Starting phenix.real_space_refine on Mon Oct 14 19:12:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jar_36132/10_2024/8jar_36132.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jar_36132/10_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_36132/10_2024/8jar_36132.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jar_36132/10_2024/8jar_36132.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jar_36132/10_2024/8jar_36132.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jar_36132/10_2024/8jar_36132.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2476 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 89 5.16 5 C 10758 2.51 5 N 2875 2.21 5 O 3118 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/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: 9.22, per 1000 atoms: 0.55 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: 4.18 Conformation dependent library (CDL) restraints added in 2.1 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: 1.59 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: 5.22 Time building geometry restraints manager: 4.85 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: 24.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 38.420 Find NCS groups from input model: 0.600 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: 0.010 Load rotamer database and sin/cos tables:3.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.430 ------------------------------------------------------------------------------- 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 : 2.069 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: 0.3746 time to fit residues: 160.8204 Evaluate side-chains 197 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 197 time to evaluate : 1.977 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 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 17205 Z= 0.202 Angle : 0.518 8.037 23220 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 *********************** 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 fitting. rotamer outliers: 17 poor density : 225 time to evaluate : 2.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 19 LYS cc_start: 0.6192 (mmmt) cc_final: 0.5838 (mmmt) REVERT: I 82 GLN cc_start: 0.5418 (pp30) cc_final: 0.5006 (pp30) outliers start: 17 outliers final: 8 residues processed: 231 average time/residue: 0.3364 time to fit residues: 113.3086 Evaluate side-chains 206 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 198 time to evaluate : 2.120 ------------------------------------------------------------------------------- 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 101 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 152 optimal weight: 0.5980 chunk 124 optimal weight: 1.9990 chunk 50 optimal weight: 0.0970 chunk 183 optimal weight: 0.8980 chunk 198 optimal weight: 9.9990 chunk 163 optimal weight: 0.5980 chunk 182 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 chunk 147 optimal weight: 1.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 578 GLN G 65 GLN ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 169 ASN E 190 HIS ** I 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 190 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17205 Z= 0.201 Angle : 0.500 9.773 23220 Z= 0.263 Chirality : 0.037 0.158 2531 Planarity : 0.004 0.042 2969 Dihedral : 4.435 71.451 2283 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 0.71 % Allowed : 10.47 % Favored : 88.82 % 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: 0.10 (0.19), residues: 2047 helix: 0.63 (0.14), residues: 1487 sheet: -1.78 (1.10), residues: 20 loop : -1.27 (0.25), residues: 540 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 B 41 TYR 0.019 0.001 TYR A 468 ARG 0.009 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 228 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 215 time to evaluate : 1.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 19 LYS cc_start: 0.6206 (mmmt) cc_final: 0.5899 (mmmt) REVERT: E 236 MET cc_start: 0.3772 (tmm) cc_final: 0.3165 (tmm) REVERT: I 82 GLN cc_start: 0.5752 (pp30) cc_final: 0.5167 (pp30) REVERT: I 86 MET cc_start: 0.7969 (tpp) cc_final: 0.7713 (tpp) outliers start: 13 outliers final: 8 residues processed: 221 average time/residue: 0.3178 time to fit residues: 106.2725 Evaluate side-chains 199 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 191 time to evaluate : 1.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain B residue 198 LYS Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain F residue -4 THR Chi-restraints excluded: chain 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: 1.9990 chunk 138 optimal weight: 4.9990 chunk 95 optimal weight: 0.0970 chunk 20 optimal weight: 0.5980 chunk 87 optimal weight: 0.9990 chunk 123 optimal weight: 3.9990 chunk 184 optimal weight: 1.9990 chunk 195 optimal weight: 0.1980 chunk 96 optimal weight: 0.7980 chunk 174 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 65 GLN ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 190 HIS ** I 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 186 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17205 Z= 0.201 Angle : 0.488 9.947 23220 Z= 0.255 Chirality : 0.037 0.135 2531 Planarity : 0.004 0.044 2969 Dihedral : 4.393 70.769 2283 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.15 % Allowed : 11.57 % Favored : 87.28 % 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: 0.22 (0.19), residues: 2047 helix: 0.74 (0.14), residues: 1485 sheet: -1.82 (1.07), residues: 20 loop : -1.29 (0.25), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP A 543 HIS 0.007 0.001 HIS A 343 PHE 0.024 0.001 PHE B 296 TYR 0.013 0.001 TYR B 468 ARG 0.010 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 224 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 203 time to evaluate : 1.970 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 MET cc_start: 0.6279 (OUTLIER) cc_final: 0.5536 (mpp) REVERT: G 19 LYS cc_start: 0.6196 (mmmt) cc_final: 0.5920 (mmmt) REVERT: E 236 MET cc_start: 0.3676 (tmm) cc_final: 0.3190 (tmm) REVERT: I 82 GLN cc_start: 0.5877 (pp30) cc_final: 0.5171 (pp30) outliers start: 21 outliers final: 12 residues processed: 216 average time/residue: 0.3224 time to fit residues: 106.4173 Evaluate side-chains 205 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 192 time to evaluate : 2.179 ------------------------------------------------------------------------------- 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 349 LYS Chi-restraints excluded: chain A residue 412 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 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 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: 0.0870 chunk 110 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 145 optimal weight: 4.9990 chunk 80 optimal weight: 0.6980 chunk 166 optimal weight: 6.9990 chunk 134 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 99 optimal weight: 0.7980 chunk 175 optimal weight: 0.3980 chunk 49 optimal weight: 0.9990 overall best weight: 0.5960 ------------------------------------------------------------------------------- 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 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.1848 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= 0.212 Angle : 0.481 8.323 23220 Z= 0.253 Chirality : 0.037 0.133 2531 Planarity : 0.003 0.047 2969 Dihedral : 4.364 70.449 2283 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.81 % Allowed : 12.50 % Favored : 85.69 % 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: 0.29 (0.19), residues: 2047 helix: 0.83 (0.14), residues: 1484 sheet: -2.45 (0.75), residues: 35 loop : -1.29 (0.26), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 543 HIS 0.007 0.001 HIS A 343 PHE 0.024 0.001 PHE I 202 TYR 0.022 0.001 TYR A 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 243 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 210 time to evaluate : 1.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 MET cc_start: 0.6303 (OUTLIER) cc_final: 0.5672 (mpp) REVERT: B 374 LEU cc_start: 0.8866 (tp) cc_final: 0.8628 (tt) REVERT: E 236 MET cc_start: 0.3618 (tmm) cc_final: 0.3204 (tmm) outliers start: 33 outliers final: 17 residues processed: 230 average time/residue: 0.2960 time to fit residues: 104.0373 Evaluate side-chains 211 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 193 time to evaluate : 2.132 ------------------------------------------------------------------------------- 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 22 SER Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 148 GLN Chi-restraints excluded: chain B residue 198 LYS Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain G residue 14 ILE Chi-restraints excluded: chain 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: 0.2980 chunk 175 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 114 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 195 optimal weight: 2.9990 chunk 162 optimal weight: 0.0770 chunk 90 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 64 optimal weight: 0.8980 chunk 102 optimal weight: 0.5980 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 65 GLN ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 190 HIS ** I 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 186 ASN I 268 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.1971 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= 0.209 Angle : 0.497 9.127 23220 Z= 0.260 Chirality : 0.037 0.134 2531 Planarity : 0.004 0.049 2969 Dihedral : 4.378 71.017 2283 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.59 % Allowed : 13.60 % Favored : 84.81 % 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: 0.87 (0.14), residues: 1484 sheet: -2.41 (0.74), residues: 35 loop : -1.31 (0.26), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP A 543 HIS 0.006 0.001 HIS A 343 PHE 0.023 0.001 PHE B 445 TYR 0.014 0.001 TYR B 468 ARG 0.013 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 233 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 204 time to evaluate : 1.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 MET cc_start: 0.6302 (OUTLIER) cc_final: 0.5774 (mpp) REVERT: B 374 LEU cc_start: 0.8869 (tp) cc_final: 0.8641 (tt) REVERT: G 19 LYS cc_start: 0.6144 (mmmt) cc_final: 0.5660 (mmmt) REVERT: E 236 MET cc_start: 0.3547 (tmm) cc_final: 0.3097 (tmm) outliers start: 29 outliers final: 19 residues processed: 222 average time/residue: 0.2960 time to fit residues: 101.3582 Evaluate side-chains 213 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 193 time to evaluate : 2.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 165 CYS Chi-restraints excluded: chain A residue 229 CYS Chi-restraints excluded: chain A residue 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 198 LYS Chi-restraints excluded: chain B residue 229 CYS Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain G residue 14 ILE Chi-restraints excluded: chain 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: 0.3980 chunk 22 optimal weight: 0.4980 chunk 111 optimal weight: 0.8980 chunk 142 optimal weight: 0.8980 chunk 110 optimal weight: 0.6980 chunk 164 optimal weight: 0.5980 chunk 109 optimal weight: 1.9990 chunk 194 optimal weight: 0.9990 chunk 121 optimal weight: 0.7980 chunk 118 optimal weight: 0.5980 chunk 89 optimal weight: 0.4980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 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 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.2071 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= 0.197 Angle : 0.495 10.096 23220 Z= 0.257 Chirality : 0.037 0.145 2531 Planarity : 0.004 0.050 2969 Dihedral : 4.355 70.817 2283 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.59 % Allowed : 13.93 % 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: 0.42 (0.19), residues: 2047 helix: 0.92 (0.14), residues: 1483 sheet: -1.61 (1.03), residues: 20 loop : -1.32 (0.26), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.002 TRP A 543 HIS 0.007 0.001 HIS B 180 PHE 0.025 0.001 PHE B 445 TYR 0.021 0.001 TYR A 468 ARG 0.012 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 235 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 206 time to evaluate : 2.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 MET cc_start: 0.6354 (OUTLIER) cc_final: 0.5803 (mpp) REVERT: B 374 LEU cc_start: 0.8871 (tp) cc_final: 0.8648 (tt) REVERT: G 5 LEU cc_start: 0.8239 (mp) cc_final: 0.7940 (mp) REVERT: G 19 LYS cc_start: 0.6188 (mmmt) cc_final: 0.5732 (mmmt) outliers start: 29 outliers final: 22 residues processed: 225 average time/residue: 0.2626 time to fit residues: 90.4486 Evaluate side-chains 221 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 198 time to evaluate : 1.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 165 CYS Chi-restraints excluded: chain A residue 229 CYS Chi-restraints excluded: chain A residue 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 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 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: 0.7980 chunk 116 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 38 optimal weight: 0.0270 chunk 37 optimal weight: 0.5980 chunk 123 optimal weight: 0.8980 chunk 132 optimal weight: 0.9990 chunk 96 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 chunk 153 optimal weight: 0.9980 overall best weight: 0.5838 ------------------------------------------------------------------------------- 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 B 404 GLN G 65 GLN ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 190 HIS ** I 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 178 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17205 Z= 0.211 Angle : 0.507 9.203 23220 Z= 0.263 Chirality : 0.037 0.149 2531 Planarity : 0.004 0.050 2969 Dihedral : 4.372 72.001 2283 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.59 % Allowed : 14.25 % Favored : 84.16 % 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: 0.40 (0.19), residues: 2047 helix: 0.90 (0.14), residues: 1492 sheet: -1.68 (1.01), residues: 20 loop : -1.34 (0.26), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP A 543 HIS 0.008 0.001 HIS B 366 PHE 0.028 0.001 PHE B 445 TYR 0.023 0.001 TYR A 468 ARG 0.013 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: 29 poor density : 206 time to evaluate : 2.068 Fit side-chains revert: symmetry clash REVERT: A 156 MET cc_start: 0.6356 (OUTLIER) cc_final: 0.5760 (mpp) REVERT: A 196 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8426 (tp) REVERT: B 374 LEU cc_start: 0.8878 (tp) cc_final: 0.8650 (tt) REVERT: G 5 LEU cc_start: 0.8276 (mp) cc_final: 0.8012 (mp) REVERT: G 19 LYS cc_start: 0.6231 (mmmt) cc_final: 0.5780 (mmmt) REVERT: H 92 GLU cc_start: 0.7695 (pt0) cc_final: 0.7427 (pt0) outliers start: 29 outliers final: 23 residues processed: 227 average time/residue: 0.2913 time to fit residues: 102.3151 Evaluate side-chains 221 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 196 time to evaluate : 2.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 165 CYS Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 229 CYS Chi-restraints excluded: chain A residue 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 177 optimal weight: 0.0060 chunk 186 optimal weight: 2.9990 chunk 170 optimal weight: 1.9990 chunk 181 optimal weight: 0.0980 chunk 109 optimal weight: 1.9990 chunk 79 optimal weight: 0.5980 chunk 142 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 163 optimal weight: 1.9990 chunk 171 optimal weight: 1.9990 chunk 180 optimal weight: 0.6980 overall best weight: 0.6798 ------------------------------------------------------------------------------- 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 ** A 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 400 GLN G 65 GLN ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 190 HIS ** I 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.2213 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= 0.234 Angle : 0.517 8.849 23220 Z= 0.269 Chirality : 0.038 0.148 2531 Planarity : 0.004 0.053 2969 Dihedral : 4.423 74.377 2283 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.64 % Allowed : 14.58 % Favored : 83.77 % 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: 0.36 (0.19), residues: 2047 helix: 0.89 (0.14), residues: 1489 sheet: -1.69 (1.01), residues: 20 loop : -1.40 (0.26), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP A 543 HIS 0.007 0.001 HIS B 366 PHE 0.032 0.001 PHE I 202 TYR 0.030 0.001 TYR A 468 ARG 0.013 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 225 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 195 time to evaluate : 2.110 Fit side-chains revert: symmetry clash REVERT: A 156 MET cc_start: 0.6357 (OUTLIER) cc_final: 0.5766 (mpp) REVERT: A 196 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8420 (tp) REVERT: B 374 LEU cc_start: 0.8897 (tp) cc_final: 0.8665 (tt) REVERT: G 5 LEU cc_start: 0.8298 (mp) cc_final: 0.8026 (mp) REVERT: G 19 LYS cc_start: 0.6256 (mmmt) cc_final: 0.5779 (mmmt) REVERT: E 236 MET cc_start: 0.3800 (OUTLIER) cc_final: 0.3543 (tmm) outliers start: 30 outliers final: 22 residues processed: 213 average time/residue: 0.3041 time to fit residues: 98.8164 Evaluate side-chains 214 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 189 time to evaluate : 1.991 ------------------------------------------------------------------------------- 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 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 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 119 optimal weight: 1.9990 chunk 191 optimal weight: 0.6980 chunk 117 optimal weight: 0.5980 chunk 91 optimal weight: 1.9990 chunk 133 optimal weight: 0.9980 chunk 201 optimal weight: 3.9990 chunk 185 optimal weight: 0.6980 chunk 160 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 123 optimal weight: 0.9980 chunk 98 optimal weight: 0.9980 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 158 HIS A 343 HIS ** A 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 404 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 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 225 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 17205 Z= 0.247 Angle : 0.530 8.919 23220 Z= 0.276 Chirality : 0.038 0.141 2531 Planarity : 0.004 0.051 2969 Dihedral : 4.475 77.108 2283 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.48 % Allowed : 14.97 % Favored : 83.55 % 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: 0.32 (0.19), residues: 2047 helix: 0.86 (0.14), residues: 1485 sheet: -1.52 (1.09), residues: 10 loop : -1.43 (0.25), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP A 543 HIS 0.007 0.001 HIS B 366 PHE 0.031 0.001 PHE B 445 TYR 0.028 0.001 TYR A 468 ARG 0.012 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 218 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 191 time to evaluate : 2.066 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 156 MET cc_start: 0.6364 (OUTLIER) cc_final: 0.5764 (mpp) REVERT: A 196 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8416 (tp) REVERT: B 374 LEU cc_start: 0.8892 (tp) cc_final: 0.8645 (tt) REVERT: B 396 LYS cc_start: 0.7588 (tptt) cc_final: 0.7344 (tppt) REVERT: B 485 MET cc_start: 0.6722 (mmm) cc_final: 0.6475 (mmm) REVERT: G 5 LEU cc_start: 0.8277 (mp) cc_final: 0.7991 (mp) REVERT: E 236 MET cc_start: 0.3870 (OUTLIER) cc_final: 0.3599 (tmm) outliers start: 27 outliers final: 23 residues processed: 209 average time/residue: 0.2929 time to fit residues: 94.7052 Evaluate side-chains 211 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 185 time to evaluate : 1.952 ------------------------------------------------------------------------------- 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 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 198 LYS Chi-restraints excluded: chain B residue 229 CYS Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain G residue 14 ILE Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain H residue 60 VAL Chi-restraints excluded: chain H residue 69 VAL Chi-restraints excluded: chain H residue 108 ASN Chi-restraints excluded: chain E residue 7 VAL Chi-restraints excluded: chain E residue 137 MET Chi-restraints excluded: chain E residue 236 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 127 optimal weight: 1.9990 chunk 170 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 147 optimal weight: 0.2980 chunk 23 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 chunk 160 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 164 optimal weight: 0.0570 chunk 20 optimal weight: 0.5980 chunk 29 optimal weight: 0.5980 overall best weight: 0.4498 ------------------------------------------------------------------------------- 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 ** A 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 24 ASN ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 404 GLN G 65 GLN ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 190 HIS ** I 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.174630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.138190 restraints weight = 22809.251| |-----------------------------------------------------------------------------| r_work (start): 0.3758 rms_B_bonded: 1.95 r_work: 0.3527 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3372 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.2304 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= 0.187 Angle : 0.502 8.936 23220 Z= 0.261 Chirality : 0.037 0.140 2531 Planarity : 0.004 0.051 2969 Dihedral : 4.411 74.380 2283 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.48 % Allowed : 15.08 % Favored : 83.44 % 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: 1480 sheet: -1.67 (1.01), residues: 10 loop : -1.39 (0.25), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP A 543 HIS 0.007 0.001 HIS B 366 PHE 0.030 0.001 PHE B 445 TYR 0.027 0.001 TYR A 468 ARG 0.012 0.000 ARG G 9 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4026.93 seconds wall clock time: 88 minutes 34.43 seconds (5314.43 seconds total)