Starting phenix.real_space_refine on Wed Apr 10 10:20:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jar_36132/04_2024/8jar_36132.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jar_36132/04_2024/8jar_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jar_36132/04_2024/8jar_36132.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jar_36132/04_2024/8jar_36132.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jar_36132/04_2024/8jar_36132.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jar_36132/04_2024/8jar_36132.pdb" } 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 Residue "D GLU 28": "OE1" <-> "OE2" Residue "B ASP 371": "OD1" <-> "OD2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 16841 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 4613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 571, 4613 Classifications: {'peptide': 571} Link IDs: {'PTRANS': 6, 'TRANS': 564} Chain: "C" Number of atoms: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 830 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 9, 'TRANS': 95} Chain: "D" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 760 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 90} Chain: "S" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 65 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 7} Chain: "B" Number of atoms: 4630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 573, 4630 Classifications: {'peptide': 573} Link IDs: {'PTRANS': 6, 'TRANS': 566} Chain: "F" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 65 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 7} Chain: "G" Number of atoms: 758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 758 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 7, 'TRANS': 88} Chain: "H" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 760 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 90} Chain: "E" Number of atoms: 2214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2214 Classifications: {'peptide': 262} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 252} Chain breaks: 1 Chain: "I" Number of atoms: 2145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 2145 Classifications: {'peptide': 254} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 244} Chain breaks: 1 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 401 SG CYS A 54 60.557 51.050 101.711 1.00 1.95 S ATOM 6678 SG CYS B 54 64.232 50.237 102.846 1.00 10.81 S Time building chain proxies: 8.91, per 1000 atoms: 0.53 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.89 Conformation dependent library (CDL) restraints added in 2.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 601 " pdb="ZN ZN B 601 " - pdb=" NE2 HIS A 89 " pdb="ZN ZN B 601 " - pdb=" NE2 HIS B 89 " pdb="ZN ZN B 601 " - pdb=" SG CYS A 54 " pdb="ZN ZN B 601 " - pdb=" SG CYS B 54 " Number of angles added : 2 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3954 Finding SS restraints... Secondary structure from input PDB file: 105 helices and 6 sheets defined 74.6% alpha, 2.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.49 Creating SS restraints... Processing helix chain 'A' and resid 12 through 24 removed outlier: 4.091A pdb=" N ASN A 24 " --> pdb=" O ALA A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 27 No H-bonds generated for 'chain 'A' and resid 25 through 27' Processing helix chain 'A' and resid 28 through 33 removed outlier: 4.009A pdb=" N ARG A 33 " --> pdb=" O ARG A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 50 removed outlier: 3.969A pdb=" N PHE A 41 " --> pdb=" O GLU A 37 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ASP A 42 " --> pdb=" O ASN A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 61 removed outlier: 3.619A pdb=" N SER A 58 " --> pdb=" O CYS A 54 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLU A 59 " --> pdb=" O GLN A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 71 removed outlier: 4.125A pdb=" N LYS A 68 " --> pdb=" O GLU A 64 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ARG A 71 " --> pdb=" O ALA A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 90 removed outlier: 3.861A pdb=" N LEU A 79 " --> pdb=" O LYS A 75 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N HIS A 81 " --> pdb=" O HIS A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 109 Processing helix chain 'A' and resid 112 through 134 removed outlier: 3.624A pdb=" N LYS A 118 " --> pdb=" O ALA A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 152 removed outlier: 4.247A pdb=" N LYS A 141 " --> pdb=" O SER A 137 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL A 142 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU A 152 " --> pdb=" O GLN A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 173 removed outlier: 3.865A pdb=" N ARG A 168 " --> pdb=" O GLU A 164 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N HIS A 171 " --> pdb=" O VAL A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 198 removed outlier: 3.837A pdb=" N GLU A 184 " --> pdb=" O HIS A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 219 removed outlier: 3.778A pdb=" N TYR A 209 " --> pdb=" O LYS A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 235 removed outlier: 3.658A pdb=" N GLU A 235 " --> pdb=" O GLU A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 259 Processing helix chain 'A' and resid 261 through 280 removed outlier: 4.411A pdb=" N GLN A 267 " --> pdb=" O LYS A 263 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU A 268 " --> pdb=" O LYS A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 300 Processing helix chain 'A' and resid 303 through 322 removed outlier: 3.572A pdb=" N VAL A 308 " --> pdb=" O ILE A 304 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N ALA A 309 " --> pdb=" O CYS A 305 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA A 313 " --> pdb=" O ALA A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 344 removed outlier: 3.549A pdb=" N TYR A 338 " --> pdb=" O GLU A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 368 removed outlier: 3.812A pdb=" N HIS A 366 " --> pdb=" O GLY A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 391 removed outlier: 3.655A pdb=" N ALA A 376 " --> pdb=" O HIS A 372 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N SER A 378 " --> pdb=" O LEU A 374 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU A 388 " --> pdb=" O LEU A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 421 removed outlier: 3.888A pdb=" N LEU A 403 " --> pdb=" O GLU A 399 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN A 404 " --> pdb=" O GLN A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 442 Processing helix chain 'A' and resid 444 through 463 Processing helix chain 'A' and resid 467 through 484 Processing helix chain 'A' and resid 487 through 507 removed outlier: 4.271A pdb=" N LYS A 493 " --> pdb=" O GLU A 489 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU A 494 " --> pdb=" O ASN A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 526 removed outlier: 4.366A pdb=" N TYR A 515 " --> pdb=" O SER A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 551 Processing helix chain 'A' and resid 566 through 577 Processing helix chain 'C' and resid 23 through 36 Processing helix chain 'C' and resid 38 through 40 No H-bonds generated for 'chain 'C' and resid 38 through 40' Processing helix chain 'C' and resid 56 through 61 removed outlier: 3.587A pdb=" N GLY C 61 " --> pdb=" O LEU C 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 37 Processing helix chain 'D' and resid 39 through 46 Processing helix chain 'D' and resid 48 through 52 removed outlier: 3.532A pdb=" N PHE D 52 " --> pdb=" O PRO D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 66 through 83 removed outlier: 3.752A pdb=" N LYS D 72 " --> pdb=" O HIS D 68 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG D 82 " --> pdb=" O THR D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 111 removed outlier: 3.516A pdb=" N MET D 105 " --> pdb=" O LEU D 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 23 Processing helix chain 'B' and resid 31 through 35 Processing helix chain 'B' and resid 36 through 50 Processing helix chain 'B' and resid 52 through 61 removed outlier: 3.853A pdb=" N GLU B 59 " --> pdb=" O GLN B 55 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N CYS B 61 " --> pdb=" O GLY B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 70 removed outlier: 3.546A pdb=" N LYS B 68 " --> pdb=" O GLU B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 90 removed outlier: 3.951A pdb=" N HIS B 81 " --> pdb=" O HIS B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 109 removed outlier: 3.923A pdb=" N SER B 106 " --> pdb=" O SER B 102 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N TYR B 107 " --> pdb=" O ARG B 103 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ILE B 108 " --> pdb=" O ARG B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 134 Processing helix chain 'B' and resid 135 through 151 removed outlier: 3.998A pdb=" N LYS B 141 " --> pdb=" O SER B 137 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N VAL B 142 " --> pdb=" O ASP B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 175 Processing helix chain 'B' and resid 178 through 199 removed outlier: 3.679A pdb=" N GLU B 183 " --> pdb=" O TYR B 179 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N GLU B 184 " --> pdb=" O HIS B 180 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N HIS B 199 " --> pdb=" O LYS B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 219 Processing helix chain 'B' and resid 221 through 235 Processing helix chain 'B' and resid 241 through 258 Processing helix chain 'B' and resid 261 through 280 removed outlier: 3.713A pdb=" N GLN B 267 " --> pdb=" O LYS B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 301 Processing helix chain 'B' and resid 303 through 322 removed outlier: 3.857A pdb=" N ALA B 309 " --> pdb=" O CYS B 305 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER B 320 " --> pdb=" O ASP B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 344 Processing helix chain 'B' and resid 351 through 360 Processing helix chain 'B' and resid 360 through 368 removed outlier: 3.866A pdb=" N ILE B 364 " --> pdb=" O ALA B 360 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N HIS B 366 " --> pdb=" O GLY B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 393 removed outlier: 3.746A pdb=" N ALA B 376 " --> pdb=" O HIS B 372 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N SER B 377 " --> pdb=" O LEU B 373 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N SER B 378 " --> pdb=" O LEU B 374 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE B 385 " --> pdb=" O VAL B 381 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU B 388 " --> pdb=" O LEU B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 421 Processing helix chain 'B' and resid 425 through 442 Processing helix chain 'B' and resid 444 through 462 removed outlier: 3.591A pdb=" N GLU B 450 " --> pdb=" O LYS B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 484 Processing helix chain 'B' and resid 487 through 507 Processing helix chain 'B' and resid 512 through 528 removed outlier: 4.030A pdb=" N ASP B 516 " --> pdb=" O GLY B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 549 Processing helix chain 'B' and resid 555 through 560 removed outlier: 3.664A pdb=" N VAL B 560 " --> pdb=" O ALA B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 577 removed outlier: 3.559A pdb=" N SER B 577 " --> pdb=" O SER B 573 " (cutoff:3.500A) Processing helix chain 'G' and resid 23 through 36 removed outlier: 4.123A pdb=" N GLY G 33 " --> pdb=" O ARG G 29 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ILE G 34 " --> pdb=" O ILE G 30 " (cutoff:3.500A) Processing helix chain 'G' and resid 38 through 42 Processing helix chain 'H' and resid 32 through 37 Processing helix chain 'H' and resid 39 through 47 Processing helix chain 'H' and resid 53 through 55 No H-bonds generated for 'chain 'H' and resid 53 through 55' Processing helix chain 'H' and resid 66 through 83 removed outlier: 4.223A pdb=" N LYS H 72 " --> pdb=" O HIS H 68 " (cutoff:3.500A) Processing helix chain 'H' and resid 99 through 109 removed outlier: 3.717A pdb=" N PHE H 109 " --> pdb=" O MET H 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 26 removed outlier: 3.572A pdb=" N THR E 13 " --> pdb=" O ASP E 9 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N THR E 20 " --> pdb=" O LYS E 16 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N MET E 26 " --> pdb=" O LYS E 22 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 47 removed outlier: 3.620A pdb=" N PHE E 39 " --> pdb=" O TRP E 35 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N SER E 40 " --> pdb=" O ASN E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 79 removed outlier: 3.758A pdb=" N SER E 79 " --> pdb=" O ARG E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 105 removed outlier: 3.588A pdb=" N GLU E 93 " --> pdb=" O ARG E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 112 Processing helix chain 'E' and resid 138 through 151 removed outlier: 3.645A pdb=" N LEU E 144 " --> pdb=" O GLY E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 172 removed outlier: 3.644A pdb=" N ILE E 167 " --> pdb=" O LEU E 163 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS E 168 " --> pdb=" O LEU E 164 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLY E 172 " --> pdb=" O LYS E 168 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 191 removed outlier: 3.880A pdb=" N ILE E 181 " --> pdb=" O ASN E 177 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N PHE E 188 " --> pdb=" O VAL E 184 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N VAL E 189 " --> pdb=" O ILE E 185 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL E 191 " --> pdb=" O SER E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 192 through 194 No H-bonds generated for 'chain 'E' and resid 192 through 194' Processing helix chain 'E' and resid 200 through 207 removed outlier: 3.541A pdb=" N GLU E 205 " --> pdb=" O LYS E 201 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 229 removed outlier: 3.625A pdb=" N THR E 213 " --> pdb=" O SER E 209 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU E 222 " --> pdb=" O TYR E 218 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ALA E 223 " --> pdb=" O TYR E 219 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER E 224 " --> pdb=" O LYS E 220 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASN E 225 " --> pdb=" O GLN E 221 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLU E 229 " --> pdb=" O ASN E 225 " (cutoff:3.500A) Processing helix chain 'E' and resid 234 through 253 removed outlier: 4.010A pdb=" N LEU E 240 " --> pdb=" O MET E 236 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY E 241 " --> pdb=" O GLU E 237 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 257 No H-bonds generated for 'chain 'E' and resid 255 through 257' Processing helix chain 'E' and resid 258 through 271 removed outlier: 4.036A pdb=" N VAL E 262 " --> pdb=" O SER E 258 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ILE E 263 " --> pdb=" O TYR E 259 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N GLN E 267 " --> pdb=" O ILE E 263 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN E 268 " --> pdb=" O HIS E 264 " (cutoff:3.500A) Processing helix chain 'E' and resid 274 through 280 removed outlier: 3.560A pdb=" N HIS E 279 " --> pdb=" O LEU E 275 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ALA E 280 " --> pdb=" O GLN E 276 " (cutoff:3.500A) Processing helix chain 'I' and resid 9 through 25 removed outlier: 3.665A pdb=" N THR I 13 " --> pdb=" O ASP I 9 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ALA I 23 " --> pdb=" O THR I 19 " (cutoff:3.500A) Processing helix chain 'I' and resid 26 through 28 No H-bonds generated for 'chain 'I' and resid 26 through 28' Processing helix chain 'I' and resid 31 through 47 removed outlier: 3.658A pdb=" N PHE I 39 " --> pdb=" O TRP I 35 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N SER I 40 " --> pdb=" O ASN I 36 " (cutoff:3.500A) Processing helix chain 'I' and resid 53 through 79 Processing helix chain 'I' and resid 82 through 105 Processing helix chain 'I' and resid 105 through 112 Processing helix chain 'I' and resid 138 through 151 removed outlier: 3.540A pdb=" N LEU I 144 " --> pdb=" O GLY I 140 " (cutoff:3.500A) Processing helix chain 'I' and resid 155 through 171 removed outlier: 3.929A pdb=" N ASP I 170 " --> pdb=" O GLU I 166 " (cutoff:3.500A) Processing helix chain 'I' and resid 177 through 191 removed outlier: 4.189A pdb=" N ILE I 181 " --> pdb=" O ASN I 177 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N PHE I 188 " --> pdb=" O VAL I 184 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N VAL I 189 " --> pdb=" O ILE I 185 " (cutoff:3.500A) Processing helix chain 'I' and resid 192 through 195 Processing helix chain 'I' and resid 200 through 205 removed outlier: 3.937A pdb=" N GLU I 205 " --> pdb=" O LYS I 201 " (cutoff:3.500A) Processing helix chain 'I' and resid 207 through 218 removed outlier: 3.724A pdb=" N THR I 213 " --> pdb=" O SER I 209 " (cutoff:3.500A) Processing helix chain 'I' and resid 218 through 226 removed outlier: 3.818A pdb=" N SER I 224 " --> pdb=" O LYS I 220 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ASN I 225 " --> pdb=" O GLN I 221 " (cutoff:3.500A) Processing helix chain 'I' and resid 234 through 254 removed outlier: 3.520A pdb=" N VAL I 239 " --> pdb=" O TYR I 235 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LEU I 240 " --> pdb=" O MET I 236 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLY I 241 " --> pdb=" O GLU I 237 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS I 252 " --> pdb=" O ILE I 248 " (cutoff:3.500A) Processing helix chain 'I' and resid 255 through 257 No H-bonds generated for 'chain 'I' and resid 255 through 257' Processing helix chain 'I' and resid 258 through 269 removed outlier: 3.607A pdb=" N VAL I 262 " --> pdb=" O SER I 258 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE I 263 " --> pdb=" O TYR I 259 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU I 265 " --> pdb=" O LYS I 261 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG I 269 " --> pdb=" O GLU I 265 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 17 through 18 removed outlier: 6.977A pdb=" N PHE C 4 " --> pdb=" O ALA C 73 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N VAL C 75 " --> pdb=" O PHE C 4 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N MET C 6 " --> pdb=" O VAL C 75 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N LEU C 77 " --> pdb=" O MET C 6 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 12 through 14 removed outlier: 6.206A pdb=" N THR C 13 " --> pdb=" O ILE D 30 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N LYS D 32 " --> pdb=" O THR C 13 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N TYR D 18 " --> pdb=" O ASN D 58 " (cutoff:3.500A) removed outlier: 8.437A pdb=" N VAL D 60 " --> pdb=" O TYR D 18 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N LYS D 20 " --> pdb=" O VAL D 60 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AA4, first strand: chain 'G' and resid 49 through 50 Processing sheet with id=AA5, first strand: chain 'G' and resid 80 through 81 Processing sheet with id=AA6, first strand: chain 'H' and resid 18 through 22 removed outlier: 3.718A pdb=" N ASN H 58 " --> pdb=" O TYR H 18 " (cutoff:3.500A) 1038 hydrogen bonds defined for protein. 3081 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.29 Time building geometry restraints manager: 7.41 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: 99.00 - 106.01: 250 106.01 - 113.02: 9297 113.02 - 120.03: 6202 120.03 - 127.04: 7307 127.04 - 134.06: 164 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 2.440 nonbonded pdb=" OH TYR A 338 " pdb=" O GLY S 0 " model vdw 2.186 2.440 nonbonded pdb=" OG SER C 94 " pdb=" OD2 ASP D 25 " model vdw 2.222 2.440 nonbonded pdb=" OE1 GLU B 334 " pdb=" OG SER B 378 " model vdw 2.231 2.440 nonbonded pdb=" OG SER B 479 " pdb=" O THR F -4 " model vdw 2.242 2.440 ... (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 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: 12.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.120 Construct map_model_manager: 0.010 Extract box with map and model: 28.540 Check model and map are aligned: 0.290 Set scattering table: 0.150 Process input model: 48.720 Find NCS groups from input model: 0.950 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 93.980 ------------------------------------------------------------------------------- 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 17205 Z= 0.242 Angle : 0.541 8.350 23220 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 295 time to evaluate : 2.044 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: 0.3199 time to fit residues: 137.8810 Evaluate side-chains 197 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 197 time to evaluate : 1.990 ------------------------------------------------------------------------------- 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: 0.9980 chunk 153 optimal weight: 0.7980 chunk 84 optimal weight: 0.5980 chunk 52 optimal weight: 0.3980 chunk 103 optimal weight: 0.6980 chunk 81 optimal weight: 0.5980 chunk 158 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 96 optimal weight: 0.8980 chunk 117 optimal weight: 3.9990 chunk 183 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 65 GLN ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 51 GLN 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.1228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17205 Z= 0.222 Angle : 0.514 8.121 23220 Z= 0.271 Chirality : 0.037 0.133 2531 Planarity : 0.004 0.049 2969 Dihedral : 4.596 79.047 2283 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.10 % Allowed : 7.73 % Favored : 91.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.18), residues: 2047 helix: 0.40 (0.13), residues: 1487 sheet: -1.57 (1.18), residues: 20 loop : -1.25 (0.25), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 543 HIS 0.011 0.001 HIS A 343 PHE 0.017 0.001 PHE A 41 TYR 0.019 0.001 TYR B 495 ARG 0.007 0.000 ARG G 9 *********************** 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 241 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 221 time to evaluate : 1.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 111 ASP cc_start: 0.8061 (t0) cc_final: 0.7852 (t0) REVERT: B 396 LYS cc_start: 0.7679 (tptt) cc_final: 0.7416 (tppt) REVERT: G 19 LYS cc_start: 0.6205 (mmmt) cc_final: 0.5878 (mmmt) REVERT: I 82 GLN cc_start: 0.5544 (pp30) cc_final: 0.5084 (pp30) outliers start: 20 outliers final: 11 residues processed: 227 average time/residue: 0.3148 time to fit residues: 106.4718 Evaluate side-chains 209 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 198 time to evaluate : 1.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 58 ASN Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 198 LYS Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain G residue 53 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 101 optimal weight: 2.9990 chunk 56 optimal weight: 0.0040 chunk 152 optimal weight: 0.3980 chunk 124 optimal weight: 0.8980 chunk 50 optimal weight: 0.0870 chunk 183 optimal weight: 0.5980 chunk 198 optimal weight: 6.9990 chunk 163 optimal weight: 0.5980 chunk 182 optimal weight: 0.7980 chunk 62 optimal weight: 0.0030 chunk 147 optimal weight: 1.9990 overall best weight: 0.2180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 84 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 E 234 GLN ** I 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 190 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 17205 Z= 0.138 Angle : 0.469 10.263 23220 Z= 0.245 Chirality : 0.035 0.137 2531 Planarity : 0.003 0.044 2969 Dihedral : 4.406 80.577 2283 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 0.71 % Allowed : 10.58 % Favored : 88.71 % 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: 0.33 (0.19), residues: 2047 helix: 0.81 (0.14), residues: 1487 sheet: -1.74 (1.08), residues: 20 loop : -1.20 (0.26), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP A 543 HIS 0.008 0.001 HIS A 343 PHE 0.015 0.001 PHE B 41 TYR 0.015 0.001 TYR B 468 ARG 0.007 0.000 ARG G 9 *********************** 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 230 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 217 time to evaluate : 1.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 343 HIS cc_start: 0.7441 (t70) cc_final: 0.7201 (t-170) REVERT: G 19 LYS cc_start: 0.6178 (mmmt) cc_final: 0.5899 (mmmt) REVERT: G 41 GLU cc_start: 0.7240 (tt0) cc_final: 0.6927 (tt0) REVERT: E 236 MET cc_start: 0.3772 (tmm) cc_final: 0.3193 (tmm) REVERT: I 82 GLN cc_start: 0.5712 (pp30) cc_final: 0.5157 (pp30) REVERT: I 86 MET cc_start: 0.7937 (tpp) cc_final: 0.7688 (tpp) outliers start: 13 outliers final: 9 residues processed: 225 average time/residue: 0.3010 time to fit residues: 101.8890 Evaluate side-chains 204 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 195 time to evaluate : 1.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 58 ASN Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 198 LYS Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain G residue 53 ASP 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 181 optimal weight: 0.0770 chunk 138 optimal weight: 0.0000 chunk 95 optimal weight: 6.9990 chunk 20 optimal weight: 0.5980 chunk 87 optimal weight: 0.6980 chunk 123 optimal weight: 3.9990 chunk 184 optimal weight: 0.8980 chunk 195 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 174 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 overall best weight: 0.4342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 395 ASN ** B 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 490 ASN G 65 GLN ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 36 ASN E 190 HIS ** I 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 268 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17205 Z= 0.175 Angle : 0.467 7.518 23220 Z= 0.245 Chirality : 0.036 0.133 2531 Planarity : 0.003 0.045 2969 Dihedral : 4.353 78.513 2283 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.48 % Allowed : 11.07 % Favored : 87.45 % 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: 0.43 (0.19), residues: 2047 helix: 0.91 (0.14), residues: 1490 sheet: -2.36 (0.76), residues: 35 loop : -1.18 (0.26), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP A 543 HIS 0.007 0.001 HIS A 343 PHE 0.018 0.001 PHE I 202 TYR 0.020 0.001 TYR A 468 ARG 0.011 0.000 ARG G 9 *********************** 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 233 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 206 time to evaluate : 1.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 MET cc_start: 0.6285 (OUTLIER) cc_final: 0.5561 (mpp) REVERT: A 343 HIS cc_start: 0.7420 (t70) cc_final: 0.7170 (t-170) REVERT: G 19 LYS cc_start: 0.6188 (mmmt) cc_final: 0.5925 (mmmt) REVERT: E 236 MET cc_start: 0.3682 (tmm) cc_final: 0.3246 (tmm) REVERT: I 82 GLN cc_start: 0.5812 (pp30) cc_final: 0.5111 (pp30) outliers start: 27 outliers final: 19 residues processed: 221 average time/residue: 0.2990 time to fit residues: 100.7077 Evaluate side-chains 214 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 194 time to evaluate : 1.961 ------------------------------------------------------------------------------- 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 229 CYS 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 C residue 64 SER Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 58 ASN Chi-restraints excluded: chain B residue 198 LYS Chi-restraints excluded: chain B residue 229 CYS Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain G residue 14 ILE Chi-restraints excluded: chain G residue 53 ASP Chi-restraints excluded: chain H residue 60 VAL 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 162 optimal weight: 0.0030 chunk 110 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 145 optimal weight: 4.9990 chunk 80 optimal weight: 0.6980 chunk 166 optimal weight: 0.9990 chunk 134 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 175 optimal weight: 0.0470 chunk 49 optimal weight: 0.8980 overall best weight: 0.5290 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 65 GLN ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 190 HIS E 234 GLN ** I 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 178 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17205 Z= 0.193 Angle : 0.474 8.913 23220 Z= 0.246 Chirality : 0.036 0.135 2531 Planarity : 0.003 0.048 2969 Dihedral : 4.357 78.093 2283 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.81 % Allowed : 12.12 % Favored : 86.07 % 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: 0.93 (0.14), residues: 1502 sheet: -2.34 (0.77), residues: 35 loop : -1.26 (0.26), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP A 543 HIS 0.007 0.001 HIS A 343 PHE 0.024 0.001 PHE I 202 TYR 0.014 0.001 TYR B 468 ARG 0.010 0.000 ARG G 9 *********************** 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 235 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 202 time to evaluate : 1.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 MET cc_start: 0.6248 (OUTLIER) cc_final: 0.5606 (mpp) REVERT: D 111 ASP cc_start: 0.7994 (t0) cc_final: 0.7769 (t0) REVERT: G 19 LYS cc_start: 0.6226 (mmmt) cc_final: 0.5937 (mmmt) REVERT: G 34 ILE cc_start: 0.7342 (mt) cc_final: 0.7139 (mt) REVERT: E 236 MET cc_start: 0.3629 (tmm) cc_final: 0.3249 (tmm) REVERT: I 82 GLN cc_start: 0.5908 (pp30) cc_final: 0.5100 (pp30) outliers start: 33 outliers final: 24 residues processed: 223 average time/residue: 0.2967 time to fit residues: 101.0065 Evaluate side-chains 216 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 191 time to evaluate : 2.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE 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 349 LYS Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 58 ASN Chi-restraints excluded: chain B residue 31 ASP 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 B residue 546 LEU Chi-restraints excluded: chain G residue 14 ILE Chi-restraints excluded: chain G residue 53 ASP Chi-restraints excluded: chain G residue 77 LEU Chi-restraints excluded: chain H residue 60 VAL Chi-restraints excluded: chain H residue 108 ASN Chi-restraints excluded: chain E residue 7 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 65 optimal weight: 0.0070 chunk 175 optimal weight: 9.9990 chunk 38 optimal weight: 0.5980 chunk 114 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 195 optimal weight: 0.7980 chunk 162 optimal weight: 0.0370 chunk 90 optimal weight: 1.9990 chunk 16 optimal weight: 0.2980 chunk 64 optimal weight: 0.9990 chunk 102 optimal weight: 0.6980 overall best weight: 0.3276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 343 HIS B 24 ASN ** B 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 65 GLN ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 190 HIS E 234 GLN I 82 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 17205 Z= 0.153 Angle : 0.463 9.057 23220 Z= 0.241 Chirality : 0.035 0.133 2531 Planarity : 0.003 0.050 2969 Dihedral : 4.293 77.891 2283 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.86 % Allowed : 12.99 % Favored : 85.14 % 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: 0.60 (0.19), residues: 2047 helix: 1.06 (0.14), residues: 1491 sheet: -2.25 (0.77), residues: 35 loop : -1.23 (0.26), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP A 543 HIS 0.004 0.001 HIS A 343 PHE 0.025 0.001 PHE B 445 TYR 0.014 0.001 TYR B 468 ARG 0.012 0.000 ARG G 9 *********************** 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 240 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 206 time to evaluate : 1.955 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 156 MET cc_start: 0.6251 (OUTLIER) cc_final: 0.5724 (mpp) REVERT: D 111 ASP cc_start: 0.7975 (t0) cc_final: 0.7768 (t0) REVERT: G 19 LYS cc_start: 0.6205 (mmmt) cc_final: 0.5900 (mmmt) outliers start: 34 outliers final: 21 residues processed: 227 average time/residue: 0.3071 time to fit residues: 106.6249 Evaluate side-chains 216 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 194 time to evaluate : 1.829 ------------------------------------------------------------------------------- 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 229 CYS 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 C residue 64 SER Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 58 ASN Chi-restraints excluded: chain D residue 92 GLU Chi-restraints excluded: chain B residue 31 ASP 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 546 LEU Chi-restraints excluded: chain G residue 14 ILE Chi-restraints excluded: chain G residue 53 ASP Chi-restraints excluded: chain G residue 77 LEU Chi-restraints excluded: chain H residue 60 VAL Chi-restraints excluded: chain H residue 108 ASN Chi-restraints excluded: chain E residue 7 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 188 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 111 optimal weight: 0.9990 chunk 142 optimal weight: 0.9980 chunk 110 optimal weight: 0.6980 chunk 164 optimal weight: 0.7980 chunk 109 optimal weight: 1.9990 chunk 194 optimal weight: 1.9990 chunk 121 optimal weight: 0.8980 chunk 118 optimal weight: 0.5980 chunk 89 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 343 HIS ** B 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 HIS G 65 GLN ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 190 HIS E 234 GLN ** I 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 17205 Z= 0.245 Angle : 0.499 9.237 23220 Z= 0.260 Chirality : 0.037 0.134 2531 Planarity : 0.004 0.049 2969 Dihedral : 4.391 76.057 2283 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.81 % Allowed : 12.83 % 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: 0.47 (0.19), residues: 2047 helix: 0.95 (0.14), residues: 1500 sheet: -2.38 (0.79), residues: 25 loop : -1.30 (0.26), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 543 HIS 0.004 0.001 HIS B 180 PHE 0.025 0.001 PHE B 445 TYR 0.015 0.001 TYR B 495 ARG 0.013 0.000 ARG G 9 *********************** 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 230 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 197 time to evaluate : 1.922 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 156 MET cc_start: 0.6339 (OUTLIER) cc_final: 0.5792 (mpp) REVERT: G 5 LEU cc_start: 0.8186 (mp) cc_final: 0.7876 (mp) REVERT: G 19 LYS cc_start: 0.6228 (mmmt) cc_final: 0.5935 (mmmt) REVERT: G 91 GLU cc_start: 0.7322 (pm20) cc_final: 0.7059 (pm20) REVERT: E 146 MET cc_start: 0.6869 (mmt) cc_final: 0.6660 (mmp) outliers start: 33 outliers final: 28 residues processed: 213 average time/residue: 0.2912 time to fit residues: 95.6491 Evaluate side-chains 219 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 190 time to evaluate : 2.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 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 349 LYS Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 58 ASN Chi-restraints excluded: chain D residue 92 GLU Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 198 LYS Chi-restraints excluded: chain B residue 229 CYS Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain G residue 14 ILE Chi-restraints excluded: chain G residue 53 ASP Chi-restraints excluded: chain G residue 77 LEU Chi-restraints excluded: chain H residue 17 MET Chi-restraints excluded: chain H residue 60 VAL Chi-restraints excluded: chain H residue 108 ASN Chi-restraints excluded: chain E residue 7 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 120 optimal weight: 0.8980 chunk 77 optimal weight: 0.6980 chunk 116 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 38 optimal weight: 0.5980 chunk 37 optimal weight: 0.6980 chunk 123 optimal weight: 0.5980 chunk 132 optimal weight: 0.9990 chunk 96 optimal weight: 0.8980 chunk 18 optimal weight: 0.3980 chunk 153 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 343 HIS B 404 GLN G 65 GLN ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 36 ASN E 190 HIS ** I 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17205 Z= 0.210 Angle : 0.493 10.468 23220 Z= 0.255 Chirality : 0.036 0.133 2531 Planarity : 0.003 0.050 2969 Dihedral : 4.400 76.813 2283 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.86 % Allowed : 13.54 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.19), residues: 2047 helix: 0.96 (0.14), residues: 1501 sheet: -1.13 (1.06), residues: 10 loop : -1.29 (0.26), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 543 HIS 0.004 0.001 HIS B 180 PHE 0.029 0.001 PHE B 445 TYR 0.014 0.001 TYR B 495 ARG 0.005 0.000 ARG G 9 *********************** 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 235 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 201 time to evaluate : 1.920 Fit side-chains revert: symmetry clash REVERT: A 156 MET cc_start: 0.6372 (OUTLIER) cc_final: 0.5839 (mpp) REVERT: G 5 LEU cc_start: 0.8213 (mp) cc_final: 0.7920 (mp) REVERT: G 91 GLU cc_start: 0.7293 (pm20) cc_final: 0.7054 (pm20) REVERT: H 92 GLU cc_start: 0.7671 (pt0) cc_final: 0.7405 (pt0) REVERT: E 236 MET cc_start: 0.3745 (OUTLIER) cc_final: 0.3407 (tmm) outliers start: 34 outliers final: 29 residues processed: 219 average time/residue: 0.2900 time to fit residues: 97.5954 Evaluate side-chains 219 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 188 time to evaluate : 1.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE 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 349 LYS Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain A residue 479 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 C residue 64 SER Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 58 ASN Chi-restraints excluded: chain D residue 92 GLU Chi-restraints excluded: chain B residue 31 ASP 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 B residue 546 LEU Chi-restraints excluded: chain G residue 14 ILE Chi-restraints excluded: chain G residue 53 ASP Chi-restraints excluded: chain G residue 77 LEU Chi-restraints excluded: chain H residue 17 MET 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 236 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 177 optimal weight: 0.9980 chunk 186 optimal weight: 0.6980 chunk 170 optimal weight: 2.9990 chunk 181 optimal weight: 0.6980 chunk 109 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 142 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 chunk 163 optimal weight: 0.6980 chunk 171 optimal weight: 0.8980 chunk 180 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 343 HIS ** B 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 400 GLN G 65 GLN ** H 35 HIS ** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 17205 Z= 0.237 Angle : 0.517 9.971 23220 Z= 0.266 Chirality : 0.037 0.140 2531 Planarity : 0.004 0.049 2969 Dihedral : 4.467 78.710 2283 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.14 % Allowed : 13.87 % Favored : 83.99 % 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: 0.95 (0.14), residues: 1487 sheet: -1.02 (1.10), residues: 10 loop : -1.34 (0.26), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP A 543 HIS 0.005 0.001 HIS B 180 PHE 0.030 0.001 PHE B 445 TYR 0.015 0.001 TYR B 495 ARG 0.012 0.000 ARG G 9 *********************** 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 227 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 188 time to evaluate : 1.974 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 156 MET cc_start: 0.6379 (OUTLIER) cc_final: 0.5846 (mpp) REVERT: B 396 LYS cc_start: 0.7679 (tptt) cc_final: 0.7384 (tppt) REVERT: G 5 LEU cc_start: 0.8221 (mp) cc_final: 0.7949 (mp) REVERT: G 19 LYS cc_start: 0.6261 (mmmt) cc_final: 0.5849 (mmmt) REVERT: G 91 GLU cc_start: 0.7349 (pm20) cc_final: 0.7109 (pm20) REVERT: I 219 TYR cc_start: 0.7094 (OUTLIER) cc_final: 0.6825 (m-10) outliers start: 39 outliers final: 31 residues processed: 208 average time/residue: 0.2958 time to fit residues: 94.5832 Evaluate side-chains 216 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 183 time to evaluate : 1.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE 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 349 LYS Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain A residue 479 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 C residue 64 SER Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 58 ASN Chi-restraints excluded: chain D residue 92 GLU Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 198 LYS Chi-restraints excluded: chain B residue 229 CYS Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain G residue 14 ILE Chi-restraints excluded: chain G residue 53 ASP Chi-restraints excluded: chain G residue 77 LEU Chi-restraints excluded: chain H residue 17 MET 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 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 119 optimal weight: 0.6980 chunk 191 optimal weight: 0.8980 chunk 117 optimal weight: 0.6980 chunk 91 optimal weight: 1.9990 chunk 133 optimal weight: 2.9990 chunk 201 optimal weight: 3.9990 chunk 185 optimal weight: 0.6980 chunk 160 optimal weight: 0.5980 chunk 16 optimal weight: 0.7980 chunk 123 optimal weight: 3.9990 chunk 98 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 343 HIS ** B 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 65 GLN ** H 35 HIS ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 17205 Z= 0.228 Angle : 0.512 9.731 23220 Z= 0.265 Chirality : 0.037 0.136 2531 Planarity : 0.003 0.048 2969 Dihedral : 4.490 81.357 2283 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.97 % Allowed : 14.09 % Favored : 83.94 % 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: 0.48 (0.19), residues: 2047 helix: 0.93 (0.14), residues: 1495 sheet: -0.92 (1.16), residues: 10 loop : -1.28 (0.26), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.002 TRP A 543 HIS 0.005 0.001 HIS B 180 PHE 0.031 0.001 PHE B 445 TYR 0.014 0.001 TYR B 536 ARG 0.005 0.000 ARG G 9 ********************** 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 223 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 187 time to evaluate : 2.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 MET cc_start: 0.6369 (OUTLIER) cc_final: 0.5836 (mpp) REVERT: G 5 LEU cc_start: 0.8261 (mp) cc_final: 0.7970 (mp) REVERT: G 91 GLU cc_start: 0.7360 (pm20) cc_final: 0.7158 (pm20) REVERT: I 219 TYR cc_start: 0.7149 (OUTLIER) cc_final: 0.6881 (m-10) outliers start: 36 outliers final: 31 residues processed: 206 average time/residue: 0.2948 time to fit residues: 93.6391 Evaluate side-chains 216 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 183 time to evaluate : 1.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE 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 349 LYS Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain A residue 479 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 C residue 64 SER Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 58 ASN Chi-restraints excluded: chain D residue 92 GLU Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 198 LYS Chi-restraints excluded: chain B residue 229 CYS Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain G residue 14 ILE Chi-restraints excluded: chain G residue 53 ASP Chi-restraints excluded: chain G residue 77 LEU Chi-restraints excluded: chain H residue 17 MET 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 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 127 optimal weight: 2.9990 chunk 170 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 147 optimal weight: 0.5980 chunk 23 optimal weight: 0.7980 chunk 44 optimal weight: 0.6980 chunk 160 optimal weight: 0.8980 chunk 67 optimal weight: 0.9980 chunk 164 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 29 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 343 HIS ** B 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 400 GLN G 65 GLN ** H 35 HIS ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.173312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.136658 restraints weight = 22891.746| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 2.09 r_work: 0.3486 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 17205 Z= 0.247 Angle : 0.522 9.587 23220 Z= 0.270 Chirality : 0.037 0.135 2531 Planarity : 0.003 0.048 2969 Dihedral : 4.545 85.500 2283 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.75 % Allowed : 14.31 % Favored : 83.94 % 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: 0.44 (0.19), residues: 2047 helix: 0.91 (0.14), residues: 1495 sheet: -1.09 (1.17), residues: 10 loop : -1.28 (0.26), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.002 TRP A 543 HIS 0.005 0.001 HIS B 180 PHE 0.032 0.001 PHE B 445 TYR 0.015 0.001 TYR B 495 ARG 0.011 0.000 ARG G 9 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3774.40 seconds wall clock time: 70 minutes 26.72 seconds (4226.72 seconds total)