Starting phenix.real_space_refine on Mon May 19 14:52:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jar_36132/05_2025/8jar_36132.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jar_36132/05_2025/8jar_36132.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jar_36132/05_2025/8jar_36132.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jar_36132/05_2025/8jar_36132.map" model { file = "/net/cci-nas-00/data/ceres_data/8jar_36132/05_2025/8jar_36132.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jar_36132/05_2025/8jar_36132.cif" } resolution = 3.3 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= 0.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2476 atoms to isotropic. 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 Zn 1 6.06 5 S 89 5.16 5 C 10758 2.51 5 N 2875 2.21 5 O 3118 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 16841 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 4613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 571, 4613 Classifications: {'peptide': 571} Link IDs: {'PTRANS': 6, 'TRANS': 564} Chain: "C" Number of atoms: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 830 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 9, 'TRANS': 95} Chain: "D" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 760 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 90} Chain: "S" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 65 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 7} Chain: "B" Number of atoms: 4630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 573, 4630 Classifications: {'peptide': 573} Link IDs: {'PTRANS': 6, 'TRANS': 566} Chain: "F" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 65 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 7} Chain: "G" Number of atoms: 758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 758 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 7, 'TRANS': 88} Chain: "H" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 760 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 90} Chain: "E" Number of atoms: 2214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2214 Classifications: {'peptide': 262} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 252} Chain breaks: 1 Chain: "I" Number of atoms: 2145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 2145 Classifications: {'peptide': 254} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 244} Chain breaks: 1 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 401 SG CYS A 54 60.557 51.050 101.711 1.00 1.95 S ATOM 6678 SG CYS B 54 64.232 50.237 102.846 1.00 10.81 S Time building chain proxies: 8.48, per 1000 atoms: 0.50 Number of scatterers: 16841 At special positions: 0 Unit cell: (119.72, 132.02, 186.96, 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) Zn 1 29.99 S 89 16.00 O 3118 8.00 N 2875 7.00 C 10758 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 3.93 Conformation dependent library (CDL) restraints added in 2.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 601 " pdb="ZN ZN B 601 " - pdb=" NE2 HIS A 89 " pdb="ZN ZN B 601 " - pdb=" NE2 HIS B 89 " pdb="ZN ZN B 601 " - pdb=" SG CYS A 54 " pdb="ZN ZN B 601 " - pdb=" SG CYS B 54 " Number of angles added : 2 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3954 Finding SS restraints... Secondary structure from input PDB file: 105 helices and 6 sheets defined 74.6% alpha, 2.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.49 Creating SS restraints... Processing helix chain 'A' and resid 12 through 24 removed outlier: 4.091A pdb=" N ASN A 24 " --> pdb=" O ALA A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 27 No H-bonds generated for 'chain 'A' and resid 25 through 27' Processing helix chain 'A' and resid 28 through 33 removed outlier: 4.009A pdb=" N ARG A 33 " --> pdb=" O ARG A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 50 removed outlier: 3.969A pdb=" N PHE A 41 " --> pdb=" O GLU A 37 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ASP A 42 " --> pdb=" O ASN A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 61 removed outlier: 3.619A pdb=" N SER A 58 " --> pdb=" O CYS A 54 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLU A 59 " --> pdb=" O GLN A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 71 removed outlier: 4.125A pdb=" N LYS A 68 " --> pdb=" O GLU A 64 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ARG A 71 " --> pdb=" O ALA A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 90 removed outlier: 3.861A pdb=" N LEU A 79 " --> pdb=" O LYS A 75 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N HIS A 81 " --> pdb=" O HIS A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 109 Processing helix chain 'A' and resid 112 through 134 removed outlier: 3.624A pdb=" N LYS A 118 " --> pdb=" O ALA A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 152 removed outlier: 4.247A pdb=" N LYS A 141 " --> pdb=" O SER A 137 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL A 142 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU A 152 " --> pdb=" O GLN A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 173 removed outlier: 3.865A pdb=" N ARG A 168 " --> pdb=" O GLU A 164 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N HIS A 171 " --> pdb=" O VAL A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 198 removed outlier: 3.837A pdb=" N GLU A 184 " --> pdb=" O HIS A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 219 removed outlier: 3.778A pdb=" N TYR A 209 " --> pdb=" O LYS A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 235 removed outlier: 3.658A pdb=" N GLU A 235 " --> pdb=" O GLU A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 259 Processing helix chain 'A' and resid 261 through 280 removed outlier: 4.411A pdb=" N GLN A 267 " --> pdb=" O LYS A 263 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU A 268 " --> pdb=" O LYS A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 300 Processing helix chain 'A' and resid 303 through 322 removed outlier: 3.572A pdb=" N VAL A 308 " --> pdb=" O ILE A 304 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N ALA A 309 " --> pdb=" O CYS A 305 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA A 313 " --> pdb=" O ALA A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 344 removed outlier: 3.549A pdb=" N TYR A 338 " --> pdb=" O GLU A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 368 removed outlier: 3.812A pdb=" N HIS A 366 " --> pdb=" O GLY A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 391 removed outlier: 3.655A pdb=" N ALA A 376 " --> pdb=" O HIS A 372 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N SER A 378 " --> pdb=" O LEU A 374 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU A 388 " --> pdb=" O LEU A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 421 removed outlier: 3.888A pdb=" N LEU A 403 " --> pdb=" O GLU A 399 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN A 404 " --> pdb=" O GLN A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 442 Processing helix chain 'A' and resid 444 through 463 Processing helix chain 'A' and resid 467 through 484 Processing helix chain 'A' and resid 487 through 507 removed outlier: 4.271A pdb=" N LYS A 493 " --> pdb=" O GLU A 489 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU A 494 " --> pdb=" O ASN A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 526 removed outlier: 4.366A pdb=" N TYR A 515 " --> pdb=" O SER A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 551 Processing helix chain 'A' and resid 566 through 577 Processing helix chain 'C' and resid 23 through 36 Processing helix chain 'C' and resid 38 through 40 No H-bonds generated for 'chain 'C' and resid 38 through 40' Processing helix chain 'C' and resid 56 through 61 removed outlier: 3.587A pdb=" N GLY C 61 " --> pdb=" O LEU C 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 37 Processing helix chain 'D' and resid 39 through 46 Processing helix chain 'D' and resid 48 through 52 removed outlier: 3.532A pdb=" N PHE D 52 " --> pdb=" O PRO D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 66 through 83 removed outlier: 3.752A pdb=" N LYS D 72 " --> pdb=" O HIS D 68 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG D 82 " --> pdb=" O THR D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 111 removed outlier: 3.516A pdb=" N MET D 105 " --> pdb=" O LEU D 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 23 Processing helix chain 'B' and resid 31 through 35 Processing helix chain 'B' and resid 36 through 50 Processing helix chain 'B' and resid 52 through 61 removed outlier: 3.853A pdb=" N GLU B 59 " --> pdb=" O GLN B 55 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N CYS B 61 " --> pdb=" O GLY B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 70 removed outlier: 3.546A pdb=" N LYS B 68 " --> pdb=" O GLU B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 90 removed outlier: 3.951A pdb=" N HIS B 81 " --> pdb=" O HIS B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 109 removed outlier: 3.923A pdb=" N SER B 106 " --> pdb=" O SER B 102 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N TYR B 107 " --> pdb=" O ARG B 103 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ILE B 108 " --> pdb=" O ARG B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 134 Processing helix chain 'B' and resid 135 through 151 removed outlier: 3.998A pdb=" N LYS B 141 " --> pdb=" O SER B 137 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N VAL B 142 " --> pdb=" O ASP B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 175 Processing helix chain 'B' and resid 178 through 199 removed outlier: 3.679A pdb=" N GLU B 183 " --> pdb=" O TYR B 179 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N GLU B 184 " --> pdb=" O HIS B 180 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N HIS B 199 " --> pdb=" O LYS B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 219 Processing helix chain 'B' and resid 221 through 235 Processing helix chain 'B' and resid 241 through 258 Processing helix chain 'B' and resid 261 through 280 removed outlier: 3.713A pdb=" N GLN B 267 " --> pdb=" O LYS B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 301 Processing helix chain 'B' and resid 303 through 322 removed outlier: 3.857A pdb=" N ALA B 309 " --> pdb=" O CYS B 305 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER B 320 " --> pdb=" O ASP B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 344 Processing helix chain 'B' and resid 351 through 360 Processing helix chain 'B' and resid 360 through 368 removed outlier: 3.866A pdb=" N ILE B 364 " --> pdb=" O ALA B 360 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N HIS B 366 " --> pdb=" O GLY B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 393 removed outlier: 3.746A pdb=" N ALA B 376 " --> pdb=" O HIS B 372 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N SER B 377 " --> pdb=" O LEU B 373 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N SER B 378 " --> pdb=" O LEU B 374 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE B 385 " --> pdb=" O VAL B 381 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU B 388 " --> pdb=" O LEU B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 421 Processing helix chain 'B' and resid 425 through 442 Processing helix chain 'B' and resid 444 through 462 removed outlier: 3.591A pdb=" N GLU B 450 " --> pdb=" O LYS B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 484 Processing helix chain 'B' and resid 487 through 507 Processing helix chain 'B' and resid 512 through 528 removed outlier: 4.030A pdb=" N ASP B 516 " --> pdb=" O GLY B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 549 Processing helix chain 'B' and resid 555 through 560 removed outlier: 3.664A pdb=" N VAL B 560 " --> pdb=" O ALA B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 577 removed outlier: 3.559A pdb=" N SER B 577 " --> pdb=" O SER B 573 " (cutoff:3.500A) Processing helix chain 'G' and resid 23 through 36 removed outlier: 4.123A pdb=" N GLY G 33 " --> pdb=" O ARG G 29 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ILE G 34 " --> pdb=" O ILE G 30 " (cutoff:3.500A) Processing helix chain 'G' and resid 38 through 42 Processing helix chain 'H' and resid 32 through 37 Processing helix chain 'H' and resid 39 through 47 Processing helix chain 'H' and resid 53 through 55 No H-bonds generated for 'chain 'H' and resid 53 through 55' Processing helix chain 'H' and resid 66 through 83 removed outlier: 4.223A pdb=" N LYS H 72 " --> pdb=" O HIS H 68 " (cutoff:3.500A) Processing helix chain 'H' and resid 99 through 109 removed outlier: 3.717A pdb=" N PHE H 109 " --> pdb=" O MET H 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 26 removed outlier: 3.572A pdb=" N THR E 13 " --> pdb=" O ASP E 9 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N THR E 20 " --> pdb=" O LYS E 16 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N MET E 26 " --> pdb=" O LYS E 22 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 47 removed outlier: 3.620A pdb=" N PHE E 39 " --> pdb=" O TRP E 35 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N SER E 40 " --> pdb=" O ASN E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 79 removed outlier: 3.758A pdb=" N SER E 79 " --> pdb=" O ARG E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 105 removed outlier: 3.588A pdb=" N GLU E 93 " --> pdb=" O ARG E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 112 Processing helix chain 'E' and resid 138 through 151 removed outlier: 3.645A pdb=" N LEU E 144 " --> pdb=" O GLY E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 172 removed outlier: 3.644A pdb=" N ILE E 167 " --> pdb=" O LEU E 163 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS E 168 " --> pdb=" O LEU E 164 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLY E 172 " --> pdb=" O LYS E 168 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 191 removed outlier: 3.880A pdb=" N ILE E 181 " --> pdb=" O ASN E 177 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N PHE E 188 " --> pdb=" O VAL E 184 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N VAL E 189 " --> pdb=" O ILE E 185 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL E 191 " --> pdb=" O SER E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 192 through 194 No H-bonds generated for 'chain 'E' and resid 192 through 194' Processing helix chain 'E' and resid 200 through 207 removed outlier: 3.541A pdb=" N GLU E 205 " --> pdb=" O LYS E 201 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 229 removed outlier: 3.625A pdb=" N THR E 213 " --> pdb=" O SER E 209 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU E 222 " --> pdb=" O TYR E 218 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ALA E 223 " --> pdb=" O TYR E 219 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER E 224 " --> pdb=" O LYS E 220 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASN E 225 " --> pdb=" O GLN E 221 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLU E 229 " --> pdb=" O ASN E 225 " (cutoff:3.500A) Processing helix chain 'E' and resid 234 through 253 removed outlier: 4.010A pdb=" N LEU E 240 " --> pdb=" O MET E 236 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY E 241 " --> pdb=" O GLU E 237 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 257 No H-bonds generated for 'chain 'E' and resid 255 through 257' Processing helix chain 'E' and resid 258 through 271 removed outlier: 4.036A pdb=" N VAL E 262 " --> pdb=" O SER E 258 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ILE E 263 " --> pdb=" O TYR E 259 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N GLN E 267 " --> pdb=" O ILE E 263 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN E 268 " --> pdb=" O HIS E 264 " (cutoff:3.500A) Processing helix chain 'E' and resid 274 through 280 removed outlier: 3.560A pdb=" N HIS E 279 " --> pdb=" O LEU E 275 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ALA E 280 " --> pdb=" O GLN E 276 " (cutoff:3.500A) Processing helix chain 'I' and resid 9 through 25 removed outlier: 3.665A pdb=" N THR I 13 " --> pdb=" O ASP I 9 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ALA I 23 " --> pdb=" O THR I 19 " (cutoff:3.500A) Processing helix chain 'I' and resid 26 through 28 No H-bonds generated for 'chain 'I' and resid 26 through 28' Processing helix chain 'I' and resid 31 through 47 removed outlier: 3.658A pdb=" N PHE I 39 " --> pdb=" O TRP I 35 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N SER I 40 " --> pdb=" O ASN I 36 " (cutoff:3.500A) Processing helix chain 'I' and resid 53 through 79 Processing helix chain 'I' and resid 82 through 105 Processing helix chain 'I' and resid 105 through 112 Processing helix chain 'I' and resid 138 through 151 removed outlier: 3.540A pdb=" N LEU I 144 " --> pdb=" O GLY I 140 " (cutoff:3.500A) Processing helix chain 'I' and resid 155 through 171 removed outlier: 3.929A pdb=" N ASP I 170 " --> pdb=" O GLU I 166 " (cutoff:3.500A) Processing helix chain 'I' and resid 177 through 191 removed outlier: 4.189A pdb=" N ILE I 181 " --> pdb=" O ASN I 177 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N PHE I 188 " --> pdb=" O VAL I 184 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N VAL I 189 " --> pdb=" O ILE I 185 " (cutoff:3.500A) Processing helix chain 'I' and resid 192 through 195 Processing helix chain 'I' and resid 200 through 205 removed outlier: 3.937A pdb=" N GLU I 205 " --> pdb=" O LYS I 201 " (cutoff:3.500A) Processing helix chain 'I' and resid 207 through 218 removed outlier: 3.724A pdb=" N THR I 213 " --> pdb=" O SER I 209 " (cutoff:3.500A) Processing helix chain 'I' and resid 218 through 226 removed outlier: 3.818A pdb=" N SER I 224 " --> pdb=" O LYS I 220 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ASN I 225 " --> pdb=" O GLN I 221 " (cutoff:3.500A) Processing helix chain 'I' and resid 234 through 254 removed outlier: 3.520A pdb=" N VAL I 239 " --> pdb=" O TYR I 235 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LEU I 240 " --> pdb=" O MET I 236 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLY I 241 " --> pdb=" O GLU I 237 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS I 252 " --> pdb=" O ILE I 248 " (cutoff:3.500A) Processing helix chain 'I' and resid 255 through 257 No H-bonds generated for 'chain 'I' and resid 255 through 257' Processing helix chain 'I' and resid 258 through 269 removed outlier: 3.607A pdb=" N VAL I 262 " --> pdb=" O SER I 258 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE I 263 " --> pdb=" O TYR I 259 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU I 265 " --> pdb=" O LYS I 261 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG I 269 " --> pdb=" O GLU I 265 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 17 through 18 removed outlier: 6.977A pdb=" N PHE C 4 " --> pdb=" O ALA C 73 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N VAL C 75 " --> pdb=" O PHE C 4 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N MET C 6 " --> pdb=" O VAL C 75 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N LEU C 77 " --> pdb=" O MET C 6 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 12 through 14 removed outlier: 6.206A pdb=" N THR C 13 " --> pdb=" O ILE D 30 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N LYS D 32 " --> pdb=" O THR C 13 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N TYR D 18 " --> pdb=" O ASN D 58 " (cutoff:3.500A) removed outlier: 8.437A pdb=" N VAL D 60 " --> pdb=" O TYR D 18 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N LYS D 20 " --> pdb=" O VAL D 60 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AA4, first strand: chain 'G' and resid 49 through 50 Processing sheet with id=AA5, first strand: chain 'G' and resid 80 through 81 Processing sheet with id=AA6, first strand: chain 'H' and resid 18 through 22 removed outlier: 3.718A pdb=" N ASN H 58 " --> pdb=" O TYR H 18 " (cutoff:3.500A) 1038 hydrogen bonds defined for protein. 3081 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: 4.97 Time building geometry restraints manager: 4.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3821 1.33 - 1.45: 3699 1.45 - 1.57: 9553 1.57 - 1.69: 0 1.69 - 1.81: 132 Bond restraints: 17205 Sorted by residual: bond pdb=" C LEU I 155 " pdb=" N GLN I 156 " ideal model delta sigma weight residual 1.335 1.306 0.029 1.36e-02 5.41e+03 4.53e+00 bond pdb=" CA LEU I 155 " pdb=" C LEU I 155 " ideal model delta sigma weight residual 1.525 1.499 0.026 1.27e-02 6.20e+03 4.12e+00 bond pdb=" C LEU I 155 " pdb=" O LEU I 155 " ideal model delta sigma weight residual 1.233 1.211 0.022 1.43e-02 4.89e+03 2.31e+00 bond pdb=" N VAL B 560 " pdb=" CA VAL B 560 " ideal model delta sigma weight residual 1.474 1.457 0.017 1.57e-02 4.06e+03 1.21e+00 bond pdb=" CB ILE A 39 " pdb=" CG2 ILE A 39 " ideal model delta sigma weight residual 1.521 1.489 0.032 3.30e-02 9.18e+02 9.36e-01 ... (remaining 17200 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.67: 22765 1.67 - 3.34: 393 3.34 - 5.01: 52 5.01 - 6.68: 8 6.68 - 8.35: 2 Bond angle restraints: 23220 Sorted by residual: angle pdb=" C THR D 84 " pdb=" N ASN D 85 " pdb=" CA ASN D 85 " ideal model delta sigma weight residual 121.54 128.24 -6.70 1.91e+00 2.74e-01 1.23e+01 angle pdb=" N VAL A 21 " pdb=" CA VAL A 21 " pdb=" C VAL A 21 " ideal model delta sigma weight residual 113.39 108.52 4.87 1.47e+00 4.63e-01 1.10e+01 angle pdb=" N VAL B 560 " pdb=" CA VAL B 560 " pdb=" C VAL B 560 " ideal model delta sigma weight residual 106.21 109.08 -2.87 1.07e+00 8.73e-01 7.20e+00 angle pdb=" C ARG B 549 " pdb=" N GLN B 550 " pdb=" CA GLN B 550 " ideal model delta sigma weight residual 121.54 126.37 -4.83 1.91e+00 2.74e-01 6.41e+00 angle pdb=" O PRO I 154 " pdb=" C PRO I 154 " pdb=" N LEU I 155 " ideal model delta sigma weight residual 122.24 125.62 -3.38 1.34e+00 5.57e-01 6.37e+00 ... (remaining 23215 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 9279 17.96 - 35.93: 918 35.93 - 53.89: 128 53.89 - 71.86: 24 71.86 - 89.82: 18 Dihedral angle restraints: 10367 sinusoidal: 4240 harmonic: 6127 Sorted by residual: dihedral pdb=" CA ILE C 7 " pdb=" C ILE C 7 " pdb=" N ARG C 8 " pdb=" CA ARG C 8 " ideal model delta harmonic sigma weight residual -180.00 -160.39 -19.61 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA LEU E 27 " pdb=" C LEU E 27 " pdb=" N GLU E 28 " pdb=" CA GLU E 28 " ideal model delta harmonic sigma weight residual 180.00 161.14 18.86 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" CA ASN B 303 " pdb=" C ASN B 303 " pdb=" N ILE B 304 " pdb=" CA ILE B 304 " ideal model delta harmonic sigma weight residual -180.00 -161.96 -18.04 0 5.00e+00 4.00e-02 1.30e+01 ... (remaining 10364 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1998 0.047 - 0.094: 475 0.094 - 0.141: 53 0.141 - 0.188: 4 0.188 - 0.235: 1 Chirality restraints: 2531 Sorted by residual: chirality pdb=" CB VAL B 301 " pdb=" CA VAL B 301 " pdb=" CG1 VAL B 301 " pdb=" CG2 VAL B 301 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CG LEU I 155 " pdb=" CB LEU I 155 " pdb=" CD1 LEU I 155 " pdb=" CD2 LEU I 155 " both_signs ideal model delta sigma weight residual False -2.59 -2.75 0.16 2.00e-01 2.50e+01 6.18e-01 chirality pdb=" CB ILE A 26 " pdb=" CA ILE A 26 " pdb=" CG1 ILE A 26 " pdb=" CG2 ILE A 26 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.91e-01 ... (remaining 2528 not shown) Planarity restraints: 2969 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER I 209 " -0.033 5.00e-02 4.00e+02 5.01e-02 4.01e+00 pdb=" N PRO I 210 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO I 210 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO I 210 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER E 209 " 0.033 5.00e-02 4.00e+02 4.95e-02 3.92e+00 pdb=" N PRO E 210 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO E 210 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO E 210 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS E 255 " -0.030 5.00e-02 4.00e+02 4.51e-02 3.25e+00 pdb=" N PRO E 256 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO E 256 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO E 256 " -0.025 5.00e-02 4.00e+02 ... (remaining 2966 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 490 2.72 - 3.26: 17562 3.26 - 3.81: 28803 3.81 - 4.35: 35377 4.35 - 4.90: 60606 Nonbonded interactions: 142838 Sorted by model distance: nonbonded pdb=" OE1 GLU A 334 " pdb=" OG SER A 378 " model vdw 2.172 3.040 nonbonded pdb=" OH TYR A 338 " pdb=" O GLY S 0 " model vdw 2.186 3.040 nonbonded pdb=" OG SER C 94 " pdb=" OD2 ASP D 25 " model vdw 2.222 3.040 nonbonded pdb=" OE1 GLU B 334 " pdb=" OG SER B 378 " model vdw 2.231 3.040 nonbonded pdb=" OG SER B 479 " pdb=" O THR F -4 " model vdw 2.242 3.040 ... (remaining 142833 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 8 through 578) } ncs_group { reference = (chain 'C' and resid 2 through 97) selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = (chain 'E' and resid 1 through 272) selection = chain 'I' } ncs_group { reference = chain 'F' selection = chain 'S' } 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 individual isotropic 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: 21.690 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 36.380 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:4.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 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 : 0.004 0.037 17209 Z= 0.162 Angle : 0.542 8.350 23222 Z= 0.296 Chirality : 0.039 0.235 2531 Planarity : 0.004 0.050 2969 Dihedral : 14.401 89.821 6413 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -0.87 (0.18), residues: 2047 helix: -0.21 (0.13), residues: 1447 sheet: -1.93 (1.23), residues: 20 loop : -1.11 (0.24), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 147 HIS 0.010 0.001 HIS B 410 PHE 0.022 0.001 PHE A 41 TYR 0.016 0.001 TYR B 294 ARG 0.011 0.000 ARG C 9 Details of bonding type rmsd hydrogen bonds : bond 0.16397 ( 1038) hydrogen bonds : angle 6.69723 ( 3081) metal coordination : bond 0.00977 ( 4) metal coordination : angle 3.17884 ( 2) covalent geometry : bond 0.00376 (17205) covalent geometry : angle 0.54146 (23220) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 295 time to evaluate : 1.782 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 468 TYR cc_start: 0.6912 (t80) cc_final: 0.6706 (t80) REVERT: C 37 ARG cc_start: 0.6674 (mmm-85) cc_final: 0.5917 (mpt180) REVERT: B 396 LYS cc_start: 0.7611 (tptt) cc_final: 0.7357 (tppt) REVERT: G 43 ARG cc_start: 0.7014 (ptp-110) cc_final: 0.6777 (mtm110) outliers start: 0 outliers final: 0 residues processed: 295 average time/residue: 0.3173 time to fit residues: 136.5431 Evaluate side-chains 197 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 197 time to evaluate : 1.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 170 optimal weight: 0.9990 chunk 153 optimal weight: 1.9990 chunk 84 optimal weight: 0.1980 chunk 52 optimal weight: 5.9990 chunk 103 optimal weight: 0.9990 chunk 81 optimal weight: 0.5980 chunk 158 optimal weight: 0.0010 chunk 61 optimal weight: 3.9990 chunk 96 optimal weight: 0.8980 chunk 117 optimal weight: 3.9990 chunk 183 optimal weight: 0.6980 overall best weight: 0.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 65 GLN ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 51 GLN ** H 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 36 ASN E 190 HIS E 279 HIS ** I 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 186 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.177182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.140191 restraints weight = 22772.425| |-----------------------------------------------------------------------------| r_work (start): 0.3768 rms_B_bonded: 2.13 r_work: 0.3609 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3461 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.1262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17209 Z= 0.139 Angle : 0.519 8.037 23222 Z= 0.274 Chirality : 0.037 0.134 2531 Planarity : 0.004 0.050 2969 Dihedral : 4.547 72.710 2283 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.93 % Allowed : 7.51 % Favored : 91.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -0.17 (0.18), residues: 2047 helix: 0.39 (0.13), residues: 1486 sheet: -1.55 (1.19), residues: 20 loop : -1.23 (0.25), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 543 HIS 0.011 0.001 HIS A 343 PHE 0.018 0.001 PHE A 41 TYR 0.018 0.001 TYR B 495 ARG 0.007 0.000 ARG G 9 Details of bonding type rmsd hydrogen bonds : bond 0.04354 ( 1038) hydrogen bonds : angle 4.62691 ( 3081) metal coordination : bond 0.00990 ( 4) metal coordination : angle 3.82161 ( 2) covalent geometry : bond 0.00311 (17205) covalent geometry : angle 0.51818 (23220) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 225 time to evaluate : 2.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 261 GLU cc_start: 0.8045 (mm-30) cc_final: 0.7837 (mm-30) REVERT: G 19 LYS cc_start: 0.5774 (mmmt) cc_final: 0.5376 (mmmt) REVERT: G 43 ARG cc_start: 0.7374 (ptp-110) cc_final: 0.6716 (mtm110) REVERT: I 82 GLN cc_start: 0.5269 (pp30) cc_final: 0.4770 (pp30) outliers start: 17 outliers final: 8 residues processed: 231 average time/residue: 0.3131 time to fit residues: 105.6577 Evaluate side-chains 207 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 199 time to evaluate : 1.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 198 LYS Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain H residue 17 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 69 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 137 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 177 optimal weight: 0.7980 chunk 56 optimal weight: 0.7980 chunk 85 optimal weight: 0.6980 chunk 22 optimal weight: 0.7980 chunk 196 optimal weight: 2.9990 chunk 82 optimal weight: 0.2980 chunk 73 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 578 GLN G 65 GLN ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 169 ASN E 190 HIS ** I 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 190 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.174891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.137534 restraints weight = 22850.318| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 2.08 r_work: 0.3587 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3436 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 17209 Z= 0.155 Angle : 0.514 10.000 23222 Z= 0.269 Chirality : 0.038 0.164 2531 Planarity : 0.004 0.042 2969 Dihedral : 4.480 71.174 2283 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.82 % Allowed : 10.69 % Favored : 88.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.01 (0.18), residues: 2047 helix: 0.58 (0.14), residues: 1487 sheet: -1.84 (1.11), residues: 20 loop : -1.34 (0.25), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP A 543 HIS 0.009 0.001 HIS A 343 PHE 0.016 0.001 PHE A 41 TYR 0.019 0.001 TYR A 468 ARG 0.009 0.000 ARG G 9 Details of bonding type rmsd hydrogen bonds : bond 0.03978 ( 1038) hydrogen bonds : angle 4.40584 ( 3081) metal coordination : bond 0.01223 ( 4) metal coordination : angle 4.14341 ( 2) covalent geometry : bond 0.00360 (17205) covalent geometry : angle 0.51244 (23220) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 214 time to evaluate : 1.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 41 GLU cc_start: 0.7305 (tt0) cc_final: 0.6955 (tt0) REVERT: B 404 GLN cc_start: 0.7707 (tp-100) cc_final: 0.7464 (tp-100) REVERT: G 19 LYS cc_start: 0.5772 (mmmt) cc_final: 0.5427 (mmmt) REVERT: G 41 GLU cc_start: 0.8145 (tt0) cc_final: 0.7892 (tt0) REVERT: E 146 MET cc_start: 0.7536 (mmt) cc_final: 0.7297 (mmp) REVERT: E 236 MET cc_start: 0.1954 (tmm) cc_final: 0.1599 (tmm) REVERT: I 82 GLN cc_start: 0.5473 (pp30) cc_final: 0.4736 (pp30) outliers start: 15 outliers final: 10 residues processed: 222 average time/residue: 0.2862 time to fit residues: 96.0572 Evaluate side-chains 204 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 194 time to evaluate : 1.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain B residue 198 LYS Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain F residue -4 THR Chi-restraints excluded: chain H residue 60 VAL Chi-restraints excluded: chain I residue 146 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 174 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 168 optimal weight: 0.3980 chunk 179 optimal weight: 0.9990 chunk 127 optimal weight: 4.9990 chunk 42 optimal weight: 0.6980 chunk 13 optimal weight: 0.4980 chunk 63 optimal weight: 1.9990 chunk 118 optimal weight: 0.6980 chunk 137 optimal weight: 0.7980 chunk 36 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 65 GLN ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 190 HIS ** I 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 186 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.174912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.137549 restraints weight = 22816.172| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 2.11 r_work: 0.3498 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17209 Z= 0.146 Angle : 0.498 9.288 23222 Z= 0.260 Chirality : 0.037 0.134 2531 Planarity : 0.004 0.044 2969 Dihedral : 4.448 71.470 2283 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.59 % Allowed : 11.51 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.16 (0.19), residues: 2047 helix: 0.70 (0.14), residues: 1482 sheet: -1.73 (1.10), residues: 20 loop : -1.32 (0.25), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP A 543 HIS 0.008 0.001 HIS A 343 PHE 0.018 0.001 PHE I 202 TYR 0.014 0.001 TYR B 468 ARG 0.010 0.000 ARG G 9 Details of bonding type rmsd hydrogen bonds : bond 0.03759 ( 1038) hydrogen bonds : angle 4.27237 ( 3081) metal coordination : bond 0.01168 ( 4) metal coordination : angle 4.14057 ( 2) covalent geometry : bond 0.00338 (17205) covalent geometry : angle 0.49667 (23220) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 205 time to evaluate : 1.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 MET cc_start: 0.6624 (OUTLIER) cc_final: 0.6017 (mpp) REVERT: B 404 GLN cc_start: 0.7651 (tp-100) cc_final: 0.7380 (tp-100) REVERT: E 162 MET cc_start: 0.7085 (mtt) cc_final: 0.6865 (mtp) REVERT: E 236 MET cc_start: 0.1984 (tmm) cc_final: 0.1702 (tmm) REVERT: I 82 GLN cc_start: 0.5602 (pp30) cc_final: 0.4763 (pp30) outliers start: 29 outliers final: 16 residues processed: 224 average time/residue: 0.2872 time to fit residues: 97.5226 Evaluate side-chains 206 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 189 time to evaluate : 1.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 165 CYS Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain C residue 22 SER Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 198 LYS Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain G residue 14 ILE Chi-restraints excluded: chain G residue 77 LEU Chi-restraints excluded: chain H residue 108 ASN Chi-restraints excluded: chain E residue 158 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 41 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 188 optimal weight: 0.9990 chunk 55 optimal weight: 4.9990 chunk 102 optimal weight: 0.5980 chunk 54 optimal weight: 3.9990 chunk 129 optimal weight: 1.9990 chunk 168 optimal weight: 0.9990 chunk 178 optimal weight: 0.8980 chunk 169 optimal weight: 0.9990 chunk 46 optimal weight: 0.0570 overall best weight: 0.7102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 ASN A 395 ASN ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 65 GLN ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 190 HIS ** I 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 186 ASN I 268 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.173996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.136688 restraints weight = 23039.386| |-----------------------------------------------------------------------------| r_work (start): 0.3738 rms_B_bonded: 2.11 r_work: 0.3489 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 17209 Z= 0.158 Angle : 0.503 8.235 23222 Z= 0.262 Chirality : 0.037 0.133 2531 Planarity : 0.004 0.046 2969 Dihedral : 4.455 74.019 2283 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.92 % Allowed : 12.55 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.20 (0.19), residues: 2047 helix: 0.74 (0.14), residues: 1484 sheet: -1.83 (1.07), residues: 20 loop : -1.34 (0.25), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP A 543 HIS 0.007 0.001 HIS A 343 PHE 0.026 0.001 PHE B 296 TYR 0.020 0.001 TYR A 468 ARG 0.011 0.000 ARG G 9 Details of bonding type rmsd hydrogen bonds : bond 0.03716 ( 1038) hydrogen bonds : angle 4.23025 ( 3081) metal coordination : bond 0.01297 ( 4) metal coordination : angle 4.13394 ( 2) covalent geometry : bond 0.00372 (17205) covalent geometry : angle 0.50149 (23220) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 203 time to evaluate : 2.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 MET cc_start: 0.6657 (OUTLIER) cc_final: 0.6132 (mpp) REVERT: B 404 GLN cc_start: 0.7669 (tp-100) cc_final: 0.7409 (tp-100) REVERT: G 19 LYS cc_start: 0.5745 (mmmt) cc_final: 0.5251 (mmmt) REVERT: G 34 ILE cc_start: 0.7555 (mt) cc_final: 0.7330 (mt) REVERT: E 162 MET cc_start: 0.7114 (mtt) cc_final: 0.6863 (mtp) REVERT: E 236 MET cc_start: 0.1883 (tmm) cc_final: 0.1622 (tmm) outliers start: 35 outliers final: 23 residues processed: 224 average time/residue: 0.3053 time to fit residues: 105.8322 Evaluate side-chains 214 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 190 time to evaluate : 2.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 165 CYS Chi-restraints excluded: chain A residue 229 CYS Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 22 SER Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 148 GLN Chi-restraints excluded: chain B residue 198 LYS Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain G residue 14 ILE Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 77 LEU Chi-restraints excluded: chain H residue 60 VAL Chi-restraints excluded: chain H residue 108 ASN Chi-restraints excluded: chain E residue 7 VAL Chi-restraints excluded: chain E residue 158 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 185 optimal weight: 2.9990 chunk 168 optimal weight: 0.8980 chunk 116 optimal weight: 0.9980 chunk 165 optimal weight: 0.9980 chunk 150 optimal weight: 0.8980 chunk 51 optimal weight: 4.9990 chunk 114 optimal weight: 0.8980 chunk 147 optimal weight: 0.6980 chunk 123 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 HIS B 490 ASN G 65 GLN ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 190 HIS ** I 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 186 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.172703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.135461 restraints weight = 23106.367| |-----------------------------------------------------------------------------| r_work (start): 0.3720 rms_B_bonded: 2.16 r_work: 0.3465 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 17209 Z= 0.179 Angle : 0.530 10.837 23222 Z= 0.274 Chirality : 0.038 0.140 2531 Planarity : 0.004 0.048 2969 Dihedral : 4.530 77.986 2283 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.03 % Allowed : 13.27 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.15 (0.19), residues: 2047 helix: 0.69 (0.14), residues: 1491 sheet: -1.77 (1.08), residues: 20 loop : -1.33 (0.26), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP A 543 HIS 0.007 0.001 HIS A 343 PHE 0.023 0.001 PHE B 445 TYR 0.014 0.001 TYR D 76 ARG 0.013 0.000 ARG G 9 Details of bonding type rmsd hydrogen bonds : bond 0.03739 ( 1038) hydrogen bonds : angle 4.23667 ( 3081) metal coordination : bond 0.01507 ( 4) metal coordination : angle 4.36172 ( 2) covalent geometry : bond 0.00423 (17205) covalent geometry : angle 0.52836 (23220) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 206 time to evaluate : 1.901 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 156 MET cc_start: 0.6644 (OUTLIER) cc_final: 0.6187 (mpp) REVERT: B 396 LYS cc_start: 0.7352 (tptt) cc_final: 0.7028 (tppt) REVERT: B 404 GLN cc_start: 0.7693 (tp-100) cc_final: 0.7427 (tp-100) REVERT: G 19 LYS cc_start: 0.5753 (mmmt) cc_final: 0.5292 (mmmt) REVERT: E 162 MET cc_start: 0.7119 (mtt) cc_final: 0.6880 (mtp) REVERT: E 236 MET cc_start: 0.1892 (tmm) cc_final: 0.1659 (tmm) outliers start: 37 outliers final: 26 residues processed: 227 average time/residue: 0.2776 time to fit residues: 96.6680 Evaluate side-chains 219 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 192 time to evaluate : 1.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 165 CYS Chi-restraints excluded: chain A residue 229 CYS Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 22 SER Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain D residue 98 GLU Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 148 GLN Chi-restraints excluded: chain B residue 198 LYS Chi-restraints excluded: chain B residue 229 CYS Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain G residue 14 ILE Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 77 LEU Chi-restraints excluded: chain H residue 60 VAL Chi-restraints excluded: chain H residue 108 ASN Chi-restraints excluded: chain E residue 7 VAL Chi-restraints excluded: chain E residue 158 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 123 optimal weight: 2.9990 chunk 169 optimal weight: 0.8980 chunk 147 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 164 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 148 optimal weight: 0.5980 chunk 116 optimal weight: 0.9980 chunk 179 optimal weight: 0.3980 chunk 141 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 HIS ** B 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 490 ASN G 65 GLN ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 190 HIS ** I 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.169534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.134391 restraints weight = 22632.472| |-----------------------------------------------------------------------------| r_work (start): 0.3741 rms_B_bonded: 1.98 r_work: 0.3490 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3334 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 17209 Z= 0.160 Angle : 0.528 10.826 23222 Z= 0.272 Chirality : 0.038 0.137 2531 Planarity : 0.004 0.049 2969 Dihedral : 4.515 78.491 2283 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.86 % Allowed : 14.42 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.21 (0.19), residues: 2047 helix: 0.74 (0.14), residues: 1494 sheet: -1.77 (1.06), residues: 20 loop : -1.34 (0.26), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP A 543 HIS 0.007 0.001 HIS B 180 PHE 0.025 0.001 PHE B 445 TYR 0.021 0.001 TYR A 468 ARG 0.013 0.000 ARG G 9 Details of bonding type rmsd hydrogen bonds : bond 0.03664 ( 1038) hydrogen bonds : angle 4.20561 ( 3081) metal coordination : bond 0.01342 ( 4) metal coordination : angle 4.37557 ( 2) covalent geometry : bond 0.00378 (17205) covalent geometry : angle 0.52634 (23220) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 201 time to evaluate : 1.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 MET cc_start: 0.6713 (OUTLIER) cc_final: 0.6272 (mpp) REVERT: B 404 GLN cc_start: 0.7800 (tp-100) cc_final: 0.7520 (tp-100) REVERT: G 5 LEU cc_start: 0.8390 (mp) cc_final: 0.8157 (mp) REVERT: G 34 ILE cc_start: 0.7520 (mt) cc_final: 0.7210 (mt) REVERT: G 41 GLU cc_start: 0.7901 (tt0) cc_final: 0.7581 (tt0) REVERT: G 91 GLU cc_start: 0.7584 (pm20) cc_final: 0.7274 (pm20) REVERT: I 219 TYR cc_start: 0.7590 (OUTLIER) cc_final: 0.7269 (m-10) outliers start: 34 outliers final: 26 residues processed: 221 average time/residue: 0.2775 time to fit residues: 92.9660 Evaluate side-chains 223 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 195 time to evaluate : 1.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 165 CYS Chi-restraints excluded: chain A residue 229 CYS Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 22 SER Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 148 GLN Chi-restraints excluded: chain B residue 198 LYS Chi-restraints excluded: chain B residue 229 CYS Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain G residue 14 ILE Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 77 LEU Chi-restraints excluded: chain H residue 60 VAL Chi-restraints excluded: chain H residue 69 VAL Chi-restraints excluded: chain H residue 108 ASN Chi-restraints excluded: chain E residue 7 VAL Chi-restraints excluded: chain I residue 219 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 154 optimal weight: 0.5980 chunk 45 optimal weight: 0.4980 chunk 188 optimal weight: 0.9980 chunk 125 optimal weight: 0.7980 chunk 96 optimal weight: 0.9980 chunk 162 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 195 optimal weight: 0.9990 chunk 102 optimal weight: 0.6980 chunk 150 optimal weight: 0.4980 chunk 59 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 HIS ** B 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 490 ASN G 65 GLN ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 190 HIS ** I 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.169883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.133954 restraints weight = 22486.012| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 1.84 r_work: 0.3510 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3356 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17209 Z= 0.147 Angle : 0.519 9.813 23222 Z= 0.268 Chirality : 0.037 0.153 2531 Planarity : 0.004 0.052 2969 Dihedral : 4.490 77.764 2283 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.97 % Allowed : 14.53 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.26 (0.19), residues: 2047 helix: 0.79 (0.14), residues: 1494 sheet: -1.83 (1.03), residues: 20 loop : -1.36 (0.26), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP A 543 HIS 0.007 0.001 HIS A 343 PHE 0.028 0.001 PHE B 445 TYR 0.015 0.001 TYR A 510 ARG 0.013 0.000 ARG G 9 Details of bonding type rmsd hydrogen bonds : bond 0.03603 ( 1038) hydrogen bonds : angle 4.17075 ( 3081) metal coordination : bond 0.01177 ( 4) metal coordination : angle 4.26531 ( 2) covalent geometry : bond 0.00344 (17205) covalent geometry : angle 0.51715 (23220) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 193 time to evaluate : 1.791 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 156 MET cc_start: 0.6698 (OUTLIER) cc_final: 0.6235 (mpp) REVERT: A 196 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8131 (tp) REVERT: A 396 LYS cc_start: 0.7634 (mptt) cc_final: 0.7329 (mmmm) REVERT: B 148 GLN cc_start: 0.7925 (OUTLIER) cc_final: 0.7648 (mt0) REVERT: B 404 GLN cc_start: 0.7743 (tp-100) cc_final: 0.7454 (tp-100) REVERT: G 34 ILE cc_start: 0.7476 (mt) cc_final: 0.7210 (mt) REVERT: G 41 GLU cc_start: 0.8035 (tt0) cc_final: 0.7807 (tt0) REVERT: G 91 GLU cc_start: 0.7577 (pm20) cc_final: 0.7273 (pm20) REVERT: E 236 MET cc_start: 0.2315 (OUTLIER) cc_final: 0.2014 (tmm) REVERT: I 219 TYR cc_start: 0.7598 (OUTLIER) cc_final: 0.7272 (m-10) outliers start: 36 outliers final: 26 residues processed: 215 average time/residue: 0.2622 time to fit residues: 87.4403 Evaluate side-chains 222 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 191 time to evaluate : 1.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 165 CYS Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 229 CYS Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 22 SER Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain D residue 98 GLU Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 148 GLN Chi-restraints excluded: chain B residue 198 LYS Chi-restraints excluded: chain B residue 229 CYS Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain G residue 14 ILE Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 77 LEU Chi-restraints excluded: chain H residue 60 VAL Chi-restraints excluded: chain H residue 69 VAL Chi-restraints excluded: chain H residue 108 ASN Chi-restraints excluded: chain E residue 7 VAL Chi-restraints excluded: chain E residue 137 MET Chi-restraints excluded: chain E residue 236 MET Chi-restraints excluded: chain I residue 219 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 76 optimal weight: 0.5980 chunk 35 optimal weight: 0.7980 chunk 132 optimal weight: 0.0170 chunk 196 optimal weight: 1.9990 chunk 157 optimal weight: 0.6980 chunk 19 optimal weight: 6.9990 chunk 170 optimal weight: 2.9990 chunk 94 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 126 optimal weight: 4.9990 chunk 128 optimal weight: 0.2980 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 HIS A 343 HIS ** B 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 400 GLN B 490 ASN G 65 GLN ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 190 HIS ** I 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 225 ASN ** I 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.171084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.134769 restraints weight = 22706.350| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 1.98 r_work: 0.3509 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3352 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17209 Z= 0.128 Angle : 0.502 9.336 23222 Z= 0.260 Chirality : 0.036 0.152 2531 Planarity : 0.004 0.051 2969 Dihedral : 4.421 75.020 2283 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.03 % Allowed : 14.64 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.34 (0.19), residues: 2047 helix: 0.89 (0.14), residues: 1490 sheet: -2.42 (0.81), residues: 25 loop : -1.40 (0.26), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP A 543 HIS 0.006 0.001 HIS B 180 PHE 0.029 0.001 PHE I 202 TYR 0.013 0.001 TYR A 510 ARG 0.013 0.000 ARG G 9 Details of bonding type rmsd hydrogen bonds : bond 0.03509 ( 1038) hydrogen bonds : angle 4.09996 ( 3081) metal coordination : bond 0.00929 ( 4) metal coordination : angle 4.13906 ( 2) covalent geometry : bond 0.00296 (17205) covalent geometry : angle 0.50038 (23220) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 194 time to evaluate : 1.781 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 156 MET cc_start: 0.6732 (OUTLIER) cc_final: 0.6255 (mpp) REVERT: A 196 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8180 (tp) REVERT: A 396 LYS cc_start: 0.7686 (mptt) cc_final: 0.7410 (mmmm) REVERT: B 148 GLN cc_start: 0.7982 (OUTLIER) cc_final: 0.7703 (mt0) REVERT: B 400 GLN cc_start: 0.6502 (mt0) cc_final: 0.6209 (mp10) REVERT: B 404 GLN cc_start: 0.7783 (tp-100) cc_final: 0.7487 (tp-100) REVERT: B 485 MET cc_start: 0.7084 (mmm) cc_final: 0.6863 (mmm) REVERT: G 91 GLU cc_start: 0.7511 (pm20) cc_final: 0.7268 (pm20) REVERT: E 206 ILE cc_start: 0.7685 (tp) cc_final: 0.7400 (tp) REVERT: E 236 MET cc_start: 0.2380 (OUTLIER) cc_final: 0.2043 (tmm) REVERT: I 219 TYR cc_start: 0.7566 (OUTLIER) cc_final: 0.7255 (m-10) outliers start: 37 outliers final: 26 residues processed: 216 average time/residue: 0.2725 time to fit residues: 90.0735 Evaluate side-chains 217 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 186 time to evaluate : 1.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 165 CYS Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 229 CYS Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 22 SER Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain D residue 98 GLU Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 148 GLN Chi-restraints excluded: chain B residue 198 LYS Chi-restraints excluded: chain B residue 229 CYS Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain G residue 14 ILE Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 77 LEU Chi-restraints excluded: chain H residue 37 LEU Chi-restraints excluded: chain H residue 60 VAL Chi-restraints excluded: chain H residue 69 VAL Chi-restraints excluded: chain H residue 108 ASN Chi-restraints excluded: chain E residue 7 VAL Chi-restraints excluded: chain E residue 137 MET Chi-restraints excluded: chain E residue 236 MET Chi-restraints excluded: chain I residue 219 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 85 optimal weight: 1.9990 chunk 1 optimal weight: 0.2980 chunk 121 optimal weight: 0.6980 chunk 52 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 chunk 19 optimal weight: 0.0670 chunk 90 optimal weight: 0.5980 chunk 182 optimal weight: 0.5980 chunk 172 optimal weight: 4.9990 chunk 184 optimal weight: 1.9990 chunk 138 optimal weight: 0.0170 overall best weight: 0.3156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 343 HIS B 24 ASN ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 490 ASN G 65 GLN ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 88 HIS E 190 HIS ** I 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 156 GLN ** 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 = 0.4151 r_free = 0.4151 target = 0.172449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.136688 restraints weight = 22509.996| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 1.86 r_work: 0.3547 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3393 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17209 Z= 0.114 Angle : 0.508 10.049 23222 Z= 0.261 Chirality : 0.036 0.148 2531 Planarity : 0.004 0.054 2969 Dihedral : 4.380 72.056 2283 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.86 % Allowed : 15.08 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.51 (0.19), residues: 2047 helix: 1.01 (0.14), residues: 1485 sheet: -1.56 (0.95), residues: 14 loop : -1.37 (0.25), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.071 0.002 TRP A 543 HIS 0.006 0.001 HIS B 180 PHE 0.030 0.001 PHE B 445 TYR 0.013 0.001 TYR D 76 ARG 0.012 0.000 ARG G 9 Details of bonding type rmsd hydrogen bonds : bond 0.03465 ( 1038) hydrogen bonds : angle 4.07015 ( 3081) metal coordination : bond 0.00662 ( 4) metal coordination : angle 3.87820 ( 2) covalent geometry : bond 0.00256 (17205) covalent geometry : angle 0.50646 (23220) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 195 time to evaluate : 2.030 Fit side-chains revert: symmetry clash REVERT: A 108 ILE cc_start: 0.8313 (tt) cc_final: 0.8049 (tt) REVERT: A 156 MET cc_start: 0.6711 (OUTLIER) cc_final: 0.6240 (mpp) REVERT: A 196 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8168 (tp) REVERT: A 396 LYS cc_start: 0.7645 (mptt) cc_final: 0.7392 (mmmm) REVERT: B 148 GLN cc_start: 0.7916 (OUTLIER) cc_final: 0.7647 (mt0) REVERT: B 404 GLN cc_start: 0.7727 (tp-100) cc_final: 0.7423 (tp-100) REVERT: B 485 MET cc_start: 0.7078 (mmm) cc_final: 0.6863 (mmm) REVERT: G 5 LEU cc_start: 0.8380 (mp) cc_final: 0.8170 (mp) REVERT: G 19 LYS cc_start: 0.5663 (mmmt) cc_final: 0.5111 (mmmt) REVERT: G 91 GLU cc_start: 0.7486 (pm20) cc_final: 0.7244 (pm20) REVERT: E 185 ILE cc_start: 0.8204 (mt) cc_final: 0.7990 (mt) REVERT: E 236 MET cc_start: 0.2319 (OUTLIER) cc_final: 0.1970 (tmm) REVERT: I 219 TYR cc_start: 0.7566 (OUTLIER) cc_final: 0.7264 (m-10) outliers start: 34 outliers final: 27 residues processed: 214 average time/residue: 0.2739 time to fit residues: 92.1071 Evaluate side-chains 215 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 183 time to evaluate : 1.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 229 CYS Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 22 SER Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain D residue 98 GLU Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 148 GLN Chi-restraints excluded: chain B residue 198 LYS Chi-restraints excluded: chain B residue 229 CYS Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain G residue 14 ILE Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 77 LEU Chi-restraints excluded: chain H residue 37 LEU Chi-restraints excluded: chain H residue 60 VAL Chi-restraints excluded: chain H residue 69 VAL Chi-restraints excluded: chain H residue 108 ASN Chi-restraints excluded: chain E residue 7 VAL Chi-restraints excluded: chain E residue 137 MET Chi-restraints excluded: chain E residue 236 MET Chi-restraints excluded: chain I residue 219 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 45 optimal weight: 0.8980 chunk 171 optimal weight: 3.9990 chunk 59 optimal weight: 0.9980 chunk 90 optimal weight: 0.0470 chunk 73 optimal weight: 0.6980 chunk 157 optimal weight: 0.6980 chunk 127 optimal weight: 0.5980 chunk 141 optimal weight: 5.9990 chunk 10 optimal weight: 0.1980 chunk 201 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 overall best weight: 0.4478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 343 HIS ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 400 GLN B 490 ASN G 65 GLN ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 190 HIS ** I 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.172060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.136165 restraints weight = 22490.021| |-----------------------------------------------------------------------------| r_work (start): 0.3765 rms_B_bonded: 1.89 r_work: 0.3537 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3382 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17209 Z= 0.127 Angle : 0.508 8.933 23222 Z= 0.263 Chirality : 0.037 0.142 2531 Planarity : 0.004 0.051 2969 Dihedral : 4.355 72.868 2283 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.70 % Allowed : 15.46 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.53 (0.19), residues: 2047 helix: 1.03 (0.14), residues: 1484 sheet: -2.28 (0.81), residues: 25 loop : -1.34 (0.26), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.002 TRP A 543 HIS 0.006 0.001 HIS B 180 PHE 0.032 0.001 PHE B 445 TYR 0.013 0.001 TYR D 76 ARG 0.011 0.000 ARG G 9 Details of bonding type rmsd hydrogen bonds : bond 0.03483 ( 1038) hydrogen bonds : angle 4.05408 ( 3081) metal coordination : bond 0.00827 ( 4) metal coordination : angle 3.86205 ( 2) covalent geometry : bond 0.00292 (17205) covalent geometry : angle 0.50704 (23220) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9473.97 seconds wall clock time: 166 minutes 3.47 seconds (9963.47 seconds total)