 11.98 % Favored : 87.41 % Rotamer: Outliers : 0.28 % Allowed : 28.47 % Favored : 71.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -2.74 (0.13), residues: 4106 helix: -0.12 (0.15), residues: 1252 sheet: -1.86 (0.28), residues: 346 loop : -2.90 (0.11), residues: 2508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 481 HIS 0.006 0.001 HIS G 378 PHE 0.023 0.001 PHE D 163 TYR 0.024 0.001 TYR G 85 ARG 0.006 0.000 ARG D 174 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8212 Ramachandran restraints generated. 4106 Oldfield, 0 Emsley, 4106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8212 Ramachandran restraints generated. 4106 Oldfield, 0 Emsley, 4106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 3537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 174 time to evaluate : 4.080 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 3 residues processed: 182 average time/residue: 0.4362 time to fit residues: 139.4681 Evaluate side-chains 158 residues out of total 3537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 155 time to evaluate : 4.100 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.3392 time to fit residues: 7.3149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 264 optimal weight: 0.8980 chunk 354 optimal weight: 5.9990 chunk 101 optimal weight: 0.6980 chunk 306 optimal weight: 0.8980 chunk 49 optimal weight: 7.9990 chunk 92 optimal weight: 4.9990 chunk 332 optimal weight: 0.0770 chunk 139 optimal weight: 0.8980 chunk 341 optimal weight: 7.9990 chunk 42 optimal weight: 0.9980 chunk 61 optimal weight: 3.9990 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 GLN ** B 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 794 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 47 ASN ** E 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.077199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.054030 restraints weight = 194494.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.055524 restraints weight = 99917.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.056462 restraints weight = 67693.776| |-----------------------------------------------------------------------------| r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3310 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3310 r_free = 0.3310 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3309 r_free = 0.3309 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3309 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.9289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 35642 Z= 0.197 Angle : 0.790 16.044 48732 Z= 0.395 Chirality : 0.045 0.225 5582 Planarity : 0.005 0.093 5940 Dihedral : 20.684 177.064 5906 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 21.40 Ramachandran Plot: Outliers : 0.61 % Allowed : 12.08 % Favored : 87.31 % Rotamer: Outliers : 0.40 % Allowed : 28.64 % Favored : 70.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -2.64 (0.13), residues: 4106 helix: -0.00 (0.15), residues: 1245 sheet: -1.79 (0.28), residues: 347 loop : -2.85 (0.11), residues: 2514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 199 HIS 0.006 0.001 HIS G 378 PHE 0.023 0.001 PHE D 163 TYR 0.020 0.001 TYR G 85 ARG 0.023 0.000 ARG B 74 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6589.93 seconds wall clock time: 121 minutes 58.13 seconds (7318.13 seconds total)