Starting phenix.real_space_refine on Mon Jun 16 12:31:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jar_36132/06_2025/8jar_36132.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jar_36132/06_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_36132/06_2025/8jar_36132.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jar_36132/06_2025/8jar_36132.map" model { file = "/net/cci-nas-00/data/ceres_data/8jar_36132/06_2025/8jar_36132.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jar_36132/06_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 11.48, per 1000 atoms: 0.68 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: 3.65 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: 1.48 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: 5.18 Time building geometry restraints manager: 4.40 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: 12.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.020 Extract box with map and model: 0.710 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 41.560 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.270 ------------------------------------------------------------------------------- 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 : 1.723 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: 0.3076 time to fit residues: 132.9683 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 : 1.771 ------------------------------------------------------------------------------- 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 = 0.140190 restraints weight = 22772.425| |-----------------------------------------------------------------------------| r_work (start): 0.3768 rms_B_bonded: 2.13 r_work: 0.3610 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3460 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3460 ------------------------------------------------------------------------------- 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 : 1.962 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: 0.5770 (mmmt) cc_final: 0.5372 (mmmt) REVERT: G 43 ARG cc_start: 0.7374 (ptp-110) cc_final: 0.6714 (mtm110) REVERT: I 82 GLN cc_start: 0.5270 (pp30) cc_final: 0.4771 (pp30) outliers start: 17 outliers final: 8 residues processed: 231 average time/residue: 0.3248 time to fit residues: 110.7278 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 : 1.914 ------------------------------------------------------------------------------- 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: 2.9990 chunk 56 optimal weight: 0.7980 chunk 85 optimal weight: 0.6980 chunk 22 optimal weight: 0.8980 chunk 196 optimal weight: 2.9990 chunk 82 optimal weight: 0.2980 chunk 73 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4159 r_free = 0.4159 target = 0.174470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.137131 restraints weight = 22859.378| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 2.18 r_work: 0.3578 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3421 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.1563 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= 0.164 Angle : 0.520 9.962 23222 Z= 0.272 Chirality : 0.038 0.163 2531 Planarity : 0.004 0.043 2969 Dihedral : 4.501 71.411 2283 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 0.82 % Allowed : 10.58 % Favored : 88.60 % 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: -0.02 (0.18), residues: 2047 helix: 0.56 (0.14), residues: 1486 sheet: -1.87 (1.11), residues: 20 loop : -1.35 (0.25), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 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 0.008 0.000 ARG G 9 Details of bonding type rmsd hydrogen bonds : bond 0.04002 ( 1038) hydrogen bonds : angle 4.42061 ( 3081) metal coordination : bond 0.01315 ( 4) metal coordination : angle 4.23591 ( 2) covalent geometry : bond 0.00383 (17205) covalent geometry : angle 0.51900 (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 : 1.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 41 GLU cc_start: 0.7304 (tt0) cc_final: 0.6939 (tt0) REVERT: B 201 GLN cc_start: 0.6848 (tp-100) cc_final: 0.6644 (mp10) REVERT: B 404 GLN cc_start: 0.7723 (tp-100) cc_final: 0.7479 (tp-100) REVERT: G 19 LYS cc_start: 0.5779 (mmmt) cc_final: 0.5434 (mmmt) REVERT: G 41 GLU cc_start: 0.8150 (tt0) cc_final: 0.7899 (tt0) REVERT: G 43 ARG cc_start: 0.7457 (ptp-110) cc_final: 0.7228 (ptp-110) REVERT: E 146 MET cc_start: 0.7568 (mmt) cc_final: 0.7326 (mmp) REVERT: E 236 MET cc_start: 0.2092 (tmm) cc_final: 0.1712 (tmm) REVERT: I 82 GLN cc_start: 0.5485 (pp30) cc_final: 0.4742 (pp30) outliers start: 15 outliers final: 11 residues processed: 222 average time/residue: 0.3014 time to fit residues: 101.0987 Evaluate side-chains 205 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 194 time to evaluate : 1.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 ASP 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 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: 0.0970 chunk 168 optimal weight: 0.1980 chunk 179 optimal weight: 0.7980 chunk 127 optimal weight: 3.9990 chunk 42 optimal weight: 0.6980 chunk 13 optimal weight: 0.7980 chunk 63 optimal weight: 0.8980 chunk 118 optimal weight: 0.5980 chunk 137 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 overall best weight: 0.4778 ------------------------------------------------------------------------------- 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 42 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 = 0.4172 r_free = 0.4172 target = 0.175746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.138510 restraints weight = 22781.637| |-----------------------------------------------------------------------------| r_work (start): 0.3762 rms_B_bonded: 2.10 r_work: 0.3515 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.1757 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= 0.128 Angle : 0.485 9.090 23222 Z= 0.254 Chirality : 0.036 0.134 2531 Planarity : 0.004 0.044 2969 Dihedral : 4.412 71.333 2283 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.26 % Allowed : 11.79 % Favored : 86.95 % 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: 1482 sheet: -1.82 (1.07), residues: 20 loop : -1.31 (0.25), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP A 543 HIS 0.008 0.001 HIS A 343 PHE 0.018 0.001 PHE I 202 TYR 0.013 0.001 TYR B 468 ARG 0.011 0.000 ARG G 9 Details of bonding type rmsd hydrogen bonds : bond 0.03691 ( 1038) hydrogen bonds : angle 4.24172 ( 3081) metal coordination : bond 0.00976 ( 4) metal coordination : angle 3.99598 ( 2) covalent geometry : bond 0.00290 (17205) covalent geometry : angle 0.48360 (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 232 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 209 time to evaluate : 1.964 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 MET cc_start: 0.6640 (OUTLIER) cc_final: 0.6040 (mpp) REVERT: B 404 GLN cc_start: 0.7623 (tp-100) cc_final: 0.7348 (tp-100) REVERT: E 162 MET cc_start: 0.7077 (mtt) cc_final: 0.6843 (mtp) REVERT: E 236 MET cc_start: 0.1900 (tmm) cc_final: 0.1627 (tmm) outliers start: 23 outliers final: 11 residues processed: 223 average time/residue: 0.2983 time to fit residues: 102.1007 Evaluate side-chains 206 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 194 time to evaluate : 1.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 G residue 14 ILE Chi-restraints excluded: chain H residue 108 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 41 optimal weight: 0.3980 chunk 29 optimal weight: 1.9990 chunk 188 optimal weight: 0.9980 chunk 55 optimal weight: 0.9990 chunk 102 optimal weight: 0.5980 chunk 54 optimal weight: 0.3980 chunk 129 optimal weight: 1.9990 chunk 168 optimal weight: 1.9990 chunk 178 optimal weight: 0.5980 chunk 169 optimal weight: 0.8980 chunk 46 optimal weight: 0.0980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 395 ASN ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 42 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 186 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.176052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.138870 restraints weight = 22971.850| |-----------------------------------------------------------------------------| r_work (start): 0.3760 rms_B_bonded: 2.07 r_work: 0.3518 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3363 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17209 Z= 0.120 Angle : 0.478 8.643 23222 Z= 0.250 Chirality : 0.036 0.135 2531 Planarity : 0.003 0.048 2969 Dihedral : 4.345 70.620 2283 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.86 % Allowed : 12.77 % Favored : 85.36 % 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: 0.38 (0.19), residues: 2047 helix: 0.87 (0.14), residues: 1487 sheet: -1.68 (1.08), residues: 20 loop : -1.26 (0.26), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 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 0.009 0.000 ARG G 9 Details of bonding type rmsd hydrogen bonds : bond 0.03568 ( 1038) hydrogen bonds : angle 4.16342 ( 3081) metal coordination : bond 0.00845 ( 4) metal coordination : angle 3.83725 ( 2) covalent geometry : bond 0.00273 (17205) covalent geometry : angle 0.47665 (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 248 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 214 time to evaluate : 2.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 MET cc_start: 0.6711 (OUTLIER) cc_final: 0.6211 (mpp) REVERT: C 41 GLU cc_start: 0.7425 (tt0) cc_final: 0.7125 (tt0) REVERT: B 148 GLN cc_start: 0.7984 (OUTLIER) cc_final: 0.7702 (mt0) REVERT: B 374 LEU cc_start: 0.8954 (tp) cc_final: 0.8728 (tt) REVERT: B 404 GLN cc_start: 0.7756 (tp-100) cc_final: 0.7466 (tp-100) REVERT: G 19 LYS cc_start: 0.5620 (mmmt) cc_final: 0.5125 (mmmt) REVERT: E 28 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.7457 (mp0) REVERT: E 162 MET cc_start: 0.7327 (mtt) cc_final: 0.7079 (mtp) REVERT: E 236 MET cc_start: 0.1969 (tmm) cc_final: 0.1707 (tmm) outliers start: 34 outliers final: 20 residues processed: 234 average time/residue: 0.3982 time to fit residues: 144.0764 Evaluate side-chains 218 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 195 time to evaluate : 1.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 229 CYS Chi-restraints excluded: chain A residue 334 GLU 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 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 462 LEU Chi-restraints excluded: chain B residue 467 ASP 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 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 28 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 185 optimal weight: 0.6980 chunk 168 optimal weight: 0.9990 chunk 116 optimal weight: 1.9990 chunk 165 optimal weight: 0.9980 chunk 150 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 114 optimal weight: 0.7980 chunk 147 optimal weight: 0.9980 chunk 123 optimal weight: 2.9990 chunk 98 optimal weight: 0.0870 chunk 60 optimal weight: 0.5980 overall best weight: 0.5758 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 42 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 268 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.175106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.138008 restraints weight = 23010.294| |-----------------------------------------------------------------------------| r_work (start): 0.3756 rms_B_bonded: 2.10 r_work: 0.3594 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3442 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17209 Z= 0.140 Angle : 0.495 8.501 23222 Z= 0.258 Chirality : 0.037 0.149 2531 Planarity : 0.004 0.049 2969 Dihedral : 4.346 70.164 2283 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.64 % Allowed : 13.87 % Favored : 84.48 % 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: 0.38 (0.19), residues: 2047 helix: 0.90 (0.14), residues: 1483 sheet: -2.35 (0.76), residues: 35 loop : -1.27 (0.26), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP A 543 HIS 0.003 0.001 HIS B 180 PHE 0.023 0.001 PHE B 445 TYR 0.013 0.001 TYR B 468 ARG 0.011 0.000 ARG G 9 Details of bonding type rmsd hydrogen bonds : bond 0.03567 ( 1038) hydrogen bonds : angle 4.14474 ( 3081) metal coordination : bond 0.01121 ( 4) metal coordination : angle 3.79402 ( 2) covalent geometry : bond 0.00325 (17205) covalent geometry : angle 0.49399 (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 233 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 203 time to evaluate : 1.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 ILE cc_start: 0.8337 (tt) cc_final: 0.8071 (tt) REVERT: A 156 MET cc_start: 0.6686 (OUTLIER) cc_final: 0.6220 (mpp) REVERT: A 396 LYS cc_start: 0.7627 (mptt) cc_final: 0.7361 (mmmm) REVERT: C 41 GLU cc_start: 0.7384 (tt0) cc_final: 0.7063 (tt0) REVERT: B 148 GLN cc_start: 0.7836 (OUTLIER) cc_final: 0.7582 (mt0) REVERT: B 374 LEU cc_start: 0.8899 (tp) cc_final: 0.8652 (tt) REVERT: B 404 GLN cc_start: 0.7680 (tp-100) cc_final: 0.7379 (tp-100) REVERT: G 19 LYS cc_start: 0.5596 (mmmt) cc_final: 0.5120 (mmmt) REVERT: E 28 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.7360 (mp0) REVERT: E 146 MET cc_start: 0.7514 (mmt) cc_final: 0.7268 (mmp) REVERT: E 162 MET cc_start: 0.7168 (mtt) cc_final: 0.6908 (mtp) REVERT: I 146 MET cc_start: 0.7860 (mmt) cc_final: 0.7564 (mmm) outliers start: 30 outliers final: 23 residues processed: 220 average time/residue: 0.2778 time to fit residues: 94.3524 Evaluate side-chains 222 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 196 time to evaluate : 1.924 ------------------------------------------------------------------------------- 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 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 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 467 ASP 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 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 28 GLU 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: 1.9990 chunk 34 optimal weight: 0.8980 chunk 164 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 148 optimal weight: 0.5980 chunk 116 optimal weight: 1.9990 chunk 179 optimal weight: 0.0270 chunk 141 optimal weight: 0.0270 chunk 109 optimal weight: 1.9990 overall best weight: 0.4696 ------------------------------------------------------------------------------- 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** ** G 42 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.182816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.138581 restraints weight = 23642.571| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 2.13 r_work: 0.3597 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3442 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17209 Z= 0.125 Angle : 0.494 9.688 23222 Z= 0.254 Chirality : 0.036 0.134 2531 Planarity : 0.003 0.051 2969 Dihedral : 4.322 70.059 2283 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.75 % Allowed : 14.14 % Favored : 84.10 % 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: 0.45 (0.19), residues: 2047 helix: 0.97 (0.14), residues: 1484 sheet: -2.30 (0.76), residues: 35 loop : -1.30 (0.26), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP A 543 HIS 0.003 0.001 HIS B 431 PHE 0.026 0.001 PHE B 445 TYR 0.014 0.001 TYR B 468 ARG 0.013 0.000 ARG G 9 Details of bonding type rmsd hydrogen bonds : bond 0.03489 ( 1038) hydrogen bonds : angle 4.09829 ( 3081) metal coordination : bond 0.00895 ( 4) metal coordination : angle 3.69332 ( 2) covalent geometry : bond 0.00288 (17205) covalent geometry : angle 0.49254 (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 239 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 207 time to evaluate : 1.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 ILE cc_start: 0.8371 (tt) cc_final: 0.8116 (tt) REVERT: A 156 MET cc_start: 0.6771 (OUTLIER) cc_final: 0.6318 (mpp) REVERT: A 396 LYS cc_start: 0.7678 (mptt) cc_final: 0.7412 (mmmm) REVERT: C 41 GLU cc_start: 0.7365 (tt0) cc_final: 0.7040 (tt0) REVERT: D 111 ASP cc_start: 0.8596 (t0) cc_final: 0.8335 (t0) REVERT: B 148 GLN cc_start: 0.7876 (OUTLIER) cc_final: 0.7623 (mt0) REVERT: B 374 LEU cc_start: 0.8927 (tp) cc_final: 0.8686 (tt) REVERT: B 404 GLN cc_start: 0.7703 (tp-100) cc_final: 0.7407 (tp-100) REVERT: G 5 LEU cc_start: 0.8447 (mp) cc_final: 0.8239 (mp) REVERT: G 19 LYS cc_start: 0.5705 (mmmt) cc_final: 0.5224 (mmmt) REVERT: G 41 GLU cc_start: 0.7792 (tt0) cc_final: 0.7481 (tt0) REVERT: G 91 GLU cc_start: 0.7477 (pm20) cc_final: 0.7191 (pm20) REVERT: I 219 TYR cc_start: 0.7526 (OUTLIER) cc_final: 0.7116 (m-10) outliers start: 32 outliers final: 22 residues processed: 226 average time/residue: 0.2823 time to fit residues: 97.6129 Evaluate side-chains 222 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 197 time to evaluate : 1.746 ------------------------------------------------------------------------------- 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 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 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 467 ASP 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 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: 0.8980 chunk 45 optimal weight: 0.8980 chunk 188 optimal weight: 0.0980 chunk 125 optimal weight: 0.7980 chunk 96 optimal weight: 1.9990 chunk 162 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 195 optimal weight: 1.9990 chunk 102 optimal weight: 0.5980 chunk 150 optimal weight: 0.0670 chunk 59 optimal weight: 0.8980 overall best weight: 0.4518 ------------------------------------------------------------------------------- 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 279 HIS 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 156 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 = 0.4172 r_free = 0.4172 target = 0.175756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.138616 restraints weight = 22715.594| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 1.96 r_work: 0.3523 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3367 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17209 Z= 0.123 Angle : 0.495 8.685 23222 Z= 0.256 Chirality : 0.036 0.142 2531 Planarity : 0.003 0.050 2969 Dihedral : 4.317 69.771 2283 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.92 % Allowed : 14.36 % 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: 0.50 (0.19), residues: 2047 helix: 1.03 (0.14), residues: 1482 sheet: -2.30 (0.76), residues: 35 loop : -1.35 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP A 543 HIS 0.008 0.001 HIS B 366 PHE 0.028 0.001 PHE B 445 TYR 0.018 0.001 TYR A 510 ARG 0.012 0.000 ARG G 9 Details of bonding type rmsd hydrogen bonds : bond 0.03443 ( 1038) hydrogen bonds : angle 4.06667 ( 3081) metal coordination : bond 0.00875 ( 4) metal coordination : angle 3.68809 ( 2) covalent geometry : bond 0.00283 (17205) covalent geometry : angle 0.49387 (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 242 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 207 time to evaluate : 1.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 ILE cc_start: 0.8346 (tt) cc_final: 0.8086 (tt) REVERT: A 156 MET cc_start: 0.6745 (OUTLIER) cc_final: 0.6273 (mpp) REVERT: A 196 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8224 (tp) REVERT: A 396 LYS cc_start: 0.7687 (mptt) cc_final: 0.7422 (mmmm) REVERT: C 41 GLU cc_start: 0.7351 (tt0) cc_final: 0.7026 (tt0) REVERT: D 111 ASP cc_start: 0.8658 (t0) cc_final: 0.8433 (t0) REVERT: B 148 GLN cc_start: 0.7963 (OUTLIER) cc_final: 0.7687 (mt0) REVERT: B 374 LEU cc_start: 0.8939 (tp) cc_final: 0.8690 (tt) REVERT: B 404 GLN cc_start: 0.7759 (tp-100) cc_final: 0.7447 (tp-100) REVERT: G 19 LYS cc_start: 0.5757 (mmmt) cc_final: 0.5253 (mmmt) REVERT: G 41 GLU cc_start: 0.7849 (tt0) cc_final: 0.7642 (tt0) REVERT: G 91 GLU cc_start: 0.7506 (pm20) cc_final: 0.7201 (pm20) REVERT: H 92 GLU cc_start: 0.8386 (pt0) cc_final: 0.8147 (pt0) REVERT: E 236 MET cc_start: 0.2275 (OUTLIER) cc_final: 0.2056 (tmm) REVERT: I 219 TYR cc_start: 0.7563 (OUTLIER) cc_final: 0.7201 (m-10) outliers start: 35 outliers final: 24 residues processed: 228 average time/residue: 0.2830 time to fit residues: 99.2136 Evaluate side-chains 232 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 203 time to evaluate : 1.816 ------------------------------------------------------------------------------- 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 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 470 VAL Chi-restraints excluded: chain G residue 14 ILE Chi-restraints excluded: chain G residue 16 THR 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 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: 0.6980 chunk 35 optimal weight: 0.9990 chunk 132 optimal weight: 2.9990 chunk 196 optimal weight: 2.9990 chunk 157 optimal weight: 0.6980 chunk 19 optimal weight: 7.9990 chunk 170 optimal weight: 0.9990 chunk 94 optimal weight: 0.6980 chunk 51 optimal weight: 3.9990 chunk 126 optimal weight: 3.9990 chunk 128 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- 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 400 GLN ** G 42 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 156 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 = 0.173388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.135869 restraints weight = 23055.304| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 2.12 r_work: 0.3481 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 17209 Z= 0.173 Angle : 0.521 9.145 23222 Z= 0.272 Chirality : 0.038 0.141 2531 Planarity : 0.004 0.051 2969 Dihedral : 4.451 75.442 2283 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.70 % Allowed : 14.80 % 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: 0.34 (0.19), residues: 2047 helix: 0.88 (0.14), residues: 1487 sheet: -2.28 (0.77), residues: 35 loop : -1.33 (0.26), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.002 TRP A 543 HIS 0.007 0.001 HIS B 366 PHE 0.031 0.002 PHE I 202 TYR 0.015 0.001 TYR B 495 ARG 0.012 0.000 ARG G 9 Details of bonding type rmsd hydrogen bonds : bond 0.03636 ( 1038) hydrogen bonds : angle 4.15472 ( 3081) metal coordination : bond 0.01386 ( 4) metal coordination : angle 3.91093 ( 2) covalent geometry : bond 0.00409 (17205) covalent geometry : angle 0.52007 (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 236 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 205 time to evaluate : 2.070 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 108 ILE cc_start: 0.8421 (tt) cc_final: 0.8191 (tt) REVERT: A 156 MET cc_start: 0.6684 (OUTLIER) cc_final: 0.6189 (mpp) REVERT: A 196 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8273 (tp) REVERT: A 396 LYS cc_start: 0.7715 (mptt) cc_final: 0.7462 (mmmm) REVERT: B 148 GLN cc_start: 0.7802 (OUTLIER) cc_final: 0.7583 (mt0) REVERT: B 374 LEU cc_start: 0.8940 (tp) cc_final: 0.8668 (tt) REVERT: B 404 GLN cc_start: 0.7681 (tp-100) cc_final: 0.7414 (tp-100) REVERT: G 91 GLU cc_start: 0.7490 (pm20) cc_final: 0.7259 (pm20) REVERT: H 92 GLU cc_start: 0.8186 (pt0) cc_final: 0.7941 (pt0) REVERT: E 236 MET cc_start: 0.2422 (OUTLIER) cc_final: 0.2166 (tmm) REVERT: I 219 TYR cc_start: 0.7592 (OUTLIER) cc_final: 0.7202 (m-10) outliers start: 31 outliers final: 21 residues processed: 224 average time/residue: 0.3245 time to fit residues: 112.3679 Evaluate side-chains 224 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 198 time to evaluate : 1.910 ------------------------------------------------------------------------------- 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 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 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 470 VAL Chi-restraints excluded: chain G residue 14 ILE Chi-restraints excluded: chain G residue 16 THR 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 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: 0.8980 chunk 1 optimal weight: 0.9980 chunk 121 optimal weight: 0.5980 chunk 52 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 19 optimal weight: 0.0050 chunk 90 optimal weight: 2.9990 chunk 182 optimal weight: 0.6980 chunk 172 optimal weight: 0.7980 chunk 184 optimal weight: 2.9990 chunk 138 optimal weight: 3.9990 overall best weight: 0.5794 ------------------------------------------------------------------------------- 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** ** G 42 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 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 225 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.170886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.135058 restraints weight = 22576.221| |-----------------------------------------------------------------------------| r_work (start): 0.3749 rms_B_bonded: 1.89 r_work: 0.3516 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3361 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.2217 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= 0.142 Angle : 0.523 9.767 23222 Z= 0.271 Chirality : 0.037 0.142 2531 Planarity : 0.004 0.054 2969 Dihedral : 4.445 75.114 2283 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.59 % Allowed : 15.46 % Favored : 82.95 % 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: 0.42 (0.19), residues: 2047 helix: 0.94 (0.14), residues: 1487 sheet: -2.28 (0.76), residues: 35 loop : -1.32 (0.26), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.002 TRP A 543 HIS 0.007 0.001 HIS B 366 PHE 0.029 0.001 PHE B 445 TYR 0.014 0.001 TYR A 510 ARG 0.012 0.000 ARG G 9 Details of bonding type rmsd hydrogen bonds : bond 0.03527 ( 1038) hydrogen bonds : angle 4.11926 ( 3081) metal coordination : bond 0.01090 ( 4) metal coordination : angle 3.94671 ( 2) covalent geometry : bond 0.00333 (17205) covalent geometry : angle 0.52209 (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 220 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 191 time to evaluate : 1.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 MET cc_start: 0.6717 (OUTLIER) cc_final: 0.6253 (mpp) REVERT: A 196 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8187 (tp) REVERT: A 396 LYS cc_start: 0.7686 (mptt) cc_final: 0.7409 (mmmm) REVERT: B 148 GLN cc_start: 0.7956 (OUTLIER) cc_final: 0.7678 (mt0) REVERT: B 374 LEU cc_start: 0.8933 (tp) cc_final: 0.8673 (tt) REVERT: B 400 GLN cc_start: 0.6892 (tm-30) cc_final: 0.6213 (mp10) REVERT: B 404 GLN cc_start: 0.7730 (tp-100) cc_final: 0.7414 (tp-100) REVERT: G 5 LEU cc_start: 0.8419 (mp) cc_final: 0.8142 (mp) REVERT: G 91 GLU cc_start: 0.7520 (pm20) cc_final: 0.7253 (pm20) REVERT: H 92 GLU cc_start: 0.8341 (pt0) cc_final: 0.8112 (pt0) REVERT: E 236 MET cc_start: 0.2445 (OUTLIER) cc_final: 0.2191 (tmm) REVERT: I 219 TYR cc_start: 0.7564 (OUTLIER) cc_final: 0.7238 (m-10) outliers start: 29 outliers final: 23 residues processed: 210 average time/residue: 0.2806 time to fit residues: 91.1400 Evaluate side-chains 217 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 189 time to evaluate : 1.724 ------------------------------------------------------------------------------- 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 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 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 470 VAL Chi-restraints excluded: chain G residue 14 ILE Chi-restraints excluded: chain G residue 16 THR 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 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: 3.9990 chunk 171 optimal weight: 4.9990 chunk 59 optimal weight: 0.5980 chunk 90 optimal weight: 1.9990 chunk 73 optimal weight: 0.5980 chunk 157 optimal weight: 0.6980 chunk 127 optimal weight: 2.9990 chunk 141 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 201 optimal weight: 4.9990 chunk 72 optimal weight: 0.0980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 42 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 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.173950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.137405 restraints weight = 22766.930| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 2.08 r_work: 0.3499 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17209 Z= 0.142 Angle : 0.511 9.029 23222 Z= 0.266 Chirality : 0.037 0.138 2531 Planarity : 0.004 0.050 2969 Dihedral : 4.438 75.648 2283 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.59 % Allowed : 15.52 % Favored : 82.89 % 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: 0.47 (0.19), residues: 2047 helix: 0.99 (0.14), residues: 1477 sheet: -2.23 (0.76), residues: 35 loop : -1.29 (0.26), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.002 TRP A 543 HIS 0.007 0.001 HIS B 366 PHE 0.028 0.001 PHE B 445 TYR 0.013 0.001 TYR B 536 ARG 0.011 0.000 ARG G 9 Details of bonding type rmsd hydrogen bonds : bond 0.03513 ( 1038) hydrogen bonds : angle 4.10278 ( 3081) metal coordination : bond 0.01108 ( 4) metal coordination : angle 4.07281 ( 2) covalent geometry : bond 0.00332 (17205) covalent geometry : angle 0.50975 (23220) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9696.14 seconds wall clock time: 170 minutes 0.81 seconds (10200.81 seconds total)