Starting phenix.real_space_refine on Sun Feb 18 05:54:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tfj_25874/02_2024/7tfj_25874_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tfj_25874/02_2024/7tfj_25874.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/7tfj_25874/02_2024/7tfj_25874.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tfj_25874/02_2024/7tfj_25874.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tfj_25874/02_2024/7tfj_25874_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tfj_25874/02_2024/7tfj_25874_updated.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= 0.042 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 370 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: 7 Type Number sf(0) Gaussians Se 18 7.20 5 P 56 5.49 5 Mg 4 5.21 5 S 81 5.16 5 C 12880 2.51 5 N 3516 2.21 5 O 4052 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 376": "OE1" <-> "OE2" Residue "D GLU 29": "OE1" <-> "OE2" Residue "D TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 94": "OE1" <-> "OE2" Residue "D GLU 141": "OE1" <-> "OE2" Residue "D GLU 258": "OE1" <-> "OE2" Residue "E GLU 58": "OE1" <-> "OE2" Residue "E GLU 302": "OE1" <-> "OE2" Residue "F GLU 3": "OE1" <-> "OE2" Residue "F GLU 7": "OE1" <-> "OE2" Residue "F PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 189": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 20607 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 3130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 3130 Classifications: {'peptide': 396} Link IDs: {'PTRANS': 14, 'TRANS': 381} Chain breaks: 1 Chain: "B" Number of atoms: 2510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2510 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 9, 'TRANS': 310} Chain: "C" Number of atoms: 2615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2615 Classifications: {'peptide': 330} Link IDs: {'PTRANS': 12, 'TRANS': 317} Chain: "D" Number of atoms: 2622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2622 Classifications: {'peptide': 331} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 318} Chain: "E" Number of atoms: 2685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2685 Classifications: {'peptide': 340} Link IDs: {'PTRANS': 14, 'TRANS': 325} Chain breaks: 1 Chain: "F" Number of atoms: 2021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2021 Classifications: {'peptide': 258} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 249} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "G" Number of atoms: 2014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2014 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 8, 'TRANS': 248} Chain: "H" Number of atoms: 1995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1995 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 8, 'TRANS': 245} Chain: "I" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 449 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "J" Number of atoms: 411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 411 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 11.44, per 1000 atoms: 0.56 Number of scatterers: 20607 At special positions: 0 Unit cell: (119.232, 122.544, 137.448, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Se 18 33.99 S 81 16.00 P 56 15.00 Mg 4 11.99 O 4052 8.00 N 3516 7.00 C 12880 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: 8.73 Conformation dependent library (CDL) restraints added in 3.6 seconds 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4728 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 104 helices and 16 sheets defined 43.6% alpha, 13.2% beta 15 base pairs and 32 stacking pairs defined. Time for finding SS restraints: 8.22 Creating SS restraints... Processing helix chain 'A' and resid 298 through 301 No H-bonds generated for 'chain 'A' and resid 298 through 301' Processing helix chain 'A' and resid 307 through 309 No H-bonds generated for 'chain 'A' and resid 307 through 309' Processing helix chain 'A' and resid 314 through 325 Processing helix chain 'A' and resid 327 through 332 Processing helix chain 'A' and resid 359 through 369 Processing helix chain 'A' and resid 385 through 389 Processing helix chain 'A' and resid 394 through 396 No H-bonds generated for 'chain 'A' and resid 394 through 396' Processing helix chain 'A' and resid 402 through 405 No H-bonds generated for 'chain 'A' and resid 402 through 405' Processing helix chain 'A' and resid 437 through 445 Processing helix chain 'A' and resid 462 through 466 Proline residue: A 465 - end of helix No H-bonds generated for 'chain 'A' and resid 462 through 466' Processing helix chain 'A' and resid 480 through 494 Processing helix chain 'A' and resid 502 through 510 Processing helix chain 'A' and resid 514 through 527 removed outlier: 4.363A pdb=" N THR A 527 " --> pdb=" O THR A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 543 Processing helix chain 'A' and resid 551 through 558 removed outlier: 3.689A pdb=" N ALA A 555 " --> pdb=" O PRO A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 571 Processing helix chain 'A' and resid 574 through 584 removed outlier: 4.186A pdb=" N ASP A 584 " --> pdb=" O LEU A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 595 removed outlier: 3.502A pdb=" N GLN A 593 " --> pdb=" O PRO A 589 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ASN A 595 " --> pdb=" O MET A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 631 removed outlier: 3.617A pdb=" N ILE A 626 " --> pdb=" O SER A 622 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL A 627 " --> pdb=" O LEU A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 648 removed outlier: 3.798A pdb=" N LEU A 641 " --> pdb=" O TRP A 638 " (cutoff:3.500A) Proline residue: A 642 - end of helix Processing helix chain 'A' and resid 650 through 654 Processing helix chain 'A' and resid 669 through 690 Processing helix chain 'B' and resid 11 through 14 No H-bonds generated for 'chain 'B' and resid 11 through 14' Processing helix chain 'B' and resid 27 through 39 Processing helix chain 'B' and resid 56 through 66 Processing helix chain 'B' and resid 71 through 74 No H-bonds generated for 'chain 'B' and resid 71 through 74' Processing helix chain 'B' and resid 86 through 98 Processing helix chain 'B' and resid 116 through 118 No H-bonds generated for 'chain 'B' and resid 116 through 118' Processing helix chain 'B' and resid 121 through 133 removed outlier: 3.538A pdb=" N ARG B 129 " --> pdb=" O GLN B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 157 Processing helix chain 'B' and resid 168 through 181 Processing helix chain 'B' and resid 188 through 198 Processing helix chain 'B' and resid 202 through 215 Processing helix chain 'B' and resid 221 through 227 Processing helix chain 'B' and resid 232 through 241 Processing helix chain 'B' and resid 245 through 255 Processing helix chain 'B' and resid 263 through 276 Processing helix chain 'B' and resid 282 through 301 Processing helix chain 'B' and resid 306 through 320 Processing helix chain 'C' and resid 15 through 18 No H-bonds generated for 'chain 'C' and resid 15 through 18' Processing helix chain 'C' and resid 32 through 43 Processing helix chain 'C' and resid 59 through 70 Processing helix chain 'C' and resid 75 through 78 No H-bonds generated for 'chain 'C' and resid 75 through 78' Processing helix chain 'C' and resid 90 through 102 removed outlier: 4.090A pdb=" N ILE C 97 " --> pdb=" O VAL C 93 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N LYS C 98 " --> pdb=" O ARG C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 136 removed outlier: 3.991A pdb=" N ARG C 132 " --> pdb=" O ASN C 128 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL C 133 " --> pdb=" O ALA C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 160 Processing helix chain 'C' and resid 171 through 185 Processing helix chain 'C' and resid 191 through 201 Processing helix chain 'C' and resid 205 through 218 Processing helix chain 'C' and resid 229 through 236 Processing helix chain 'C' and resid 241 through 253 Processing helix chain 'C' and resid 256 through 270 removed outlier: 4.077A pdb=" N LYS C 270 " --> pdb=" O VAL C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 287 removed outlier: 4.021A pdb=" N ASP C 287 " --> pdb=" O LYS C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 311 Processing helix chain 'C' and resid 316 through 332 Processing helix chain 'D' and resid 27 through 30 No H-bonds generated for 'chain 'D' and resid 27 through 30' Processing helix chain 'D' and resid 36 through 38 No H-bonds generated for 'chain 'D' and resid 36 through 38' Processing helix chain 'D' and resid 43 through 54 removed outlier: 3.914A pdb=" N LYS D 54 " --> pdb=" O LYS D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 82 Processing helix chain 'D' and resid 88 through 91 No H-bonds generated for 'chain 'D' and resid 88 through 91' Processing helix chain 'D' and resid 103 through 115 removed outlier: 3.823A pdb=" N VAL D 110 " --> pdb=" O VAL D 106 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N LYS D 111 " --> pdb=" O ARG D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 128 Processing helix chain 'D' and resid 142 through 144 No H-bonds generated for 'chain 'D' and resid 142 through 144' Processing helix chain 'D' and resid 147 through 162 removed outlier: 4.339A pdb=" N ARG D 155 " --> pdb=" O SER D 151 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N THR D 156 " --> pdb=" O ALA D 152 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N SER D 161 " --> pdb=" O MET D 157 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N GLY D 162 " --> pdb=" O GLU D 158 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 183 Processing helix chain 'D' and resid 198 through 208 Processing helix chain 'D' and resid 216 through 223 Processing helix chain 'D' and resid 228 through 245 Processing helix chain 'D' and resid 253 through 259 Processing helix chain 'D' and resid 265 through 276 Processing helix chain 'D' and resid 280 through 293 Processing helix chain 'D' and resid 297 through 308 Processing helix chain 'D' and resid 316 through 334 removed outlier: 3.773A pdb=" N TRP D 324 " --> pdb=" O ASN D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 339 through 352 Processing helix chain 'E' and resid 4 through 7 No H-bonds generated for 'chain 'E' and resid 4 through 7' Processing helix chain 'E' and resid 20 through 31 Processing helix chain 'E' and resid 49 through 60 Processing helix chain 'E' and resid 106 through 118 removed outlier: 3.543A pdb=" N GLN E 118 " --> pdb=" O LYS E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 145 No H-bonds generated for 'chain 'E' and resid 143 through 145' Processing helix chain 'E' and resid 148 through 160 removed outlier: 4.016A pdb=" N ARG E 156 " --> pdb=" O ALA E 152 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 176 No H-bonds generated for 'chain 'E' and resid 174 through 176' Processing helix chain 'E' and resid 179 through 184 Processing helix chain 'E' and resid 195 through 208 Processing helix chain 'E' and resid 217 through 226 Processing helix chain 'E' and resid 230 through 243 Processing helix chain 'E' and resid 258 through 272 Processing helix chain 'E' and resid 276 through 291 Processing helix chain 'E' and resid 296 through 307 Processing helix chain 'E' and resid 315 through 333 Processing helix chain 'E' and resid 340 through 352 Processing helix chain 'F' and resid 10 through 19 removed outlier: 3.727A pdb=" N PHE F 19 " --> pdb=" O ILE F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 72 through 79 Processing helix chain 'F' and resid 141 through 152 Processing helix chain 'F' and resid 191 through 193 No H-bonds generated for 'chain 'F' and resid 191 through 193' Processing helix chain 'F' and resid 209 through 220 removed outlier: 4.156A pdb=" N GLY F 218 " --> pdb=" O ASP F 214 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N SER F 219 " --> pdb=" O ILE F 215 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N SER F 220 " --> pdb=" O ILE F 216 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 19 removed outlier: 3.852A pdb=" N PHE G 19 " --> pdb=" O ILE G 15 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 81 removed outlier: 4.689A pdb=" N CYS G 81 " --> pdb=" O LYS G 77 " (cutoff:3.500A) Processing helix chain 'G' and resid 141 through 152 Processing helix chain 'G' and resid 191 through 193 No H-bonds generated for 'chain 'G' and resid 191 through 193' Processing helix chain 'G' and resid 210 through 218 removed outlier: 4.291A pdb=" N GLY G 218 " --> pdb=" O ASP G 214 " (cutoff:3.500A) Processing helix chain 'H' and resid 9 through 18 Processing helix chain 'H' and resid 72 through 81 Processing helix chain 'H' and resid 141 through 154 removed outlier: 3.748A pdb=" N LEU H 154 " --> pdb=" O ASP H 150 " (cutoff:3.500A) Processing helix chain 'H' and resid 209 through 220 removed outlier: 3.948A pdb=" N ILE H 216 " --> pdb=" O LEU H 212 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N LYS H 217 " --> pdb=" O LEU H 213 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N GLY H 218 " --> pdb=" O ASP H 214 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N SER H 219 " --> pdb=" O ILE H 215 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N SER H 220 " --> pdb=" O ILE H 216 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 348 through 352 removed outlier: 6.061A pdb=" N LEU A 451 " --> pdb=" O ALA A 349 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N LEU A 351 " --> pdb=" O LEU A 451 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N LEU A 453 " --> pdb=" O LEU A 351 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ASP A 373 " --> pdb=" O VAL A 420 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N ILE A 422 " --> pdb=" O ASP A 373 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N LEU A 375 " --> pdb=" O ILE A 422 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 159 through 162 removed outlier: 3.615A pdb=" N MET B 45 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N LYS B 109 " --> pdb=" O ARG B 139 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N ALA B 141 " --> pdb=" O LYS B 109 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N VAL B 111 " --> pdb=" O ALA B 141 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N ALA B 143 " --> pdb=" O VAL B 111 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N LEU B 113 " --> pdb=" O ALA B 143 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 162 through 166 removed outlier: 3.871A pdb=" N GLY C 53 " --> pdb=" O ALA C 147 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N LYS C 112 " --> pdb=" O ARG C 142 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N CYS C 144 " --> pdb=" O LYS C 112 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ILE C 114 " --> pdb=" O CYS C 144 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N LEU C 146 " --> pdb=" O ILE C 114 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N LEU C 116 " --> pdb=" O LEU C 146 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 185 through 189 removed outlier: 4.008A pdb=" N GLY D 65 " --> pdb=" O CYS D 170 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N LYS D 135 " --> pdb=" O ARG D 165 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N CYS D 167 " --> pdb=" O LYS D 135 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ILE D 137 " --> pdb=" O CYS D 167 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N ILE D 169 " --> pdb=" O ILE D 137 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N LEU D 139 " --> pdb=" O ILE D 169 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'E' and resid 186 through 190 removed outlier: 6.280A pdb=" N LYS E 136 " --> pdb=" O ARG E 166 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N ILE E 168 " --> pdb=" O LYS E 136 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N VAL E 138 " --> pdb=" O ILE E 168 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N VAL E 170 " --> pdb=" O VAL E 138 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N ILE E 140 " --> pdb=" O VAL E 170 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N HIS E 93 " --> pdb=" O SER E 90 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N SER E 90 " --> pdb=" O HIS E 93 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL E 88 " --> pdb=" O GLU E 95 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N THR E 97 " --> pdb=" O ASN E 86 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N ASN E 86 " --> pdb=" O THR E 97 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LEU E 83 " --> pdb=" O PHE E 75 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU E 85 " --> pdb=" O ARG E 73 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'F' and resid 2 through 6 removed outlier: 3.738A pdb=" N LEU F 88 " --> pdb=" O PHE F 6 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU F 116 " --> pdb=" O ILE F 99 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'F' and resid 66 through 68 removed outlier: 4.481A pdb=" N ASP F 240 " --> pdb=" O ARG F 224 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ARG F 224 " --> pdb=" O ASP F 240 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'F' and resid 157 through 160 Processing sheet with id= I, first strand: chain 'F' and resid 167 through 170 Processing sheet with id= J, first strand: chain 'G' and resid 66 through 68 removed outlier: 3.783A pdb=" N ASN G 27 " --> pdb=" O GLN G 38 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN G 38 " --> pdb=" O ASN G 27 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ASP G 240 " --> pdb=" O ARG G 224 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ARG G 224 " --> pdb=" O ASP G 240 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N THR G 136 " --> pdb=" O GLU G 198 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'G' and resid 87 through 92 removed outlier: 3.766A pdb=" N LEU G 102 " --> pdb=" O THR G 89 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'G' and resid 167 through 172 removed outlier: 3.715A pdb=" N ILE G 167 " --> pdb=" O ILE G 182 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'H' and resid 3 through 5 Processing sheet with id= N, first strand: chain 'H' and resid 66 through 68 removed outlier: 3.546A pdb=" N VAL H 66 " --> pdb=" O CYS H 30 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLN H 29 " --> pdb=" O ILE H 36 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ILE H 36 " --> pdb=" O GLN H 29 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ASP H 240 " --> pdb=" O ARG H 224 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ARG H 224 " --> pdb=" O ASP H 240 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS H 196 " --> pdb=" O SER H 138 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'H' and resid 157 through 160 Processing sheet with id= P, first strand: chain 'H' and resid 166 through 172 856 hydrogen bonds defined for protein. 2478 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 37 hydrogen bonds 70 hydrogen bond angles 0 basepair planarities 15 basepair parallelities 32 stacking parallelities Total time for adding SS restraints: 6.84 Time building geometry restraints manager: 9.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.37: 6811 1.37 - 1.52: 8059 1.52 - 1.67: 5998 1.67 - 1.82: 115 1.82 - 1.97: 40 Bond restraints: 21023 Sorted by residual: bond pdb=" N GLU B 287 " pdb=" CA GLU B 287 " ideal model delta sigma weight residual 1.459 1.486 -0.026 1.19e-02 7.06e+03 4.94e+00 bond pdb=" CG GLU C 307 " pdb=" CD GLU C 307 " ideal model delta sigma weight residual 1.516 1.461 0.055 2.50e-02 1.60e+03 4.78e+00 bond pdb=" N GLN E 110 " pdb=" CA GLN E 110 " ideal model delta sigma weight residual 1.459 1.484 -0.024 1.19e-02 7.06e+03 4.20e+00 bond pdb=" N ARG A 434 " pdb=" CA ARG A 434 " ideal model delta sigma weight residual 1.461 1.490 -0.029 1.49e-02 4.50e+03 3.69e+00 bond pdb=" C LYS A 550 " pdb=" N PRO A 551 " ideal model delta sigma weight residual 1.333 1.358 -0.025 1.44e-02 4.82e+03 3.01e+00 ... (remaining 21018 not shown) Histogram of bond angle deviations from ideal: 96.62 - 104.56: 414 104.56 - 112.50: 11287 112.50 - 120.44: 8912 120.44 - 128.39: 7854 128.39 - 136.33: 134 Bond angle restraints: 28601 Sorted by residual: angle pdb=" N GLU C 307 " pdb=" CA GLU C 307 " pdb=" CB GLU C 307 " ideal model delta sigma weight residual 110.28 118.10 -7.82 1.55e+00 4.16e-01 2.54e+01 angle pdb=" CA ARG E 106 " pdb=" CB ARG E 106 " pdb=" CG ARG E 106 " ideal model delta sigma weight residual 114.10 122.74 -8.64 2.00e+00 2.50e-01 1.87e+01 angle pdb=" CA GLU C 307 " pdb=" CB GLU C 307 " pdb=" CG GLU C 307 " ideal model delta sigma weight residual 114.10 121.59 -7.49 2.00e+00 2.50e-01 1.40e+01 angle pdb=" N VAL A 401 " pdb=" CA VAL A 401 " pdb=" C VAL A 401 " ideal model delta sigma weight residual 112.96 109.23 3.73 1.00e+00 1.00e+00 1.39e+01 angle pdb=" C GLU A 293 " pdb=" N GLU A 294 " pdb=" CA GLU A 294 " ideal model delta sigma weight residual 122.61 128.22 -5.61 1.56e+00 4.11e-01 1.29e+01 ... (remaining 28596 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.79: 12302 30.79 - 61.58: 497 61.58 - 92.37: 22 92.37 - 123.17: 1 123.17 - 153.96: 2 Dihedral angle restraints: 12824 sinusoidal: 5560 harmonic: 7264 Sorted by residual: dihedral pdb=" O1B ADP E 500 " pdb=" O3A ADP E 500 " pdb=" PB ADP E 500 " pdb=" PA ADP E 500 " ideal model delta sinusoidal sigma weight residual -60.00 -178.91 118.91 1 2.00e+01 2.50e-03 3.56e+01 dihedral pdb=" O1A AGS D 401 " pdb=" O3A AGS D 401 " pdb=" PA AGS D 401 " pdb=" PB AGS D 401 " ideal model delta sinusoidal sigma weight residual -67.73 86.23 -153.96 1 3.00e+01 1.11e-03 2.03e+01 dihedral pdb=" C4' DT J 19 " pdb=" C3' DT J 19 " pdb=" O3' DT J 19 " pdb=" P DA J 20 " ideal model delta sinusoidal sigma weight residual 220.00 85.93 134.07 1 3.50e+01 8.16e-04 1.33e+01 ... (remaining 12821 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 2314 0.037 - 0.075: 759 0.075 - 0.112: 204 0.112 - 0.150: 48 0.150 - 0.187: 5 Chirality restraints: 3330 Sorted by residual: chirality pdb=" CA ASP D 178 " pdb=" N ASP D 178 " pdb=" C ASP D 178 " pdb=" CB ASP D 178 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.78e-01 chirality pdb=" CA PHE H 19 " pdb=" N PHE H 19 " pdb=" C PHE H 19 " pdb=" CB PHE H 19 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.27e-01 chirality pdb=" CB THR H 193 " pdb=" CA THR H 193 " pdb=" OG1 THR H 193 " pdb=" CG2 THR H 193 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.18 2.00e-01 2.50e+01 7.84e-01 ... (remaining 3327 not shown) Planarity restraints: 3483 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA H 251 " 0.088 5.00e-02 4.00e+02 1.32e-01 2.78e+01 pdb=" N PRO H 252 " -0.228 5.00e-02 4.00e+02 pdb=" CA PRO H 252 " 0.071 5.00e-02 4.00e+02 pdb=" CD PRO H 252 " 0.069 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY E 62 " 0.061 5.00e-02 4.00e+02 8.90e-02 1.27e+01 pdb=" N PRO E 63 " -0.154 5.00e-02 4.00e+02 pdb=" CA PRO E 63 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO E 63 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 680 " 0.012 2.00e-02 2.50e+03 2.32e-02 5.38e+00 pdb=" C TYR A 680 " -0.040 2.00e-02 2.50e+03 pdb=" O TYR A 680 " 0.015 2.00e-02 2.50e+03 pdb=" N ARG A 681 " 0.014 2.00e-02 2.50e+03 ... (remaining 3480 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 304 2.65 - 3.21: 19017 3.21 - 3.78: 32119 3.78 - 4.34: 44249 4.34 - 4.90: 72632 Nonbonded interactions: 168321 Sorted by model distance: nonbonded pdb=" OG1 THR D 72 " pdb="MG MG D 402 " model vdw 2.088 2.170 nonbonded pdb=" O2G AGS C 401 " pdb="MG MG C 402 " model vdw 2.105 2.170 nonbonded pdb=" OG1 THR A 360 " pdb="MG MG A 902 " model vdw 2.142 2.170 nonbonded pdb=" O3G AGS D 401 " pdb="MG MG D 402 " model vdw 2.151 2.170 nonbonded pdb=" O2G AGS B 401 " pdb="MG MG B 402 " model vdw 2.164 2.170 ... (remaining 168316 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 'F' and resid 1 through 254) selection = (chain 'G' and resid 1 through 254) selection = chain 'H' } 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: 2.620 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: 0.020 Extract box with map and model: 14.130 Check model and map are aligned: 0.300 Set scattering table: 0.180 Process input model: 60.430 Find NCS groups from input model: 1.080 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 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 : 0.003 0.079 21023 Z= 0.208 Angle : 0.623 10.361 28601 Z= 0.330 Chirality : 0.041 0.187 3330 Planarity : 0.005 0.132 3483 Dihedral : 15.192 153.957 8096 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.09 % Allowed : 0.50 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.17), residues: 2466 helix: 1.09 (0.16), residues: 1127 sheet: -0.35 (0.25), residues: 469 loop : -0.77 (0.21), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 543 HIS 0.004 0.001 HIS B 232 PHE 0.028 0.001 PHE A 335 TYR 0.016 0.001 TYR A 596 ARG 0.011 0.000 ARG G 80 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 2207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 367 time to evaluate : 2.349 Fit side-chains revert: symmetry clash REVERT: A 376 GLU cc_start: 0.7704 (pm20) cc_final: 0.6718 (tt0) REVERT: A 399 MET cc_start: 0.7742 (ppp) cc_final: 0.7037 (ppp) REVERT: A 414 LEU cc_start: 0.7176 (mm) cc_final: 0.6861 (mm) REVERT: A 660 MET cc_start: 0.7036 (mtm) cc_final: 0.6800 (ttm) REVERT: A 666 PHE cc_start: 0.6949 (t80) cc_final: 0.6279 (t80) REVERT: D 115 ARG cc_start: 0.7579 (mtm-85) cc_final: 0.7303 (ttp-170) REVERT: E 258 ASP cc_start: 0.7952 (p0) cc_final: 0.7742 (p0) REVERT: G 149 ARG cc_start: 0.8370 (mtm110) cc_final: 0.8056 (mtm180) REVERT: G 228 ARG cc_start: 0.8199 (mtt-85) cc_final: 0.7847 (mtt90) REVERT: H 215 ILE cc_start: 0.7806 (pt) cc_final: 0.7526 (pt) REVERT: H 238 GLN cc_start: 0.7922 (tt0) cc_final: 0.6981 (tm-30) outliers start: 2 outliers final: 1 residues processed: 368 average time/residue: 0.3363 time to fit residues: 187.7703 Evaluate side-chains 284 residues out of total 2207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 283 time to evaluate : 2.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 146 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 211 optimal weight: 8.9990 chunk 189 optimal weight: 2.9990 chunk 105 optimal weight: 0.1980 chunk 64 optimal weight: 3.9990 chunk 127 optimal weight: 5.9990 chunk 101 optimal weight: 0.8980 chunk 195 optimal weight: 1.9990 chunk 75 optimal weight: 0.6980 chunk 119 optimal weight: 0.0060 chunk 145 optimal weight: 0.9980 chunk 227 optimal weight: 2.9990 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 HIS B 146 GLN ** B 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 184 HIS ** E 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 238 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.0892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21023 Z= 0.169 Angle : 0.532 11.123 28601 Z= 0.275 Chirality : 0.039 0.150 3330 Planarity : 0.004 0.081 3483 Dihedral : 14.178 149.621 3208 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.95 % Allowed : 7.66 % Favored : 91.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.17), residues: 2466 helix: 1.39 (0.16), residues: 1126 sheet: -0.20 (0.26), residues: 449 loop : -0.74 (0.20), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 298 HIS 0.007 0.001 HIS E 93 PHE 0.016 0.001 PHE H 19 TYR 0.020 0.001 TYR B 186 ARG 0.004 0.000 ARG D 175 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 314 time to evaluate : 2.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 376 GLU cc_start: 0.7693 (pm20) cc_final: 0.6793 (tt0) REVERT: A 399 MET cc_start: 0.7631 (ppp) cc_final: 0.5555 (mtt) REVERT: A 666 PHE cc_start: 0.6985 (t80) cc_final: 0.6261 (t80) REVERT: B 129 ARG cc_start: 0.7605 (tpp-160) cc_final: 0.6959 (tpp-160) REVERT: B 133 LEU cc_start: 0.7966 (OUTLIER) cc_final: 0.7553 (mp) REVERT: C 83 ASN cc_start: 0.7145 (m-40) cc_final: 0.6901 (m110) REVERT: C 140 ASN cc_start: 0.7449 (p0) cc_final: 0.7248 (p0) REVERT: C 307 GLU cc_start: 0.6484 (mp0) cc_final: 0.6239 (mp0) REVERT: E 258 ASP cc_start: 0.7956 (p0) cc_final: 0.7709 (p0) REVERT: G 149 ARG cc_start: 0.8412 (mtm110) cc_final: 0.8090 (mtm110) REVERT: H 61 ARG cc_start: 0.6683 (ttm170) cc_final: 0.5988 (ptt90) REVERT: H 238 GLN cc_start: 0.7976 (tt0) cc_final: 0.6997 (tm-30) outliers start: 21 outliers final: 16 residues processed: 326 average time/residue: 0.3690 time to fit residues: 180.9732 Evaluate side-chains 298 residues out of total 2207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 281 time to evaluate : 2.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 368 GLN Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain A residue 508 GLN Chi-restraints excluded: chain A residue 595 ASN Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain D residue 124 HIS Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain F residue 21 ASP Chi-restraints excluded: chain G residue 83 ASN Chi-restraints excluded: chain G residue 93 ASP Chi-restraints excluded: chain H residue 2 LEU Chi-restraints excluded: chain H residue 175 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 126 optimal weight: 8.9990 chunk 70 optimal weight: 1.9990 chunk 188 optimal weight: 2.9990 chunk 154 optimal weight: 4.9990 chunk 62 optimal weight: 0.8980 chunk 227 optimal weight: 9.9990 chunk 245 optimal weight: 4.9990 chunk 202 optimal weight: 0.0970 chunk 225 optimal weight: 20.0000 chunk 77 optimal weight: 0.6980 chunk 182 optimal weight: 4.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 108 HIS ** B 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 124 HIS ** E 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 27 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.1316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 21023 Z= 0.259 Angle : 0.549 9.442 28601 Z= 0.281 Chirality : 0.040 0.156 3330 Planarity : 0.004 0.061 3483 Dihedral : 14.417 151.188 3205 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.86 % Allowed : 10.79 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.17), residues: 2466 helix: 1.40 (0.16), residues: 1125 sheet: -0.23 (0.25), residues: 467 loop : -0.70 (0.21), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 298 HIS 0.005 0.001 HIS E 93 PHE 0.022 0.002 PHE G 169 TYR 0.024 0.001 TYR B 186 ARG 0.005 0.000 ARG G 80 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 297 time to evaluate : 2.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 376 GLU cc_start: 0.7747 (pm20) cc_final: 0.6826 (tt0) REVERT: A 399 MET cc_start: 0.7668 (ppp) cc_final: 0.5703 (mtt) REVERT: B 129 ARG cc_start: 0.7732 (tpp-160) cc_final: 0.7472 (tpp-160) REVERT: C 307 GLU cc_start: 0.6416 (mp0) cc_final: 0.6110 (mp0) REVERT: E 258 ASP cc_start: 0.7999 (p0) cc_final: 0.7764 (p0) REVERT: G 84 ASN cc_start: 0.8314 (p0) cc_final: 0.7989 (p0) REVERT: G 149 ARG cc_start: 0.8471 (mtm110) cc_final: 0.8100 (mtm110) REVERT: H 61 ARG cc_start: 0.6729 (ttm170) cc_final: 0.5983 (ptt90) outliers start: 41 outliers final: 33 residues processed: 321 average time/residue: 0.3485 time to fit residues: 169.0588 Evaluate side-chains 310 residues out of total 2207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 277 time to evaluate : 2.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain A residue 429 MET Chi-restraints excluded: chain A residue 508 GLN Chi-restraints excluded: chain A residue 595 ASN Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 77 GLU Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain B residue 270 SER Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 291 GLN Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 124 HIS Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 259 TRP Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain F residue 21 ASP Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain G residue 93 ASP Chi-restraints excluded: chain G residue 177 SER Chi-restraints excluded: chain G residue 229 LEU Chi-restraints excluded: chain H residue 2 LEU Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 175 ILE Chi-restraints excluded: chain H residue 193 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 224 optimal weight: 9.9990 chunk 170 optimal weight: 0.8980 chunk 118 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 108 optimal weight: 0.6980 chunk 152 optimal weight: 3.9990 chunk 228 optimal weight: 3.9990 chunk 241 optimal weight: 5.9990 chunk 119 optimal weight: 0.5980 chunk 216 optimal weight: 0.9990 chunk 65 optimal weight: 0.6980 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 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 HIS ** B 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.1438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21023 Z= 0.176 Angle : 0.510 9.270 28601 Z= 0.261 Chirality : 0.039 0.141 3330 Planarity : 0.004 0.053 3483 Dihedral : 14.289 147.421 3205 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.90 % Allowed : 12.47 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.17), residues: 2466 helix: 1.54 (0.16), residues: 1124 sheet: -0.32 (0.24), residues: 494 loop : -0.59 (0.21), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 298 HIS 0.005 0.001 HIS D 124 PHE 0.028 0.001 PHE G 169 TYR 0.023 0.001 TYR B 186 ARG 0.006 0.000 ARG D 175 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 291 time to evaluate : 2.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 376 GLU cc_start: 0.7772 (pm20) cc_final: 0.6843 (tt0) REVERT: A 399 MET cc_start: 0.7592 (ppp) cc_final: 0.5612 (mtt) REVERT: A 666 PHE cc_start: 0.7065 (t80) cc_final: 0.6269 (t80) REVERT: B 129 ARG cc_start: 0.7649 (tpp-160) cc_final: 0.7079 (tpp-160) REVERT: B 133 LEU cc_start: 0.8215 (OUTLIER) cc_final: 0.7654 (mp) REVERT: C 17 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7801 (pt0) REVERT: C 52 TYR cc_start: 0.8274 (t80) cc_final: 0.8011 (t80) REVERT: C 69 GLU cc_start: 0.8096 (tm-30) cc_final: 0.7846 (tm-30) REVERT: C 140 ASN cc_start: 0.7462 (p0) cc_final: 0.7068 (p0) REVERT: C 307 GLU cc_start: 0.6252 (mp0) cc_final: 0.6037 (mp0) REVERT: G 84 ASN cc_start: 0.8335 (p0) cc_final: 0.8050 (p0) REVERT: G 149 ARG cc_start: 0.8472 (mtm110) cc_final: 0.8112 (mtm110) REVERT: G 228 ARG cc_start: 0.8207 (mtt-85) cc_final: 0.7834 (mtt-85) REVERT: H 14 ARG cc_start: 0.8931 (mtm-85) cc_final: 0.8217 (mtm180) REVERT: H 61 ARG cc_start: 0.6756 (ttm170) cc_final: 0.6064 (ptt90) REVERT: H 238 GLN cc_start: 0.8012 (tt0) cc_final: 0.7127 (tm-30) outliers start: 42 outliers final: 35 residues processed: 319 average time/residue: 0.3586 time to fit residues: 172.8020 Evaluate side-chains 310 residues out of total 2207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 273 time to evaluate : 2.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain A residue 508 GLN Chi-restraints excluded: chain A residue 591 MET Chi-restraints excluded: chain A residue 595 ASN Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 77 GLU Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain B residue 270 SER Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 291 GLN Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 124 HIS Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 259 TRP Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain F residue 21 ASP Chi-restraints excluded: chain F residue 22 CYS Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 93 ASP Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 229 LEU Chi-restraints excluded: chain H residue 2 LEU Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 137 LEU Chi-restraints excluded: chain H residue 175 ILE Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain H residue 193 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 201 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 179 optimal weight: 0.9980 chunk 99 optimal weight: 5.9990 chunk 206 optimal weight: 0.4980 chunk 167 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 chunk 123 optimal weight: 2.9990 chunk 216 optimal weight: 0.9980 chunk 60 optimal weight: 10.0000 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 108 HIS ** B 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 83 ASN G 83 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21023 Z= 0.220 Angle : 0.518 8.788 28601 Z= 0.265 Chirality : 0.039 0.182 3330 Planarity : 0.004 0.047 3483 Dihedral : 14.306 148.245 3205 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.40 % Allowed : 13.28 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.17), residues: 2466 helix: 1.52 (0.16), residues: 1126 sheet: -0.35 (0.23), residues: 497 loop : -0.55 (0.21), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 298 HIS 0.004 0.001 HIS B 108 PHE 0.026 0.001 PHE G 169 TYR 0.024 0.001 TYR B 186 ARG 0.007 0.000 ARG D 175 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 2207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 286 time to evaluate : 2.375 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 376 GLU cc_start: 0.7802 (pm20) cc_final: 0.6872 (tt0) REVERT: A 399 MET cc_start: 0.7588 (ppp) cc_final: 0.5624 (mtt) REVERT: A 628 GLU cc_start: 0.7921 (tm-30) cc_final: 0.7307 (tm-30) REVERT: B 129 ARG cc_start: 0.7616 (tpp-160) cc_final: 0.7162 (tpp-160) REVERT: B 133 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.7657 (mp) REVERT: C 52 TYR cc_start: 0.8284 (t80) cc_final: 0.8043 (t80) REVERT: C 99 ASP cc_start: 0.7692 (p0) cc_final: 0.7477 (p0) REVERT: C 307 GLU cc_start: 0.6242 (mp0) cc_final: 0.6037 (mp0) REVERT: G 84 ASN cc_start: 0.8337 (p0) cc_final: 0.8071 (p0) REVERT: G 149 ARG cc_start: 0.8501 (mtm110) cc_final: 0.7958 (mtm110) REVERT: H 14 ARG cc_start: 0.8929 (mtm-85) cc_final: 0.8246 (mtm180) REVERT: H 61 ARG cc_start: 0.6772 (ttm170) cc_final: 0.6075 (ptt90) REVERT: H 79 LEU cc_start: 0.8636 (mp) cc_final: 0.8179 (mt) outliers start: 53 outliers final: 40 residues processed: 320 average time/residue: 0.3507 time to fit residues: 170.5778 Evaluate side-chains 309 residues out of total 2207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 268 time to evaluate : 2.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain A residue 595 ASN Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 77 GLU Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain B residue 270 SER Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 291 GLN Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 124 HIS Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 259 TRP Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain F residue 21 ASP Chi-restraints excluded: chain F residue 22 CYS Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 93 ASP Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 177 SER Chi-restraints excluded: chain H residue 2 LEU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 81 CYS Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 137 LEU Chi-restraints excluded: chain H residue 175 ILE Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain H residue 193 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 81 optimal weight: 0.9980 chunk 217 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 chunk 141 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 241 optimal weight: 0.9990 chunk 200 optimal weight: 3.9990 chunk 111 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 80 optimal weight: 0.9990 chunk 126 optimal weight: 5.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 108 HIS ** B 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21023 Z= 0.204 Angle : 0.514 8.664 28601 Z= 0.263 Chirality : 0.039 0.173 3330 Planarity : 0.003 0.047 3483 Dihedral : 14.255 147.351 3205 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.40 % Allowed : 14.10 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.17), residues: 2466 helix: 1.58 (0.16), residues: 1121 sheet: -0.33 (0.23), residues: 503 loop : -0.55 (0.21), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 298 HIS 0.004 0.001 HIS B 108 PHE 0.025 0.001 PHE G 169 TYR 0.024 0.001 TYR B 186 ARG 0.006 0.000 ARG D 175 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 282 time to evaluate : 2.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 376 GLU cc_start: 0.7825 (pm20) cc_final: 0.6902 (tt0) REVERT: A 399 MET cc_start: 0.7567 (ppp) cc_final: 0.5645 (mtt) REVERT: A 628 GLU cc_start: 0.7950 (tm-30) cc_final: 0.7346 (tm-30) REVERT: B 129 ARG cc_start: 0.7625 (tpp-160) cc_final: 0.7206 (tpp-160) REVERT: B 133 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.7546 (mp) REVERT: C 52 TYR cc_start: 0.8294 (t80) cc_final: 0.7945 (t80) REVERT: C 69 GLU cc_start: 0.8120 (tm-30) cc_final: 0.7891 (tm-30) REVERT: C 307 GLU cc_start: 0.6340 (mp0) cc_final: 0.6128 (mp0) REVERT: D 322 ILE cc_start: 0.8425 (OUTLIER) cc_final: 0.8222 (tt) REVERT: E 68 LEU cc_start: 0.8137 (mm) cc_final: 0.7907 (mm) REVERT: E 106 ARG cc_start: 0.7449 (OUTLIER) cc_final: 0.6383 (tpt90) REVERT: G 149 ARG cc_start: 0.8512 (mtm110) cc_final: 0.8167 (mtm110) REVERT: G 199 MSE cc_start: 0.5707 (tpp) cc_final: 0.4022 (mmm) REVERT: H 14 ARG cc_start: 0.8943 (mtm-85) cc_final: 0.8257 (mtm180) REVERT: H 61 ARG cc_start: 0.6798 (ttm170) cc_final: 0.6044 (ptt90) REVERT: H 79 LEU cc_start: 0.8671 (mp) cc_final: 0.8204 (mt) REVERT: H 238 GLN cc_start: 0.8050 (tt0) cc_final: 0.7050 (tm-30) outliers start: 53 outliers final: 43 residues processed: 317 average time/residue: 0.3405 time to fit residues: 163.4685 Evaluate side-chains 312 residues out of total 2207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 266 time to evaluate : 2.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain A residue 536 ILE Chi-restraints excluded: chain A residue 595 ASN Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 77 GLU Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain B residue 270 SER Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 291 GLN Chi-restraints excluded: chain C residue 316 ASP Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 124 HIS Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 322 ILE Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 106 ARG Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 259 TRP Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain F residue 21 ASP Chi-restraints excluded: chain F residue 22 CYS Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain G residue 93 ASP Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 177 SER Chi-restraints excluded: chain H residue 2 LEU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 81 CYS Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 137 LEU Chi-restraints excluded: chain H residue 175 ILE Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain H residue 193 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 233 optimal weight: 7.9990 chunk 27 optimal weight: 1.9990 chunk 137 optimal weight: 2.9990 chunk 176 optimal weight: 2.9990 chunk 136 optimal weight: 2.9990 chunk 203 optimal weight: 4.9990 chunk 135 optimal weight: 2.9990 chunk 240 optimal weight: 10.0000 chunk 150 optimal weight: 2.9990 chunk 146 optimal weight: 0.3980 chunk 111 optimal weight: 5.9990 overall best weight: 2.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 610 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 HIS ** B 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 124 HIS ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 238 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 21023 Z= 0.400 Angle : 0.622 8.254 28601 Z= 0.318 Chirality : 0.043 0.199 3330 Planarity : 0.004 0.047 3483 Dihedral : 14.623 156.002 3205 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 2.81 % Allowed : 14.87 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.17), residues: 2466 helix: 1.16 (0.16), residues: 1136 sheet: -0.44 (0.23), residues: 506 loop : -0.69 (0.21), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 638 HIS 0.007 0.001 HIS B 60 PHE 0.017 0.002 PHE F 185 TYR 0.027 0.002 TYR B 186 ARG 0.007 0.001 ARG G 80 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 280 time to evaluate : 2.386 Fit side-chains revert: symmetry clash REVERT: A 376 GLU cc_start: 0.7846 (pm20) cc_final: 0.7010 (tt0) REVERT: A 399 MET cc_start: 0.7573 (ppp) cc_final: 0.5547 (mtt) REVERT: A 594 GLU cc_start: 0.6903 (OUTLIER) cc_final: 0.6069 (tp30) REVERT: B 129 ARG cc_start: 0.7568 (tpp-160) cc_final: 0.7195 (tpp-160) REVERT: B 133 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.7422 (mp) REVERT: C 307 GLU cc_start: 0.6565 (mt-10) cc_final: 0.6302 (mp0) REVERT: D 134 TYR cc_start: 0.8932 (p90) cc_final: 0.8651 (p90) REVERT: D 322 ILE cc_start: 0.8554 (OUTLIER) cc_final: 0.8321 (tt) REVERT: E 106 ARG cc_start: 0.7626 (OUTLIER) cc_final: 0.6509 (tpt90) REVERT: F 78 ILE cc_start: 0.8822 (mm) cc_final: 0.8589 (mt) REVERT: G 149 ARG cc_start: 0.8560 (mtm110) cc_final: 0.8196 (mtm110) REVERT: H 14 ARG cc_start: 0.8942 (mtm-85) cc_final: 0.8259 (mtm180) REVERT: H 238 GLN cc_start: 0.8201 (tt0) cc_final: 0.7068 (tm-30) outliers start: 62 outliers final: 49 residues processed: 322 average time/residue: 0.3496 time to fit residues: 169.5349 Evaluate side-chains 322 residues out of total 2207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 269 time to evaluate : 2.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain A residue 536 ILE Chi-restraints excluded: chain A residue 594 GLU Chi-restraints excluded: chain A residue 595 ASN Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 77 GLU Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 270 SER Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 291 GLN Chi-restraints excluded: chain C residue 316 ASP Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 88 MET Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 124 HIS Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 322 ILE Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 106 ARG Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 259 TRP Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain F residue 22 CYS Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 93 ASP Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 177 SER Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 81 CYS Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 137 LEU Chi-restraints excluded: chain H residue 175 ILE Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain H residue 193 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 149 optimal weight: 0.7980 chunk 96 optimal weight: 0.7980 chunk 143 optimal weight: 5.9990 chunk 72 optimal weight: 0.6980 chunk 47 optimal weight: 0.7980 chunk 46 optimal weight: 3.9990 chunk 153 optimal weight: 0.7980 chunk 164 optimal weight: 2.9990 chunk 119 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 189 optimal weight: 3.9990 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 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 HIS ** B 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 96 ASN ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21023 Z= 0.190 Angle : 0.534 8.395 28601 Z= 0.273 Chirality : 0.039 0.167 3330 Planarity : 0.003 0.046 3483 Dihedral : 14.366 147.766 3205 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.40 % Allowed : 15.96 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.17), residues: 2466 helix: 1.43 (0.16), residues: 1119 sheet: -0.37 (0.23), residues: 509 loop : -0.61 (0.21), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 543 HIS 0.005 0.001 HIS B 108 PHE 0.021 0.001 PHE A 335 TYR 0.024 0.001 TYR B 186 ARG 0.008 0.000 ARG G 80 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 2207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 281 time to evaluate : 2.485 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 376 GLU cc_start: 0.7815 (pm20) cc_final: 0.6996 (tt0) REVERT: A 399 MET cc_start: 0.7521 (ppp) cc_final: 0.5606 (mtt) REVERT: A 594 GLU cc_start: 0.6743 (OUTLIER) cc_final: 0.5951 (tp30) REVERT: A 667 THR cc_start: 0.7184 (p) cc_final: 0.6733 (p) REVERT: B 129 ARG cc_start: 0.7528 (tpp-160) cc_final: 0.7289 (tpp-160) REVERT: B 133 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.7330 (mp) REVERT: C 307 GLU cc_start: 0.6340 (mt-10) cc_final: 0.6117 (mp0) REVERT: E 68 LEU cc_start: 0.8141 (mm) cc_final: 0.7898 (mm) REVERT: E 106 ARG cc_start: 0.7573 (OUTLIER) cc_final: 0.6493 (tpt90) REVERT: G 149 ARG cc_start: 0.8530 (mtm110) cc_final: 0.8212 (mtm110) REVERT: G 223 ASP cc_start: 0.6678 (p0) cc_final: 0.6268 (p0) REVERT: H 14 ARG cc_start: 0.8939 (mtm-85) cc_final: 0.8242 (mtm180) REVERT: H 61 ARG cc_start: 0.6478 (mtm110) cc_final: 0.4764 (ptt-90) outliers start: 53 outliers final: 45 residues processed: 315 average time/residue: 0.3488 time to fit residues: 166.5110 Evaluate side-chains 312 residues out of total 2207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 264 time to evaluate : 2.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain A residue 536 ILE Chi-restraints excluded: chain A residue 594 GLU Chi-restraints excluded: chain A residue 595 ASN Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 77 GLU Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 136 ASN Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 270 SER Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 316 ASP Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 124 HIS Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 106 ARG Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain F residue 21 ASP Chi-restraints excluded: chain F residue 22 CYS Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 93 ASP Chi-restraints excluded: chain G residue 94 ASN Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 177 SER Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 81 CYS Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 137 LEU Chi-restraints excluded: chain H residue 175 ILE Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain H residue 193 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 219 optimal weight: 0.4980 chunk 230 optimal weight: 1.9990 chunk 210 optimal weight: 1.9990 chunk 224 optimal weight: 5.9990 chunk 135 optimal weight: 3.9990 chunk 97 optimal weight: 0.7980 chunk 176 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 202 optimal weight: 5.9990 chunk 212 optimal weight: 2.9990 chunk 223 optimal weight: 3.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 610 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 HIS ** B 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 21023 Z= 0.281 Angle : 0.563 7.690 28601 Z= 0.287 Chirality : 0.041 0.175 3330 Planarity : 0.004 0.046 3483 Dihedral : 14.430 149.969 3205 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.58 % Allowed : 16.00 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.17), residues: 2466 helix: 1.33 (0.16), residues: 1126 sheet: -0.32 (0.24), residues: 496 loop : -0.67 (0.21), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 638 HIS 0.005 0.001 HIS B 108 PHE 0.014 0.002 PHE F 185 TYR 0.027 0.001 TYR B 186 ARG 0.009 0.000 ARG G 80 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 265 time to evaluate : 2.458 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 306 ASN cc_start: 0.8387 (p0) cc_final: 0.8172 (p0) REVERT: A 399 MET cc_start: 0.7511 (ppp) cc_final: 0.5621 (mtt) REVERT: A 594 GLU cc_start: 0.6683 (OUTLIER) cc_final: 0.5880 (tp30) REVERT: A 625 ASP cc_start: 0.8334 (t0) cc_final: 0.8118 (t0) REVERT: A 663 ARG cc_start: 0.4506 (tpt90) cc_final: 0.4206 (tmt-80) REVERT: A 667 THR cc_start: 0.7208 (p) cc_final: 0.6838 (p) REVERT: B 133 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.7360 (mp) REVERT: D 322 ILE cc_start: 0.8471 (OUTLIER) cc_final: 0.8234 (tt) REVERT: E 106 ARG cc_start: 0.7634 (OUTLIER) cc_final: 0.6523 (tpt90) REVERT: F 78 ILE cc_start: 0.8847 (mm) cc_final: 0.8606 (mt) REVERT: G 84 ASN cc_start: 0.8335 (p0) cc_final: 0.8035 (p0) REVERT: G 149 ARG cc_start: 0.8534 (mtm110) cc_final: 0.8029 (mtm110) REVERT: H 14 ARG cc_start: 0.8943 (mtm-85) cc_final: 0.8239 (mtm180) REVERT: H 61 ARG cc_start: 0.6285 (mtm110) cc_final: 0.4534 (ptt90) REVERT: H 238 GLN cc_start: 0.8115 (tt0) cc_final: 0.7141 (tm-30) outliers start: 57 outliers final: 50 residues processed: 303 average time/residue: 0.3481 time to fit residues: 159.9277 Evaluate side-chains 317 residues out of total 2207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 263 time to evaluate : 2.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain A residue 536 ILE Chi-restraints excluded: chain A residue 594 GLU Chi-restraints excluded: chain A residue 595 ASN Chi-restraints excluded: chain A residue 660 MET Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 77 GLU Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 108 HIS Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 136 ASN Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 270 SER Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 316 ASP Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 88 MET Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 124 HIS Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 322 ILE Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 106 ARG Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 259 TRP Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain F residue 21 ASP Chi-restraints excluded: chain F residue 22 CYS Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 93 ASP Chi-restraints excluded: chain G residue 94 ASN Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 177 SER Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 81 CYS Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 137 LEU Chi-restraints excluded: chain H residue 175 ILE Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain H residue 193 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 147 optimal weight: 9.9990 chunk 237 optimal weight: 1.9990 chunk 144 optimal weight: 7.9990 chunk 112 optimal weight: 0.8980 chunk 165 optimal weight: 1.9990 chunk 249 optimal weight: 4.9990 chunk 229 optimal weight: 9.9990 chunk 198 optimal weight: 4.9990 chunk 20 optimal weight: 0.9980 chunk 153 optimal weight: 0.7980 chunk 121 optimal weight: 0.7980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 HIS ** B 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 64 HIS H 238 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 21023 Z= 0.231 Angle : 0.555 8.698 28601 Z= 0.281 Chirality : 0.040 0.170 3330 Planarity : 0.004 0.065 3483 Dihedral : 14.373 148.104 3205 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.58 % Allowed : 16.14 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.17), residues: 2466 helix: 1.39 (0.16), residues: 1123 sheet: -0.30 (0.23), residues: 496 loop : -0.68 (0.21), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 638 HIS 0.015 0.001 HIS B 108 PHE 0.013 0.001 PHE F 185 TYR 0.025 0.001 TYR B 186 ARG 0.011 0.000 ARG B 129 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 273 time to evaluate : 2.875 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 306 ASN cc_start: 0.8354 (p0) cc_final: 0.8117 (p0) REVERT: A 376 GLU cc_start: 0.7854 (pm20) cc_final: 0.7056 (tt0) REVERT: A 399 MET cc_start: 0.7446 (ppp) cc_final: 0.5556 (mtt) REVERT: A 594 GLU cc_start: 0.6622 (OUTLIER) cc_final: 0.5904 (tp30) REVERT: A 663 ARG cc_start: 0.4515 (tpt90) cc_final: 0.4221 (tmt-80) REVERT: C 227 ILE cc_start: 0.8987 (OUTLIER) cc_final: 0.8780 (mt) REVERT: D 322 ILE cc_start: 0.8446 (OUTLIER) cc_final: 0.8210 (tt) REVERT: E 68 LEU cc_start: 0.8108 (mm) cc_final: 0.7870 (mm) REVERT: E 106 ARG cc_start: 0.7595 (OUTLIER) cc_final: 0.6519 (tpt90) REVERT: E 193 PRO cc_start: 0.7436 (Cg_exo) cc_final: 0.7219 (Cg_endo) REVERT: G 84 ASN cc_start: 0.8350 (p0) cc_final: 0.8041 (p0) REVERT: G 149 ARG cc_start: 0.8510 (mtm110) cc_final: 0.8143 (mtm110) REVERT: G 199 MSE cc_start: 0.5520 (tpp) cc_final: 0.4322 (mmm) REVERT: G 223 ASP cc_start: 0.6718 (p0) cc_final: 0.6307 (p0) REVERT: H 14 ARG cc_start: 0.8940 (mtm-85) cc_final: 0.8232 (mtm180) REVERT: H 61 ARG cc_start: 0.6231 (mtm110) cc_final: 0.4514 (ptt-90) REVERT: H 238 GLN cc_start: 0.8106 (tt0) cc_final: 0.6993 (tm-30) outliers start: 57 outliers final: 47 residues processed: 309 average time/residue: 0.3522 time to fit residues: 164.4638 Evaluate side-chains 317 residues out of total 2207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 266 time to evaluate : 2.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain A residue 536 ILE Chi-restraints excluded: chain A residue 594 GLU Chi-restraints excluded: chain A residue 595 ASN Chi-restraints excluded: chain A residue 660 MET Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 77 GLU Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 108 HIS Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 136 ASN Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 270 SER Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 227 ILE Chi-restraints excluded: chain C residue 316 ASP Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 88 MET Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 124 HIS Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 322 ILE Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 106 ARG Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain F residue 21 ASP Chi-restraints excluded: chain F residue 22 CYS Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 93 ASP Chi-restraints excluded: chain G residue 94 ASN Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 177 SER Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 81 CYS Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 137 LEU Chi-restraints excluded: chain H residue 175 ILE Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain H residue 193 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 157 optimal weight: 3.9990 chunk 211 optimal weight: 4.9990 chunk 60 optimal weight: 0.9980 chunk 182 optimal weight: 2.9990 chunk 29 optimal weight: 0.4980 chunk 55 optimal weight: 0.6980 chunk 198 optimal weight: 0.9980 chunk 83 optimal weight: 0.5980 chunk 203 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 36 optimal weight: 0.0980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 HIS ** B 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.160737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.120226 restraints weight = 27058.923| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 2.61 r_work: 0.3363 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21023 Z= 0.168 Angle : 0.536 10.357 28601 Z= 0.271 Chirality : 0.039 0.261 3330 Planarity : 0.003 0.047 3483 Dihedral : 14.247 144.737 3205 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.09 % Allowed : 16.59 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.17), residues: 2466 helix: 1.55 (0.16), residues: 1115 sheet: -0.28 (0.23), residues: 496 loop : -0.62 (0.21), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 259 HIS 0.020 0.001 HIS B 108 PHE 0.013 0.001 PHE F 185 TYR 0.026 0.001 TYR B 186 ARG 0.009 0.000 ARG G 80 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4581.36 seconds wall clock time: 84 minutes 7.22 seconds (5047.22 seconds total)