Starting phenix.real_space_refine on Fri Feb 16 11:28:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wm1_32597/02_2024/7wm1_32597_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wm1_32597/02_2024/7wm1_32597.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wm1_32597/02_2024/7wm1_32597.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wm1_32597/02_2024/7wm1_32597.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wm1_32597/02_2024/7wm1_32597_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wm1_32597/02_2024/7wm1_32597_neut_updated.pdb" } resolution = 2.8 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= 0.013 sd= 0.144 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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: 6 Type Number sf(0) Gaussians K 3 8.98 5 P 4 5.49 5 S 72 5.16 5 C 9948 2.51 5 N 2516 2.21 5 O 2654 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 61": "OE1" <-> "OE2" Residue "A ARG 83": "NH1" <-> "NH2" Residue "A ARG 86": "NH1" <-> "NH2" Residue "A PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 147": "OE1" <-> "OE2" Residue "A ARG 151": "NH1" <-> "NH2" Residue "A ARG 169": "NH1" <-> "NH2" Residue "A ARG 177": "NH1" <-> "NH2" Residue "A GLU 179": "OE1" <-> "OE2" Residue "A ARG 182": "NH1" <-> "NH2" Residue "A ARG 215": "NH1" <-> "NH2" Residue "A ARG 239": "NH1" <-> "NH2" Residue "A GLU 266": "OE1" <-> "OE2" Residue "A ARG 300": "NH1" <-> "NH2" Residue "A ARG 315": "NH1" <-> "NH2" Residue "A ARG 321": "NH1" <-> "NH2" Residue "A ARG 335": "NH1" <-> "NH2" Residue "A GLU 339": "OE1" <-> "OE2" Residue "A ARG 374": "NH1" <-> "NH2" Residue "A GLU 391": "OE1" <-> "OE2" Residue "A GLU 397": "OE1" <-> "OE2" Residue "A PHE 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 431": "NH1" <-> "NH2" Residue "A GLU 432": "OE1" <-> "OE2" Residue "A GLU 441": "OE1" <-> "OE2" Residue "A ARG 448": "NH1" <-> "NH2" Residue "A ARG 455": "NH1" <-> "NH2" Residue "A ARG 464": "NH1" <-> "NH2" Residue "B ARG 84": "NH1" <-> "NH2" Residue "B ARG 85": "NH1" <-> "NH2" Residue "B GLU 90": "OE1" <-> "OE2" Residue "B GLU 111": "OE1" <-> "OE2" Residue "B ARG 159": "NH1" <-> "NH2" Residue "B ARG 189": "NH1" <-> "NH2" Residue "B ARG 205": "NH1" <-> "NH2" Residue "B GLU 209": "OE1" <-> "OE2" Residue "B ARG 213": "NH1" <-> "NH2" Residue "B GLU 215": "OE1" <-> "OE2" Residue "B ARG 254": "NH1" <-> "NH2" Residue "B PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 270": "NH1" <-> "NH2" Residue "B ARG 301": "NH1" <-> "NH2" Residue "B GLU 302": "OE1" <-> "OE2" Residue "B ARG 334": "NH1" <-> "NH2" Residue "B ARG 347": "NH1" <-> "NH2" Residue "B ARG 353": "NH1" <-> "NH2" Residue "B ARG 359": "NH1" <-> "NH2" Residue "B GLU 374": "OE1" <-> "OE2" Residue "B ARG 376": "NH1" <-> "NH2" Residue "B GLU 378": "OE1" <-> "OE2" Residue "B ARG 398": "NH1" <-> "NH2" Residue "B GLU 402": "OE1" <-> "OE2" Residue "B GLU 412": "OE1" <-> "OE2" Residue "B GLU 432": "OE1" <-> "OE2" Residue "B GLU 475": "OE1" <-> "OE2" Residue "B ARG 491": "NH1" <-> "NH2" Residue "B ARG 498": "NH1" <-> "NH2" Residue "B GLU 506": "OE1" <-> "OE2" Residue "C GLU 61": "OE1" <-> "OE2" Residue "C ARG 83": "NH1" <-> "NH2" Residue "C ARG 86": "NH1" <-> "NH2" Residue "C PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 147": "OE1" <-> "OE2" Residue "C ARG 151": "NH1" <-> "NH2" Residue "C ARG 169": "NH1" <-> "NH2" Residue "C ARG 177": "NH1" <-> "NH2" Residue "C GLU 179": "OE1" <-> "OE2" Residue "C ARG 182": "NH1" <-> "NH2" Residue "C ARG 215": "NH1" <-> "NH2" Residue "C ARG 239": "NH1" <-> "NH2" Residue "C GLU 266": "OE1" <-> "OE2" Residue "C ARG 315": "NH1" <-> "NH2" Residue "C ARG 321": "NH1" <-> "NH2" Residue "C ARG 335": "NH1" <-> "NH2" Residue "C ASP 337": "OD1" <-> "OD2" Residue "C GLU 339": "OE1" <-> "OE2" Residue "C ARG 374": "NH1" <-> "NH2" Residue "C GLU 391": "OE1" <-> "OE2" Residue "C GLU 397": "OE1" <-> "OE2" Residue "C PHE 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 431": "NH1" <-> "NH2" Residue "C GLU 441": "OE1" <-> "OE2" Residue "C ARG 448": "NH1" <-> "NH2" Residue "C ARG 455": "NH1" <-> "NH2" Residue "C ARG 464": "NH1" <-> "NH2" Residue "D ARG 85": "NH1" <-> "NH2" Residue "D GLU 90": "OE1" <-> "OE2" Residue "D GLU 111": "OE1" <-> "OE2" Residue "D ARG 159": "NH1" <-> "NH2" Residue "D ARG 189": "NH1" <-> "NH2" Residue "D ARG 205": "NH1" <-> "NH2" Residue "D GLU 209": "OE1" <-> "OE2" Residue "D ARG 213": "NH1" <-> "NH2" Residue "D GLU 215": "OE1" <-> "OE2" Residue "D ARG 254": "NH1" <-> "NH2" Residue "D PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 270": "NH1" <-> "NH2" Residue "D ARG 301": "NH1" <-> "NH2" Residue "D GLU 302": "OE1" <-> "OE2" Residue "D ARG 339": "NH1" <-> "NH2" Residue "D ARG 347": "NH1" <-> "NH2" Residue "D ARG 353": "NH1" <-> "NH2" Residue "D ARG 359": "NH1" <-> "NH2" Residue "D GLU 374": "OE1" <-> "OE2" Residue "D ARG 376": "NH1" <-> "NH2" Residue "D GLU 378": "OE1" <-> "OE2" Residue "D ARG 398": "NH1" <-> "NH2" Residue "D GLU 402": "OE1" <-> "OE2" Residue "D GLU 412": "OE1" <-> "OE2" Residue "D GLU 432": "OE1" <-> "OE2" Residue "D GLU 475": "OE1" <-> "OE2" Residue "D ARG 491": "NH1" <-> "NH2" Residue "D ARG 498": "NH1" <-> "NH2" Residue "D GLU 506": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 15197 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3669 Classifications: {'peptide': 449} Link IDs: {'PTRANS': 15, 'TRANS': 433} Chain: "B" Number of atoms: 3850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 473, 3850 Classifications: {'peptide': 473} Link IDs: {'PTRANS': 15, 'TRANS': 457} Chain: "C" Number of atoms: 3669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3669 Classifications: {'peptide': 449} Link IDs: {'PTRANS': 15, 'TRANS': 433} Chain: "D" Number of atoms: 3850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 473, 3850 Classifications: {'peptide': 473} Link IDs: {'PTRANS': 15, 'TRANS': 457} Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 42 Unusual residues: {' K': 3, 'POV': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Time building chain proxies: 8.40, per 1000 atoms: 0.55 Number of scatterers: 15197 At special positions: 0 Unit cell: (115.271, 113.117, 123.89, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) K 3 19.00 S 72 16.00 P 4 15.00 O 2654 8.00 N 2516 7.00 C 9948 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: 5.79 Conformation dependent library (CDL) restraints added in 2.9 seconds 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3512 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 78 helices and 8 sheets defined 50.5% alpha, 5.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.85 Creating SS restraints... Processing helix chain 'A' and resid 55 through 66 removed outlier: 4.394A pdb=" N VAL A 65 " --> pdb=" O GLU A 61 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N VAL A 66 " --> pdb=" O ALA A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 80 removed outlier: 3.575A pdb=" N TRP A 73 " --> pdb=" O VAL A 69 " (cutoff:3.500A) Proline residue: A 76 - end of helix Processing helix chain 'A' and resid 87 through 108 removed outlier: 3.575A pdb=" N ILE A 91 " --> pdb=" O PRO A 87 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N THR A 92 " --> pdb=" O PRO A 88 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ASN A 94 " --> pdb=" O SER A 90 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N PHE A 108 " --> pdb=" O ILE A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 131 removed outlier: 4.361A pdb=" N PHE A 129 " --> pdb=" O LYS A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 141 No H-bonds generated for 'chain 'A' and resid 138 through 141' Processing helix chain 'A' and resid 146 through 152 removed outlier: 3.717A pdb=" N ARG A 151 " --> pdb=" O GLU A 147 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE A 152 " --> pdb=" O ALA A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 166 removed outlier: 3.581A pdb=" N MET A 162 " --> pdb=" O GLY A 158 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LEU A 163 " --> pdb=" O LEU A 159 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ARG A 164 " --> pdb=" O PHE A 160 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N LEU A 165 " --> pdb=" O ASN A 161 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N TRP A 166 " --> pdb=" O MET A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 180 removed outlier: 3.510A pdb=" N GLU A 179 " --> pdb=" O PHE A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 214 removed outlier: 4.111A pdb=" N ALA A 192 " --> pdb=" O TRP A 188 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TYR A 210 " --> pdb=" O ALA A 206 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA A 213 " --> pdb=" O TYR A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 251 removed outlier: 3.599A pdb=" N TYR A 240 " --> pdb=" O LEU A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 289 Processing helix chain 'A' and resid 297 through 300 No H-bonds generated for 'chain 'A' and resid 297 through 300' Processing helix chain 'A' and resid 303 through 306 No H-bonds generated for 'chain 'A' and resid 303 through 306' Processing helix chain 'A' and resid 308 through 315 removed outlier: 3.763A pdb=" N ALA A 313 " --> pdb=" O ALA A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 338 Processing helix chain 'A' and resid 347 through 349 No H-bonds generated for 'chain 'A' and resid 347 through 349' Processing helix chain 'A' and resid 355 through 369 removed outlier: 3.585A pdb=" N SER A 359 " --> pdb=" O ARG A 355 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE A 363 " --> pdb=" O SER A 359 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N SER A 365 " --> pdb=" O PHE A 361 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N LEU A 366 " --> pdb=" O LEU A 362 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LYS A 369 " --> pdb=" O SER A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 386 Processing helix chain 'A' and resid 441 through 444 No H-bonds generated for 'chain 'A' and resid 441 through 444' Processing helix chain 'A' and resid 467 through 475 Processing helix chain 'A' and resid 480 through 490 Processing helix chain 'B' and resid 55 through 58 No H-bonds generated for 'chain 'B' and resid 55 through 58' Processing helix chain 'B' and resid 84 through 109 removed outlier: 3.835A pdb=" N TYR B 99 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N TRP B 102 " --> pdb=" O GLY B 98 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU B 105 " --> pdb=" O ALA B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 128 removed outlier: 3.528A pdb=" N PHE B 128 " --> pdb=" O VAL B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 156 No H-bonds generated for 'chain 'B' and resid 153 through 156' Processing helix chain 'B' and resid 164 through 172 Processing helix chain 'B' and resid 176 through 181 Processing helix chain 'B' and resid 197 through 213 removed outlier: 3.748A pdb=" N ARG B 203 " --> pdb=" O ARG B 200 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA B 208 " --> pdb=" O ARG B 205 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N PHE B 211 " --> pdb=" O ALA B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 250 removed outlier: 3.547A pdb=" N ARG B 226 " --> pdb=" O TYR B 222 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU B 230 " --> pdb=" O ARG B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 287 removed outlier: 3.506A pdb=" N THR B 277 " --> pdb=" O TRP B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 324 removed outlier: 3.800A pdb=" N LEU B 311 " --> pdb=" O MET B 307 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE B 314 " --> pdb=" O MET B 310 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLY B 315 " --> pdb=" O LEU B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 351 removed outlier: 3.765A pdb=" N SER B 340 " --> pdb=" O PHE B 336 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ASP B 344 " --> pdb=" O SER B 340 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ILE B 345 " --> pdb=" O ALA B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 375 removed outlier: 3.636A pdb=" N ALA B 364 " --> pdb=" O GLU B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 396 removed outlier: 3.632A pdb=" N HIS B 395 " --> pdb=" O SER B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 401 No H-bonds generated for 'chain 'B' and resid 398 through 401' Processing helix chain 'B' and resid 412 through 421 removed outlier: 4.432A pdb=" N GLN B 421 " --> pdb=" O GLN B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 480 Processing helix chain 'B' and resid 504 through 509 Processing helix chain 'B' and resid 519 through 525 Processing helix chain 'C' and resid 55 through 80 removed outlier: 3.515A pdb=" N ALA C 72 " --> pdb=" O VAL C 68 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N TRP C 73 " --> pdb=" O VAL C 69 " (cutoff:3.500A) Proline residue: C 76 - end of helix Processing helix chain 'C' and resid 87 through 108 removed outlier: 3.574A pdb=" N ILE C 91 " --> pdb=" O PRO C 87 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N THR C 92 " --> pdb=" O PRO C 88 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ASN C 94 " --> pdb=" O SER C 90 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N PHE C 108 " --> pdb=" O ILE C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 131 removed outlier: 4.306A pdb=" N PHE C 129 " --> pdb=" O LYS C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 141 No H-bonds generated for 'chain 'C' and resid 138 through 141' Processing helix chain 'C' and resid 146 through 152 removed outlier: 3.717A pdb=" N ARG C 151 " --> pdb=" O GLU C 147 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE C 152 " --> pdb=" O ALA C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 166 removed outlier: 3.582A pdb=" N MET C 162 " --> pdb=" O GLY C 158 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LEU C 163 " --> pdb=" O LEU C 159 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ARG C 164 " --> pdb=" O PHE C 160 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N LEU C 165 " --> pdb=" O ASN C 161 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N TRP C 166 " --> pdb=" O MET C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 180 removed outlier: 3.512A pdb=" N GLU C 179 " --> pdb=" O PHE C 175 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 190 No H-bonds generated for 'chain 'C' and resid 187 through 190' Processing helix chain 'C' and resid 193 through 214 removed outlier: 3.600A pdb=" N THR C 198 " --> pdb=" O LEU C 194 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TYR C 210 " --> pdb=" O ALA C 206 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ALA C 213 " --> pdb=" O TYR C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 252 removed outlier: 3.599A pdb=" N TYR C 240 " --> pdb=" O LEU C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 289 Processing helix chain 'C' and resid 297 through 300 No H-bonds generated for 'chain 'C' and resid 297 through 300' Processing helix chain 'C' and resid 303 through 306 No H-bonds generated for 'chain 'C' and resid 303 through 306' Processing helix chain 'C' and resid 308 through 315 removed outlier: 3.763A pdb=" N ALA C 313 " --> pdb=" O ALA C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 338 Processing helix chain 'C' and resid 347 through 349 No H-bonds generated for 'chain 'C' and resid 347 through 349' Processing helix chain 'C' and resid 355 through 369 removed outlier: 3.585A pdb=" N SER C 359 " --> pdb=" O ARG C 355 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE C 363 " --> pdb=" O SER C 359 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N SER C 365 " --> pdb=" O PHE C 361 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N LEU C 366 " --> pdb=" O LEU C 362 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LYS C 369 " --> pdb=" O SER C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 386 Processing helix chain 'C' and resid 441 through 444 No H-bonds generated for 'chain 'C' and resid 441 through 444' Processing helix chain 'C' and resid 467 through 475 Processing helix chain 'C' and resid 480 through 490 Processing helix chain 'D' and resid 55 through 59 Processing helix chain 'D' and resid 84 through 109 removed outlier: 3.835A pdb=" N TYR D 99 " --> pdb=" O ILE D 95 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N TRP D 102 " --> pdb=" O GLY D 98 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU D 105 " --> pdb=" O ALA D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 128 removed outlier: 3.529A pdb=" N PHE D 128 " --> pdb=" O VAL D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 153 through 156 No H-bonds generated for 'chain 'D' and resid 153 through 156' Processing helix chain 'D' and resid 164 through 172 Processing helix chain 'D' and resid 176 through 181 Processing helix chain 'D' and resid 197 through 213 removed outlier: 3.747A pdb=" N ARG D 203 " --> pdb=" O ARG D 200 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA D 208 " --> pdb=" O ARG D 205 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N PHE D 211 " --> pdb=" O ALA D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 250 removed outlier: 3.535A pdb=" N LEU D 230 " --> pdb=" O ARG D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 287 removed outlier: 3.506A pdb=" N THR D 277 " --> pdb=" O TRP D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 324 removed outlier: 3.801A pdb=" N LEU D 311 " --> pdb=" O MET D 307 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ILE D 314 " --> pdb=" O MET D 310 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLY D 315 " --> pdb=" O LEU D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 333 through 351 removed outlier: 4.076A pdb=" N ASP D 344 " --> pdb=" O SER D 340 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ILE D 345 " --> pdb=" O ALA D 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 356 through 375 removed outlier: 3.635A pdb=" N ALA D 364 " --> pdb=" O GLU D 360 " (cutoff:3.500A) Processing helix chain 'D' and resid 386 through 396 removed outlier: 3.633A pdb=" N HIS D 395 " --> pdb=" O SER D 391 " (cutoff:3.500A) Processing helix chain 'D' and resid 398 through 401 No H-bonds generated for 'chain 'D' and resid 398 through 401' Processing helix chain 'D' and resid 412 through 421 removed outlier: 4.433A pdb=" N GLN D 421 " --> pdb=" O GLN D 417 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 480 Processing helix chain 'D' and resid 504 through 509 Processing helix chain 'D' and resid 519 through 525 Processing sheet with id= A, first strand: chain 'A' and resid 389 through 393 removed outlier: 3.597A pdb=" N ASN A 414 " --> pdb=" O GLN A 461 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N LEU A 463 " --> pdb=" O LEU A 412 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N LEU A 412 " --> pdb=" O LEU A 463 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N MET A 465 " --> pdb=" O TYR A 410 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N TYR A 410 " --> pdb=" O MET A 465 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 417 through 420 Processing sheet with id= C, first strand: chain 'B' and resid 424 through 427 removed outlier: 3.662A pdb=" N SER B 448 " --> pdb=" O GLN B 495 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ILE B 497 " --> pdb=" O ILE B 446 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N ILE B 446 " --> pdb=" O ILE B 497 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ILE B 499 " --> pdb=" O TYR B 444 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N TYR B 444 " --> pdb=" O ILE B 499 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 487 through 490 removed outlier: 3.932A pdb=" N ALA B 465 " --> pdb=" O ILE B 453 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N ALA B 455 " --> pdb=" O VAL B 463 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N VAL B 463 " --> pdb=" O ALA B 455 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 389 through 393 removed outlier: 3.597A pdb=" N ASN C 414 " --> pdb=" O GLN C 461 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N LEU C 463 " --> pdb=" O LEU C 412 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N LEU C 412 " --> pdb=" O LEU C 463 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N MET C 465 " --> pdb=" O TYR C 410 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N TYR C 410 " --> pdb=" O MET C 465 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 417 through 420 Processing sheet with id= G, first strand: chain 'D' and resid 424 through 427 removed outlier: 3.662A pdb=" N SER D 448 " --> pdb=" O GLN D 495 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ILE D 497 " --> pdb=" O ILE D 446 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N ILE D 446 " --> pdb=" O ILE D 497 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ILE D 499 " --> pdb=" O TYR D 444 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N TYR D 444 " --> pdb=" O ILE D 499 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 487 through 490 removed outlier: 3.932A pdb=" N ALA D 465 " --> pdb=" O ILE D 453 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N ALA D 455 " --> pdb=" O VAL D 463 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N VAL D 463 " --> pdb=" O ALA D 455 " (cutoff:3.500A) 576 hydrogen bonds defined for protein. 1626 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.81 Time building geometry restraints manager: 6.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.98 - 1.15: 26 1.15 - 1.31: 2358 1.31 - 1.48: 6419 1.48 - 1.65: 6637 1.65 - 1.81: 126 Bond restraints: 15566 Sorted by residual: bond pdb=" C TRP C 73 " pdb=" O TRP C 73 " ideal model delta sigma weight residual 1.236 0.982 0.254 1.15e-02 7.56e+03 4.89e+02 bond pdb=" C ALA C 72 " pdb=" O ALA C 72 " ideal model delta sigma weight residual 1.237 0.982 0.255 1.16e-02 7.43e+03 4.83e+02 bond pdb=" C THR C 71 " pdb=" O THR C 71 " ideal model delta sigma weight residual 1.236 1.010 0.226 1.28e-02 6.10e+03 3.11e+02 bond pdb=" C PRO C 76 " pdb=" O PRO C 76 " ideal model delta sigma weight residual 1.237 1.041 0.196 1.26e-02 6.30e+03 2.42e+02 bond pdb=" C PHE C 77 " pdb=" O PHE C 77 " ideal model delta sigma weight residual 1.236 1.044 0.192 1.26e-02 6.30e+03 2.33e+02 ... (remaining 15561 not shown) Histogram of bond angle deviations from ideal: 87.74 - 97.64: 12 97.64 - 107.53: 628 107.53 - 117.42: 10334 117.42 - 127.31: 9944 127.31 - 137.20: 168 Bond angle restraints: 21086 Sorted by residual: angle pdb=" C LEU D 60 " pdb=" N PRO D 61 " pdb=" CA PRO D 61 " ideal model delta sigma weight residual 119.90 135.40 -15.50 1.05e+00 9.07e-01 2.18e+02 angle pdb=" C TYR A 57 " pdb=" CA TYR A 57 " pdb=" CB TYR A 57 " ideal model delta sigma weight residual 110.88 87.74 23.14 1.57e+00 4.06e-01 2.17e+02 angle pdb=" C TYR C 57 " pdb=" CA TYR C 57 " pdb=" CB TYR C 57 " ideal model delta sigma weight residual 110.88 87.77 23.11 1.57e+00 4.06e-01 2.17e+02 angle pdb=" O MET A 106 " pdb=" C MET A 106 " pdb=" N THR A 107 " ideal model delta sigma weight residual 122.39 101.53 20.86 1.48e+00 4.57e-01 1.99e+02 angle pdb=" CA MET A 106 " pdb=" C MET A 106 " pdb=" N THR A 107 " ideal model delta sigma weight residual 118.44 135.44 -17.00 1.41e+00 5.03e-01 1.45e+02 ... (remaining 21081 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.62: 8266 26.62 - 53.25: 792 53.25 - 79.87: 130 79.87 - 106.49: 16 106.49 - 133.11: 2 Dihedral angle restraints: 9206 sinusoidal: 3770 harmonic: 5436 Sorted by residual: dihedral pdb=" C TYR A 57 " pdb=" N TYR A 57 " pdb=" CA TYR A 57 " pdb=" CB TYR A 57 " ideal model delta harmonic sigma weight residual -122.60 -95.90 -26.70 0 2.50e+00 1.60e-01 1.14e+02 dihedral pdb=" C TYR C 57 " pdb=" N TYR C 57 " pdb=" CA TYR C 57 " pdb=" CB TYR C 57 " ideal model delta harmonic sigma weight residual -122.60 -95.92 -26.68 0 2.50e+00 1.60e-01 1.14e+02 dihedral pdb=" C ASP C 54 " pdb=" N ASP C 54 " pdb=" CA ASP C 54 " pdb=" CB ASP C 54 " ideal model delta harmonic sigma weight residual -122.60 -144.47 21.87 0 2.50e+00 1.60e-01 7.65e+01 ... (remaining 9203 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.170: 2275 0.170 - 0.340: 71 0.340 - 0.510: 19 0.510 - 0.680: 2 0.680 - 0.851: 3 Chirality restraints: 2370 Sorted by residual: chirality pdb=" CA PRO C 76 " pdb=" N PRO C 76 " pdb=" C PRO C 76 " pdb=" CB PRO C 76 " both_signs ideal model delta sigma weight residual False 2.72 1.87 0.85 2.00e-01 2.50e+01 1.81e+01 chirality pdb=" CA ASP C 54 " pdb=" N ASP C 54 " pdb=" C ASP C 54 " pdb=" CB ASP C 54 " both_signs ideal model delta sigma weight residual False 2.51 1.70 0.81 2.00e-01 2.50e+01 1.64e+01 chirality pdb=" CA ASP A 54 " pdb=" N ASP A 54 " pdb=" C ASP A 54 " pdb=" CB ASP A 54 " both_signs ideal model delta sigma weight residual False 2.51 1.70 0.81 2.00e-01 2.50e+01 1.64e+01 ... (remaining 2367 not shown) Planarity restraints: 2622 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C28 POV B 701 " -0.252 2.00e-02 2.50e+03 2.37e-01 5.63e+02 pdb=" C29 POV B 701 " 0.308 2.00e-02 2.50e+03 pdb="C210 POV B 701 " 0.153 2.00e-02 2.50e+03 pdb="C211 POV B 701 " -0.209 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV C 901 " 0.141 2.00e-02 2.50e+03 1.41e-01 1.99e+02 pdb=" C29 POV C 901 " -0.139 2.00e-02 2.50e+03 pdb="C210 POV C 901 " -0.143 2.00e-02 2.50e+03 pdb="C211 POV C 901 " 0.141 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV D 701 " 0.119 2.00e-02 2.50e+03 1.18e-01 1.39e+02 pdb=" C29 POV D 701 " -0.127 2.00e-02 2.50e+03 pdb="C210 POV D 701 " -0.109 2.00e-02 2.50e+03 pdb="C211 POV D 701 " 0.116 2.00e-02 2.50e+03 ... (remaining 2619 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.69: 665 2.69 - 3.30: 17167 3.30 - 3.92: 27849 3.92 - 4.53: 39514 4.53 - 5.14: 61326 Nonbonded interactions: 146521 Sorted by model distance: nonbonded pdb=" N ASP D 344 " pdb=" OD1 ASP D 344 " model vdw 2.080 2.520 nonbonded pdb=" O THR D 288 " pdb=" OG1 THR D 289 " model vdw 2.144 2.440 nonbonded pdb=" O THR B 288 " pdb=" OG1 THR B 289 " model vdw 2.144 2.440 nonbonded pdb=" OH TYR A 283 " pdb=" O22 POV A 901 " model vdw 2.200 2.440 nonbonded pdb=" N ASP B 452 " pdb=" OD1 ASP B 452 " model vdw 2.206 2.520 ... (remaining 146516 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 44 through 492 or resid 901)) selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } 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: 0.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.750 Check model and map are aligned: 0.200 Set scattering table: 0.140 Process input model: 41.530 Find NCS groups from input model: 0.900 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: 0.000 Load rotamer database and sin/cos tables:14.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 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 : 0.012 0.255 15566 Z= 0.782 Angle : 1.248 23.135 21086 Z= 0.816 Chirality : 0.082 0.851 2370 Planarity : 0.010 0.237 2622 Dihedral : 20.137 133.112 5694 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 15.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 15.89 % Allowed : 23.78 % Favored : 60.33 % Cbeta Deviations : 1.94 % 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: -4.36 (0.16), residues: 1836 helix: -2.85 (0.12), residues: 1044 sheet: -1.83 (0.46), residues: 100 loop : -2.87 (0.21), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.083 0.005 TRP C 73 HIS 0.009 0.001 HIS B 365 PHE 0.061 0.003 PHE B 63 TYR 0.039 0.003 TYR C 70 ARG 0.009 0.001 ARG B 226 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 554 residues out of total 1636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 260 poor density : 294 time to evaluate : 1.697 Fit side-chains revert: symmetry clash REVERT: A 44 LYS cc_start: 0.3386 (OUTLIER) cc_final: 0.2968 (mtmm) REVERT: A 47 ARG cc_start: 0.4883 (OUTLIER) cc_final: 0.4458 (ptt180) REVERT: A 54 ASP cc_start: 0.7599 (OUTLIER) cc_final: 0.7317 (p0) REVERT: A 55 HIS cc_start: 0.7439 (OUTLIER) cc_final: 0.7224 (m170) REVERT: A 233 GLU cc_start: 0.7125 (pm20) cc_final: 0.6912 (pp20) REVERT: A 322 LEU cc_start: 0.8129 (OUTLIER) cc_final: 0.7898 (mt) REVERT: A 342 GLN cc_start: 0.7746 (mm-40) cc_final: 0.7464 (mm-40) REVERT: A 356 SER cc_start: 0.8771 (p) cc_final: 0.8436 (m) REVERT: A 368 ASP cc_start: 0.7536 (OUTLIER) cc_final: 0.7283 (t70) REVERT: A 429 ILE cc_start: 0.7109 (OUTLIER) cc_final: 0.6731 (tt) REVERT: B 319 TYR cc_start: 0.7854 (t80) cc_final: 0.7499 (t80) REVERT: B 324 MET cc_start: 0.8008 (tpp) cc_final: 0.7705 (tpt) REVERT: B 394 GLN cc_start: 0.7835 (OUTLIER) cc_final: 0.7615 (tm130) REVERT: B 418 LEU cc_start: 0.7620 (OUTLIER) cc_final: 0.7199 (mt) REVERT: B 519 ILE cc_start: 0.6694 (OUTLIER) cc_final: 0.6379 (pp) REVERT: B 520 ILE cc_start: 0.7511 (OUTLIER) cc_final: 0.7216 (mm) REVERT: C 44 LYS cc_start: 0.3295 (OUTLIER) cc_final: 0.2990 (mtmt) REVERT: C 47 ARG cc_start: 0.5109 (OUTLIER) cc_final: 0.4660 (ptt180) REVERT: C 55 HIS cc_start: 0.7461 (OUTLIER) cc_final: 0.7136 (m170) REVERT: C 151 ARG cc_start: 0.7491 (tpp80) cc_final: 0.7030 (mmt90) REVERT: C 188 TRP cc_start: 0.8076 (m100) cc_final: 0.7737 (m100) REVERT: C 322 LEU cc_start: 0.8264 (OUTLIER) cc_final: 0.7945 (mt) REVERT: C 342 GLN cc_start: 0.7856 (mm-40) cc_final: 0.7637 (mm-40) REVERT: C 368 ASP cc_start: 0.7406 (OUTLIER) cc_final: 0.6975 (p0) REVERT: C 387 GLU cc_start: 0.7345 (OUTLIER) cc_final: 0.7129 (mp0) REVERT: C 392 TYR cc_start: 0.7968 (m-80) cc_final: 0.7707 (m-80) REVERT: C 429 ILE cc_start: 0.7111 (OUTLIER) cc_final: 0.6756 (tt) REVERT: C 448 ARG cc_start: 0.7319 (ptp-110) cc_final: 0.7068 (ptp90) REVERT: D 167 VAL cc_start: 0.8407 (p) cc_final: 0.8195 (m) REVERT: D 280 MET cc_start: 0.8336 (OUTLIER) cc_final: 0.8062 (mmm) REVERT: D 319 TYR cc_start: 0.7779 (t80) cc_final: 0.7447 (t80) REVERT: D 324 MET cc_start: 0.7990 (tpp) cc_final: 0.7710 (tpt) REVERT: D 336 PHE cc_start: 0.5908 (OUTLIER) cc_final: 0.5209 (t80) REVERT: D 338 MET cc_start: 0.6954 (tpp) cc_final: 0.6639 (ttm) REVERT: D 359 ARG cc_start: 0.6590 (ttm110) cc_final: 0.6229 (ttm110) REVERT: D 520 ILE cc_start: 0.7672 (OUTLIER) cc_final: 0.7386 (mm) outliers start: 260 outliers final: 89 residues processed: 504 average time/residue: 1.0891 time to fit residues: 612.6892 Evaluate side-chains 328 residues out of total 1636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 218 time to evaluate : 1.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LYS Chi-restraints excluded: chain A residue 46 ARG Chi-restraints excluded: chain A residue 47 ARG Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 55 HIS Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 191 CYS Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 283 TYR Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 379 ASP Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 423 ASP Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 458 ARG Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain B residue 394 GLN Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 420 SER Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain C residue 44 LYS Chi-restraints excluded: chain C residue 46 ARG Chi-restraints excluded: chain C residue 47 ARG Chi-restraints excluded: chain C residue 55 HIS Chi-restraints excluded: chain C residue 56 LYS Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 63 PHE Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 70 TYR Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 191 CYS Chi-restraints excluded: chain C residue 204 CYS Chi-restraints excluded: chain C residue 217 SER Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 263 ASN Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 305 THR Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 335 ARG Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain C residue 337 ASP Chi-restraints excluded: chain C residue 338 SER Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain C residue 379 ASP Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 387 GLU Chi-restraints excluded: chain C residue 407 THR Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 423 ASP Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 474 ILE Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 74 SER Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 280 MET Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 336 PHE Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 390 SER Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 460 SER Chi-restraints excluded: chain D residue 520 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 153 optimal weight: 0.7980 chunk 137 optimal weight: 0.9980 chunk 76 optimal weight: 6.9990 chunk 47 optimal weight: 0.7980 chunk 93 optimal weight: 0.7980 chunk 73 optimal weight: 4.9990 chunk 142 optimal weight: 0.7980 chunk 55 optimal weight: 0.4980 chunk 86 optimal weight: 6.9990 chunk 106 optimal weight: 0.5980 chunk 165 optimal weight: 5.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 ASN A 218 ASN A 294 HIS A 323 GLN A 342 GLN A 378 ASN A 461 GLN A 487 ASN B 219 HIS B 299 ASN B 330 HIS B 436 GLN B 495 GLN B 501 HIS B 502 HIS B 522 ASN C 97 ASN C 218 ASN C 323 GLN C 342 GLN C 378 ASN C 461 GLN C 487 ASN D 219 HIS D 299 ASN D 330 HIS D 436 GLN D 501 HIS D 502 HIS D 509 GLN D 522 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15566 Z= 0.170 Angle : 0.582 9.100 21086 Z= 0.304 Chirality : 0.042 0.173 2370 Planarity : 0.004 0.041 2622 Dihedral : 13.069 109.165 2360 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 8.86 % Allowed : 27.81 % Favored : 63.33 % 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: -2.52 (0.19), residues: 1836 helix: -1.34 (0.15), residues: 1038 sheet: -1.43 (0.46), residues: 104 loop : -2.02 (0.23), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 60 HIS 0.007 0.001 HIS D 365 PHE 0.018 0.001 PHE B 486 TYR 0.021 0.001 TYR A 334 ARG 0.005 0.000 ARG C 300 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 1636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 248 time to evaluate : 1.711 Fit side-chains revert: symmetry clash REVERT: A 46 ARG cc_start: 0.6391 (OUTLIER) cc_final: 0.5717 (mmt-90) REVERT: A 47 ARG cc_start: 0.4923 (OUTLIER) cc_final: 0.4436 (ptt90) REVERT: A 55 HIS cc_start: 0.7465 (OUTLIER) cc_final: 0.7042 (m170) REVERT: A 155 GLN cc_start: 0.6024 (mm-40) cc_final: 0.5798 (tp40) REVERT: A 168 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8248 (mp) REVERT: A 343 GLN cc_start: 0.6428 (OUTLIER) cc_final: 0.5569 (tp40) REVERT: A 465 MET cc_start: 0.8008 (OUTLIER) cc_final: 0.7538 (tpt) REVERT: B 142 LEU cc_start: 0.8556 (tt) cc_final: 0.8320 (tt) REVERT: B 143 ASP cc_start: 0.7377 (OUTLIER) cc_final: 0.6981 (m-30) REVERT: B 319 TYR cc_start: 0.7839 (t80) cc_final: 0.7562 (t80) REVERT: B 394 GLN cc_start: 0.7654 (OUTLIER) cc_final: 0.7118 (tm-30) REVERT: B 418 LEU cc_start: 0.7593 (OUTLIER) cc_final: 0.7271 (mt) REVERT: C 47 ARG cc_start: 0.4839 (OUTLIER) cc_final: 0.4570 (ptt90) REVERT: C 55 HIS cc_start: 0.7582 (OUTLIER) cc_final: 0.7329 (m170) REVERT: C 151 ARG cc_start: 0.7296 (tpp80) cc_final: 0.6867 (mmt90) REVERT: C 188 TRP cc_start: 0.8103 (m100) cc_final: 0.7708 (m100) REVERT: C 343 GLN cc_start: 0.6545 (OUTLIER) cc_final: 0.5896 (tp40) REVERT: C 465 MET cc_start: 0.7959 (OUTLIER) cc_final: 0.7532 (tpt) REVERT: D 155 LEU cc_start: 0.8260 (OUTLIER) cc_final: 0.8025 (mt) REVERT: D 319 TYR cc_start: 0.7779 (t80) cc_final: 0.7537 (t80) REVERT: D 394 GLN cc_start: 0.7684 (OUTLIER) cc_final: 0.7332 (tm-30) REVERT: D 418 LEU cc_start: 0.7604 (OUTLIER) cc_final: 0.7337 (mt) REVERT: D 519 ILE cc_start: 0.6857 (OUTLIER) cc_final: 0.6310 (pp) outliers start: 145 outliers final: 41 residues processed: 362 average time/residue: 1.0713 time to fit residues: 432.5582 Evaluate side-chains 268 residues out of total 1636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 210 time to evaluate : 1.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ARG Chi-restraints excluded: chain A residue 47 ARG Chi-restraints excluded: chain A residue 55 HIS Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 204 CYS Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 263 ASN Chi-restraints excluded: chain A residue 343 GLN Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 383 GLN Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 143 ASP Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 382 GLN Chi-restraints excluded: chain B residue 394 GLN Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 432 GLU Chi-restraints excluded: chain C residue 46 ARG Chi-restraints excluded: chain C residue 47 ARG Chi-restraints excluded: chain C residue 55 HIS Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 204 CYS Chi-restraints excluded: chain C residue 217 SER Chi-restraints excluded: chain C residue 263 ASN Chi-restraints excluded: chain C residue 337 ASP Chi-restraints excluded: chain C residue 343 GLN Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 383 GLN Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 465 MET Chi-restraints excluded: chain C residue 474 ILE Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 155 LEU Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 382 GLN Chi-restraints excluded: chain D residue 394 GLN Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 519 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 91 optimal weight: 20.0000 chunk 51 optimal weight: 0.0870 chunk 137 optimal weight: 0.0980 chunk 112 optimal weight: 2.9990 chunk 45 optimal weight: 8.9990 chunk 165 optimal weight: 4.9990 chunk 178 optimal weight: 0.9990 chunk 147 optimal weight: 4.9990 chunk 164 optimal weight: 0.9980 chunk 56 optimal weight: 3.9990 chunk 132 optimal weight: 5.9990 overall best weight: 1.0362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 219 HIS B 352 ASN B 522 ASN D 219 HIS D 352 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.2627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15566 Z= 0.177 Angle : 0.543 8.867 21086 Z= 0.282 Chirality : 0.041 0.139 2370 Planarity : 0.004 0.041 2622 Dihedral : 10.804 91.038 2232 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.68 % Favored : 95.26 % Rotamer: Outliers : 7.40 % Allowed : 31.05 % Favored : 61.55 % 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: -1.68 (0.19), residues: 1836 helix: -0.66 (0.16), residues: 1064 sheet: -0.39 (0.49), residues: 88 loop : -1.80 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 237 HIS 0.007 0.001 HIS D 365 PHE 0.017 0.001 PHE B 110 TYR 0.020 0.001 TYR D 405 ARG 0.004 0.000 ARG C 374 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 1636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 234 time to evaluate : 1.727 Fit side-chains REVERT: A 47 ARG cc_start: 0.5000 (OUTLIER) cc_final: 0.4376 (ptt90) REVERT: A 55 HIS cc_start: 0.7232 (OUTLIER) cc_final: 0.6875 (m170) REVERT: A 106 MET cc_start: 0.7076 (tmm) cc_final: 0.6824 (tmm) REVERT: A 168 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.8062 (mp) REVERT: A 335 ARG cc_start: 0.6765 (OUTLIER) cc_final: 0.6536 (tpp80) REVERT: A 343 GLN cc_start: 0.6569 (OUTLIER) cc_final: 0.5689 (tp40) REVERT: A 465 MET cc_start: 0.7938 (OUTLIER) cc_final: 0.7679 (tpt) REVERT: B 142 LEU cc_start: 0.8580 (tt) cc_final: 0.8339 (tt) REVERT: B 197 ASN cc_start: 0.8327 (OUTLIER) cc_final: 0.8074 (p0) REVERT: B 319 TYR cc_start: 0.7920 (t80) cc_final: 0.7699 (t80) REVERT: B 394 GLN cc_start: 0.7704 (OUTLIER) cc_final: 0.7139 (tm-30) REVERT: B 418 LEU cc_start: 0.7672 (OUTLIER) cc_final: 0.7410 (mt) REVERT: B 519 ILE cc_start: 0.6921 (OUTLIER) cc_final: 0.6325 (pp) REVERT: C 47 ARG cc_start: 0.5106 (OUTLIER) cc_final: 0.4561 (ptt90) REVERT: C 55 HIS cc_start: 0.7650 (OUTLIER) cc_final: 0.7387 (m170) REVERT: C 151 ARG cc_start: 0.7284 (tpp80) cc_final: 0.6866 (mmt90) REVERT: C 155 GLN cc_start: 0.5932 (mm-40) cc_final: 0.5678 (tp40) REVERT: C 188 TRP cc_start: 0.8037 (m100) cc_final: 0.7674 (m100) REVERT: C 337 ASP cc_start: 0.6136 (OUTLIER) cc_final: 0.5932 (p0) REVERT: C 343 GLN cc_start: 0.6490 (OUTLIER) cc_final: 0.5639 (tp40) REVERT: C 465 MET cc_start: 0.7887 (OUTLIER) cc_final: 0.7576 (tpt) REVERT: D 197 ASN cc_start: 0.8358 (OUTLIER) cc_final: 0.8104 (p0) REVERT: D 319 TYR cc_start: 0.7860 (t80) cc_final: 0.7552 (t80) REVERT: D 394 GLN cc_start: 0.7667 (OUTLIER) cc_final: 0.7303 (tm-30) REVERT: D 418 LEU cc_start: 0.7695 (OUTLIER) cc_final: 0.7413 (mt) REVERT: D 519 ILE cc_start: 0.6941 (OUTLIER) cc_final: 0.6358 (pp) outliers start: 121 outliers final: 50 residues processed: 331 average time/residue: 1.1284 time to fit residues: 415.3010 Evaluate side-chains 287 residues out of total 1636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 218 time to evaluate : 1.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ARG Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 55 HIS Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 204 CYS Chi-restraints excluded: chain A residue 263 ASN Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 325 GLN Chi-restraints excluded: chain A residue 335 ARG Chi-restraints excluded: chain A residue 343 GLN Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 383 GLN Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 197 ASN Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 382 GLN Chi-restraints excluded: chain B residue 394 GLN Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 425 GLU Chi-restraints excluded: chain B residue 432 GLU Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain C residue 47 ARG Chi-restraints excluded: chain C residue 55 HIS Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 204 CYS Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 263 ASN Chi-restraints excluded: chain C residue 337 ASP Chi-restraints excluded: chain C residue 343 GLN Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 383 GLN Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 465 MET Chi-restraints excluded: chain C residue 474 ILE Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 197 ASN Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 336 PHE Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 382 GLN Chi-restraints excluded: chain D residue 394 GLN Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 425 GLU Chi-restraints excluded: chain D residue 431 MET Chi-restraints excluded: chain D residue 519 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 163 optimal weight: 10.0000 chunk 124 optimal weight: 10.0000 chunk 85 optimal weight: 10.0000 chunk 18 optimal weight: 5.9990 chunk 79 optimal weight: 0.9980 chunk 111 optimal weight: 0.9980 chunk 166 optimal weight: 0.6980 chunk 175 optimal weight: 4.9990 chunk 86 optimal weight: 4.9990 chunk 157 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 219 HIS B 484 GLN B 512 ASN C 466 ASN D 219 HIS D 484 GLN D 512 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 15566 Z= 0.243 Angle : 0.562 8.245 21086 Z= 0.295 Chirality : 0.043 0.149 2370 Planarity : 0.004 0.041 2622 Dihedral : 10.299 87.728 2216 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.74 % Favored : 95.21 % Rotamer: Outliers : 7.46 % Allowed : 32.15 % Favored : 60.39 % 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: -1.32 (0.20), residues: 1836 helix: -0.37 (0.16), residues: 1084 sheet: -0.44 (0.51), residues: 92 loop : -1.66 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 273 HIS 0.007 0.001 HIS B 365 PHE 0.021 0.002 PHE B 110 TYR 0.018 0.002 TYR A 283 ARG 0.003 0.000 ARG C 374 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 1636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 229 time to evaluate : 1.714 Fit side-chains revert: symmetry clash REVERT: A 47 ARG cc_start: 0.5073 (OUTLIER) cc_final: 0.4461 (ptt90) REVERT: A 55 HIS cc_start: 0.7285 (OUTLIER) cc_final: 0.6969 (m170) REVERT: A 106 MET cc_start: 0.7219 (tmm) cc_final: 0.6972 (tmm) REVERT: A 168 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8012 (mp) REVERT: A 335 ARG cc_start: 0.6864 (OUTLIER) cc_final: 0.6491 (tpp80) REVERT: A 465 MET cc_start: 0.7925 (OUTLIER) cc_final: 0.7479 (tpt) REVERT: A 471 LEU cc_start: 0.7405 (OUTLIER) cc_final: 0.6995 (mp) REVERT: B 142 LEU cc_start: 0.8611 (tt) cc_final: 0.8369 (tt) REVERT: B 143 ASP cc_start: 0.7405 (OUTLIER) cc_final: 0.6831 (m-30) REVERT: B 418 LEU cc_start: 0.7680 (OUTLIER) cc_final: 0.7408 (mt) REVERT: B 426 TYR cc_start: 0.8048 (m-80) cc_final: 0.7400 (m-80) REVERT: B 489 ARG cc_start: 0.7353 (ttp80) cc_final: 0.7137 (ttp-110) REVERT: B 519 ILE cc_start: 0.7005 (OUTLIER) cc_final: 0.6392 (pp) REVERT: C 47 ARG cc_start: 0.5034 (OUTLIER) cc_final: 0.4486 (ptt90) REVERT: C 55 HIS cc_start: 0.7703 (OUTLIER) cc_final: 0.7436 (m170) REVERT: C 188 TRP cc_start: 0.8027 (m100) cc_final: 0.7668 (m100) REVERT: C 343 GLN cc_start: 0.6403 (OUTLIER) cc_final: 0.5722 (tp40) REVERT: C 465 MET cc_start: 0.7897 (OUTLIER) cc_final: 0.7606 (tpt) REVERT: D 319 TYR cc_start: 0.7842 (t80) cc_final: 0.7622 (t80) REVERT: D 336 PHE cc_start: 0.4954 (OUTLIER) cc_final: 0.4642 (p90) REVERT: D 394 GLN cc_start: 0.7674 (OUTLIER) cc_final: 0.7169 (tm-30) REVERT: D 418 LEU cc_start: 0.7697 (OUTLIER) cc_final: 0.7380 (mt) REVERT: D 519 ILE cc_start: 0.6998 (OUTLIER) cc_final: 0.6387 (pp) outliers start: 122 outliers final: 50 residues processed: 326 average time/residue: 1.1349 time to fit residues: 411.6781 Evaluate side-chains 288 residues out of total 1636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 221 time to evaluate : 1.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ARG Chi-restraints excluded: chain A residue 55 HIS Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 204 CYS Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 263 ASN Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 335 ARG Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 383 GLN Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 143 ASP Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 324 MET Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 382 GLN Chi-restraints excluded: chain B residue 394 GLN Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 425 GLU Chi-restraints excluded: chain B residue 432 GLU Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 517 LYS Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain C residue 47 ARG Chi-restraints excluded: chain C residue 55 HIS Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 263 ASN Chi-restraints excluded: chain C residue 343 GLN Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 383 GLN Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 465 MET Chi-restraints excluded: chain C residue 474 ILE Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 336 PHE Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 382 GLN Chi-restraints excluded: chain D residue 394 GLN Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 425 GLU Chi-restraints excluded: chain D residue 431 MET Chi-restraints excluded: chain D residue 432 GLU Chi-restraints excluded: chain D residue 459 VAL Chi-restraints excluded: chain D residue 519 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 146 optimal weight: 6.9990 chunk 99 optimal weight: 5.9990 chunk 2 optimal weight: 0.2980 chunk 130 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 150 optimal weight: 0.6980 chunk 121 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 89 optimal weight: 6.9990 chunk 157 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 342 GLN B 219 HIS B 512 ASN D 219 HIS D 330 HIS D 512 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.3041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.075 15566 Z= 0.162 Angle : 0.512 8.174 21086 Z= 0.267 Chirality : 0.041 0.141 2370 Planarity : 0.004 0.041 2622 Dihedral : 9.371 86.992 2208 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.63 % Favored : 95.26 % Rotamer: Outliers : 6.66 % Allowed : 32.15 % Favored : 61.19 % 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: -0.97 (0.20), residues: 1836 helix: 0.01 (0.16), residues: 1064 sheet: -0.38 (0.50), residues: 92 loop : -1.64 (0.23), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 237 HIS 0.007 0.001 HIS D 365 PHE 0.014 0.001 PHE D 110 TYR 0.022 0.001 TYR D 405 ARG 0.003 0.000 ARG C 190 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 232 time to evaluate : 1.652 Fit side-chains REVERT: A 47 ARG cc_start: 0.4911 (OUTLIER) cc_final: 0.4417 (ptt90) REVERT: A 55 HIS cc_start: 0.7289 (OUTLIER) cc_final: 0.6901 (m170) REVERT: A 106 MET cc_start: 0.7219 (tmm) cc_final: 0.6956 (tmm) REVERT: A 182 ARG cc_start: 0.6902 (OUTLIER) cc_final: 0.6190 (mpp80) REVERT: A 343 GLN cc_start: 0.6459 (OUTLIER) cc_final: 0.5777 (tp40) REVERT: A 465 MET cc_start: 0.7861 (OUTLIER) cc_final: 0.7482 (tpt) REVERT: B 142 LEU cc_start: 0.8598 (tt) cc_final: 0.8370 (tt) REVERT: B 143 ASP cc_start: 0.7276 (OUTLIER) cc_final: 0.6775 (m-30) REVERT: B 197 ASN cc_start: 0.8278 (OUTLIER) cc_final: 0.8031 (p0) REVERT: B 394 GLN cc_start: 0.7633 (OUTLIER) cc_final: 0.7111 (tm-30) REVERT: B 418 LEU cc_start: 0.7597 (OUTLIER) cc_final: 0.7277 (mt) REVERT: B 426 TYR cc_start: 0.7964 (m-80) cc_final: 0.7533 (m-80) REVERT: B 519 ILE cc_start: 0.6976 (OUTLIER) cc_final: 0.6389 (pp) REVERT: C 47 ARG cc_start: 0.5078 (OUTLIER) cc_final: 0.4462 (ptt90) REVERT: C 55 HIS cc_start: 0.7556 (OUTLIER) cc_final: 0.7299 (m170) REVERT: C 188 TRP cc_start: 0.8026 (m100) cc_final: 0.7702 (m100) REVERT: C 343 GLN cc_start: 0.6280 (OUTLIER) cc_final: 0.5813 (tp40) REVERT: C 465 MET cc_start: 0.7794 (OUTLIER) cc_final: 0.7491 (tpt) REVERT: D 197 ASN cc_start: 0.8309 (OUTLIER) cc_final: 0.8061 (p0) REVERT: D 319 TYR cc_start: 0.7852 (t80) cc_final: 0.7602 (t80) REVERT: D 394 GLN cc_start: 0.7635 (OUTLIER) cc_final: 0.7323 (tm-30) REVERT: D 418 LEU cc_start: 0.7634 (OUTLIER) cc_final: 0.7311 (mt) REVERT: D 519 ILE cc_start: 0.6950 (OUTLIER) cc_final: 0.6370 (pp) outliers start: 109 outliers final: 50 residues processed: 315 average time/residue: 1.2172 time to fit residues: 424.9658 Evaluate side-chains 281 residues out of total 1636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 213 time to evaluate : 1.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ARG Chi-restraints excluded: chain A residue 55 HIS Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 182 ARG Chi-restraints excluded: chain A residue 204 CYS Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 263 ASN Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 343 GLN Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 383 GLN Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 143 ASP Chi-restraints excluded: chain B residue 197 ASN Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 324 MET Chi-restraints excluded: chain B residue 382 GLN Chi-restraints excluded: chain B residue 394 GLN Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 432 GLU Chi-restraints excluded: chain B residue 448 SER Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 517 LYS Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain C residue 47 ARG Chi-restraints excluded: chain C residue 55 HIS Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 263 ASN Chi-restraints excluded: chain C residue 343 GLN Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 383 GLN Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 465 MET Chi-restraints excluded: chain C residue 474 ILE Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 197 ASN Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 324 MET Chi-restraints excluded: chain D residue 345 ILE Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 394 GLN Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 420 SER Chi-restraints excluded: chain D residue 425 GLU Chi-restraints excluded: chain D residue 431 MET Chi-restraints excluded: chain D residue 432 GLU Chi-restraints excluded: chain D residue 459 VAL Chi-restraints excluded: chain D residue 519 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 59 optimal weight: 0.7980 chunk 158 optimal weight: 0.4980 chunk 34 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 chunk 43 optimal weight: 7.9990 chunk 176 optimal weight: 9.9990 chunk 146 optimal weight: 0.9980 chunk 81 optimal weight: 5.9990 chunk 14 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 92 optimal weight: 10.0000 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 466 ASN B 219 HIS B 512 ASN D 219 HIS D 330 HIS D 512 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 15566 Z= 0.261 Angle : 0.560 8.211 21086 Z= 0.293 Chirality : 0.043 0.156 2370 Planarity : 0.004 0.041 2622 Dihedral : 9.613 89.319 2201 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.68 % Favored : 95.21 % Rotamer: Outliers : 6.78 % Allowed : 32.52 % Favored : 60.70 % 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: -1.02 (0.20), residues: 1836 helix: -0.08 (0.16), residues: 1088 sheet: -0.31 (0.50), residues: 102 loop : -1.64 (0.24), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 273 HIS 0.007 0.001 HIS D 365 PHE 0.023 0.002 PHE D 110 TYR 0.016 0.002 TYR A 283 ARG 0.003 0.000 ARG D 189 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 221 time to evaluate : 1.640 Fit side-chains REVERT: A 47 ARG cc_start: 0.5014 (OUTLIER) cc_final: 0.4429 (ptt90) REVERT: A 55 HIS cc_start: 0.7322 (OUTLIER) cc_final: 0.6981 (m170) REVERT: A 106 MET cc_start: 0.7278 (tmm) cc_final: 0.7045 (tmm) REVERT: A 182 ARG cc_start: 0.6897 (OUTLIER) cc_final: 0.6194 (mpp80) REVERT: A 343 GLN cc_start: 0.6401 (OUTLIER) cc_final: 0.5587 (tp40) REVERT: A 465 MET cc_start: 0.7855 (OUTLIER) cc_final: 0.7651 (tpt) REVERT: B 143 ASP cc_start: 0.7393 (OUTLIER) cc_final: 0.6849 (m-30) REVERT: B 197 ASN cc_start: 0.8353 (OUTLIER) cc_final: 0.8067 (p0) REVERT: B 307 MET cc_start: 0.8411 (ptt) cc_final: 0.8141 (ptt) REVERT: B 418 LEU cc_start: 0.7646 (OUTLIER) cc_final: 0.7277 (mt) REVERT: B 426 TYR cc_start: 0.8047 (m-80) cc_final: 0.7551 (m-80) REVERT: B 519 ILE cc_start: 0.7031 (OUTLIER) cc_final: 0.6456 (pp) REVERT: C 47 ARG cc_start: 0.5099 (OUTLIER) cc_final: 0.4536 (ptt90) REVERT: C 55 HIS cc_start: 0.7572 (OUTLIER) cc_final: 0.7303 (m170) REVERT: C 188 TRP cc_start: 0.8046 (m100) cc_final: 0.7783 (m100) REVERT: C 343 GLN cc_start: 0.6291 (OUTLIER) cc_final: 0.5800 (tp40) REVERT: C 465 MET cc_start: 0.7816 (OUTLIER) cc_final: 0.7566 (tpt) REVERT: D 197 ASN cc_start: 0.8365 (OUTLIER) cc_final: 0.8078 (p0) REVERT: D 319 TYR cc_start: 0.7875 (t80) cc_final: 0.7659 (t80) REVERT: D 394 GLN cc_start: 0.7645 (OUTLIER) cc_final: 0.7156 (tm-30) REVERT: D 418 LEU cc_start: 0.7638 (OUTLIER) cc_final: 0.7253 (mt) REVERT: D 519 ILE cc_start: 0.7056 (OUTLIER) cc_final: 0.6420 (pp) outliers start: 111 outliers final: 57 residues processed: 310 average time/residue: 1.1414 time to fit residues: 392.3673 Evaluate side-chains 279 residues out of total 1636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 205 time to evaluate : 1.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ARG Chi-restraints excluded: chain A residue 55 HIS Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 182 ARG Chi-restraints excluded: chain A residue 204 CYS Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 263 ASN Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 343 GLN Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 383 GLN Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain B residue 100 SER Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 143 ASP Chi-restraints excluded: chain B residue 197 ASN Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 382 GLN Chi-restraints excluded: chain B residue 394 GLN Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 425 GLU Chi-restraints excluded: chain B residue 432 GLU Chi-restraints excluded: chain B residue 448 SER Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 517 LYS Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain C residue 47 ARG Chi-restraints excluded: chain C residue 55 HIS Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 263 ASN Chi-restraints excluded: chain C residue 343 GLN Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 383 GLN Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 407 THR Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 442 ILE Chi-restraints excluded: chain C residue 465 MET Chi-restraints excluded: chain C residue 474 ILE Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 197 ASN Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 345 ILE Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 394 GLN Chi-restraints excluded: chain D residue 405 TYR Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 425 GLU Chi-restraints excluded: chain D residue 431 MET Chi-restraints excluded: chain D residue 432 GLU Chi-restraints excluded: chain D residue 448 SER Chi-restraints excluded: chain D residue 459 VAL Chi-restraints excluded: chain D residue 519 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 169 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 100 optimal weight: 0.0870 chunk 128 optimal weight: 7.9990 chunk 99 optimal weight: 2.9990 chunk 148 optimal weight: 0.0060 chunk 98 optimal weight: 7.9990 chunk 175 optimal weight: 0.0040 chunk 109 optimal weight: 0.8980 chunk 106 optimal weight: 0.7980 chunk 80 optimal weight: 0.8980 overall best weight: 0.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 290 ASN B 219 HIS B 512 ASN D 219 HIS D 330 HIS D 495 GLN D 512 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.3458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.076 15566 Z= 0.132 Angle : 0.497 8.707 21086 Z= 0.255 Chirality : 0.040 0.140 2370 Planarity : 0.004 0.043 2622 Dihedral : 8.782 87.624 2200 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.03 % Favored : 95.86 % Rotamer: Outliers : 5.32 % Allowed : 34.05 % Favored : 60.64 % 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: -0.66 (0.20), residues: 1836 helix: 0.36 (0.16), residues: 1070 sheet: -1.04 (0.48), residues: 106 loop : -1.59 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 237 HIS 0.006 0.001 HIS B 365 PHE 0.015 0.001 PHE C 361 TYR 0.024 0.001 TYR B 405 ARG 0.004 0.000 ARG B 189 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 239 time to evaluate : 1.776 Fit side-chains revert: symmetry clash REVERT: A 47 ARG cc_start: 0.5034 (OUTLIER) cc_final: 0.4458 (ptt90) REVERT: A 55 HIS cc_start: 0.7330 (OUTLIER) cc_final: 0.6979 (m170) REVERT: A 106 MET cc_start: 0.7216 (tmm) cc_final: 0.6977 (tmm) REVERT: A 162 MET cc_start: 0.8879 (tpt) cc_final: 0.8368 (mmm) REVERT: A 182 ARG cc_start: 0.6888 (OUTLIER) cc_final: 0.6264 (mpp80) REVERT: A 343 GLN cc_start: 0.6714 (OUTLIER) cc_final: 0.6066 (tp40) REVERT: A 465 MET cc_start: 0.7740 (OUTLIER) cc_final: 0.7417 (tpt) REVERT: B 142 LEU cc_start: 0.8581 (tt) cc_final: 0.8367 (tt) REVERT: B 394 GLN cc_start: 0.7568 (OUTLIER) cc_final: 0.7035 (tm-30) REVERT: B 418 LEU cc_start: 0.7699 (OUTLIER) cc_final: 0.7394 (mt) REVERT: B 421 GLN cc_start: 0.7786 (mp10) cc_final: 0.7555 (mp10) REVERT: B 426 TYR cc_start: 0.7940 (m-80) cc_final: 0.7561 (m-80) REVERT: B 519 ILE cc_start: 0.6940 (OUTLIER) cc_final: 0.6397 (pt) REVERT: C 47 ARG cc_start: 0.5045 (OUTLIER) cc_final: 0.4511 (ptt90) REVERT: C 55 HIS cc_start: 0.7343 (OUTLIER) cc_final: 0.7017 (m170) REVERT: C 162 MET cc_start: 0.8765 (tpt) cc_final: 0.8269 (mmm) REVERT: C 182 ARG cc_start: 0.6933 (OUTLIER) cc_final: 0.6330 (mpp80) REVERT: C 188 TRP cc_start: 0.8016 (m100) cc_final: 0.7740 (m100) REVERT: C 343 GLN cc_start: 0.6152 (OUTLIER) cc_final: 0.5666 (tp40) REVERT: D 319 TYR cc_start: 0.7847 (t80) cc_final: 0.7584 (t80) REVERT: D 394 GLN cc_start: 0.7578 (OUTLIER) cc_final: 0.7362 (tm-30) REVERT: D 418 LEU cc_start: 0.7714 (OUTLIER) cc_final: 0.7414 (mt) REVERT: D 519 ILE cc_start: 0.6900 (OUTLIER) cc_final: 0.6364 (pp) outliers start: 87 outliers final: 33 residues processed: 309 average time/residue: 1.2039 time to fit residues: 411.3585 Evaluate side-chains 263 residues out of total 1636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 215 time to evaluate : 1.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ARG Chi-restraints excluded: chain A residue 55 HIS Chi-restraints excluded: chain A residue 182 ARG Chi-restraints excluded: chain A residue 343 GLN Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 383 GLN Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 324 MET Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 394 GLN Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 425 GLU Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain C residue 47 ARG Chi-restraints excluded: chain C residue 55 HIS Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 182 ARG Chi-restraints excluded: chain C residue 263 ASN Chi-restraints excluded: chain C residue 343 GLN Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 407 THR Chi-restraints excluded: chain C residue 474 ILE Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 324 MET Chi-restraints excluded: chain D residue 345 ILE Chi-restraints excluded: chain D residue 394 GLN Chi-restraints excluded: chain D residue 405 TYR Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 425 GLU Chi-restraints excluded: chain D residue 459 VAL Chi-restraints excluded: chain D residue 519 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 108 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 104 optimal weight: 8.9990 chunk 52 optimal weight: 7.9990 chunk 34 optimal weight: 8.9990 chunk 33 optimal weight: 5.9990 chunk 111 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 86 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 137 optimal weight: 3.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 HIS B 330 HIS B 495 GLN B 512 ASN D 81 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.3287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 15566 Z= 0.291 Angle : 0.587 8.461 21086 Z= 0.303 Chirality : 0.044 0.169 2370 Planarity : 0.004 0.044 2622 Dihedral : 9.415 89.342 2197 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.30 % Favored : 95.59 % Rotamer: Outliers : 5.38 % Allowed : 34.17 % Favored : 60.45 % 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: -0.75 (0.20), residues: 1836 helix: 0.23 (0.16), residues: 1054 sheet: -0.93 (0.50), residues: 106 loop : -1.50 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 273 HIS 0.007 0.001 HIS D 365 PHE 0.023 0.002 PHE B 110 TYR 0.018 0.002 TYR A 283 ARG 0.005 0.000 ARG B 489 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 213 time to evaluate : 1.673 Fit side-chains revert: symmetry clash REVERT: A 47 ARG cc_start: 0.5071 (OUTLIER) cc_final: 0.4441 (ptt90) REVERT: A 55 HIS cc_start: 0.7328 (OUTLIER) cc_final: 0.7010 (m170) REVERT: A 106 MET cc_start: 0.7249 (tmm) cc_final: 0.7020 (tmm) REVERT: A 182 ARG cc_start: 0.6909 (OUTLIER) cc_final: 0.6212 (mpp80) REVERT: A 465 MET cc_start: 0.7813 (OUTLIER) cc_final: 0.7547 (tpt) REVERT: B 142 LEU cc_start: 0.8588 (tt) cc_final: 0.8357 (tt) REVERT: B 197 ASN cc_start: 0.8287 (OUTLIER) cc_final: 0.8017 (p0) REVERT: B 418 LEU cc_start: 0.7703 (OUTLIER) cc_final: 0.7321 (mt) REVERT: B 519 ILE cc_start: 0.7045 (OUTLIER) cc_final: 0.6470 (pp) REVERT: C 47 ARG cc_start: 0.5155 (OUTLIER) cc_final: 0.4554 (ptt90) REVERT: C 55 HIS cc_start: 0.7474 (OUTLIER) cc_final: 0.7190 (m170) REVERT: C 106 MET cc_start: 0.6926 (ttp) cc_final: 0.6704 (tmm) REVERT: C 188 TRP cc_start: 0.8010 (m100) cc_final: 0.7736 (m100) REVERT: C 343 GLN cc_start: 0.6183 (OUTLIER) cc_final: 0.5916 (tp-100) REVERT: C 441 GLU cc_start: 0.6460 (OUTLIER) cc_final: 0.6036 (pt0) REVERT: D 197 ASN cc_start: 0.8313 (OUTLIER) cc_final: 0.8045 (p0) REVERT: D 319 TYR cc_start: 0.7912 (t80) cc_final: 0.7668 (t80) REVERT: D 366 MET cc_start: 0.6963 (tmm) cc_final: 0.6743 (ttp) REVERT: D 394 GLN cc_start: 0.7657 (OUTLIER) cc_final: 0.7313 (tm-30) REVERT: D 418 LEU cc_start: 0.7710 (OUTLIER) cc_final: 0.7333 (mt) REVERT: D 432 GLU cc_start: 0.6905 (OUTLIER) cc_final: 0.6066 (pt0) REVERT: D 519 ILE cc_start: 0.7049 (OUTLIER) cc_final: 0.6441 (pp) outliers start: 88 outliers final: 41 residues processed: 285 average time/residue: 1.1892 time to fit residues: 375.3702 Evaluate side-chains 266 residues out of total 1636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 209 time to evaluate : 1.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ARG Chi-restraints excluded: chain A residue 55 HIS Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 182 ARG Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 383 GLN Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 197 ASN Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 394 GLN Chi-restraints excluded: chain B residue 405 TYR Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 425 GLU Chi-restraints excluded: chain B residue 448 SER Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain C residue 47 ARG Chi-restraints excluded: chain C residue 55 HIS Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 263 ASN Chi-restraints excluded: chain C residue 343 GLN Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 407 THR Chi-restraints excluded: chain C residue 441 GLU Chi-restraints excluded: chain C residue 442 ILE Chi-restraints excluded: chain C residue 474 ILE Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 197 ASN Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 345 ILE Chi-restraints excluded: chain D residue 394 GLN Chi-restraints excluded: chain D residue 405 TYR Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 425 GLU Chi-restraints excluded: chain D residue 432 GLU Chi-restraints excluded: chain D residue 448 SER Chi-restraints excluded: chain D residue 459 VAL Chi-restraints excluded: chain D residue 519 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 159 optimal weight: 0.9980 chunk 168 optimal weight: 4.9990 chunk 153 optimal weight: 0.9990 chunk 163 optimal weight: 9.9990 chunk 98 optimal weight: 0.0170 chunk 71 optimal weight: 0.7980 chunk 128 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 147 optimal weight: 0.0770 chunk 154 optimal weight: 0.0010 chunk 162 optimal weight: 5.9990 overall best weight: 0.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 219 HIS B 330 HIS B 495 GLN B 512 ASN D 219 HIS D 330 HIS D 512 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.3641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.077 15566 Z= 0.140 Angle : 0.524 9.414 21086 Z= 0.266 Chirality : 0.040 0.155 2370 Planarity : 0.004 0.049 2622 Dihedral : 8.643 87.600 2197 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.76 % Favored : 96.13 % Rotamer: Outliers : 3.73 % Allowed : 36.19 % Favored : 60.09 % 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 (0.20), residues: 1836 helix: 0.47 (0.16), residues: 1070 sheet: 0.01 (0.51), residues: 88 loop : -1.59 (0.23), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 188 HIS 0.007 0.001 HIS B 365 PHE 0.013 0.001 PHE A 187 TYR 0.019 0.001 TYR A 283 ARG 0.005 0.000 ARG C 431 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 222 time to evaluate : 1.879 Fit side-chains revert: symmetry clash REVERT: A 47 ARG cc_start: 0.5138 (OUTLIER) cc_final: 0.4510 (ptt90) REVERT: A 55 HIS cc_start: 0.7346 (OUTLIER) cc_final: 0.7031 (m170) REVERT: A 64 LEU cc_start: 0.7258 (OUTLIER) cc_final: 0.7008 (mt) REVERT: A 106 MET cc_start: 0.7189 (tmm) cc_final: 0.6949 (tmm) REVERT: A 162 MET cc_start: 0.8815 (tpt) cc_final: 0.8388 (mmm) REVERT: A 182 ARG cc_start: 0.6895 (OUTLIER) cc_final: 0.6273 (mpp80) REVERT: A 465 MET cc_start: 0.7744 (OUTLIER) cc_final: 0.7516 (tpp) REVERT: B 68 GLU cc_start: 0.6980 (mm-30) cc_final: 0.6334 (tp30) REVERT: B 142 LEU cc_start: 0.8577 (tt) cc_final: 0.8373 (tt) REVERT: B 394 GLN cc_start: 0.7573 (OUTLIER) cc_final: 0.7065 (tm-30) REVERT: B 418 LEU cc_start: 0.7702 (OUTLIER) cc_final: 0.7386 (mt) REVERT: B 421 GLN cc_start: 0.7728 (mp10) cc_final: 0.7516 (mp10) REVERT: B 426 TYR cc_start: 0.8021 (m-80) cc_final: 0.7739 (m-80) REVERT: B 461 GLU cc_start: 0.6010 (pp20) cc_final: 0.5731 (pp20) REVERT: B 489 ARG cc_start: 0.7232 (ttp80) cc_final: 0.7007 (ttp-110) REVERT: B 519 ILE cc_start: 0.6949 (OUTLIER) cc_final: 0.6410 (pt) REVERT: C 47 ARG cc_start: 0.5252 (OUTLIER) cc_final: 0.4685 (ptt90) REVERT: C 55 HIS cc_start: 0.7389 (OUTLIER) cc_final: 0.7074 (m170) REVERT: C 162 MET cc_start: 0.8760 (tpt) cc_final: 0.8316 (mmm) REVERT: C 182 ARG cc_start: 0.6896 (OUTLIER) cc_final: 0.6315 (mpp80) REVERT: C 188 TRP cc_start: 0.8003 (m100) cc_final: 0.7760 (m100) REVERT: C 343 GLN cc_start: 0.6122 (OUTLIER) cc_final: 0.5748 (tp-100) REVERT: D 319 TYR cc_start: 0.7851 (t80) cc_final: 0.7593 (t80) REVERT: D 394 GLN cc_start: 0.7580 (OUTLIER) cc_final: 0.7317 (tm-30) REVERT: D 418 LEU cc_start: 0.7724 (OUTLIER) cc_final: 0.7413 (mt) REVERT: D 489 ARG cc_start: 0.7164 (ttp80) cc_final: 0.6867 (ttp-110) REVERT: D 519 ILE cc_start: 0.6879 (OUTLIER) cc_final: 0.6341 (pp) outliers start: 61 outliers final: 32 residues processed: 272 average time/residue: 1.2045 time to fit residues: 363.0109 Evaluate side-chains 256 residues out of total 1636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 209 time to evaluate : 1.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ARG Chi-restraints excluded: chain A residue 55 HIS Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 182 ARG Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 383 GLN Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 324 MET Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 394 GLN Chi-restraints excluded: chain B residue 405 TYR Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain C residue 47 ARG Chi-restraints excluded: chain C residue 55 HIS Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 182 ARG Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 263 ASN Chi-restraints excluded: chain C residue 343 GLN Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 407 THR Chi-restraints excluded: chain C residue 474 ILE Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 324 MET Chi-restraints excluded: chain D residue 345 ILE Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 394 GLN Chi-restraints excluded: chain D residue 405 TYR Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 425 GLU Chi-restraints excluded: chain D residue 459 VAL Chi-restraints excluded: chain D residue 519 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 107 optimal weight: 1.9990 chunk 172 optimal weight: 4.9990 chunk 105 optimal weight: 10.0000 chunk 82 optimal weight: 2.9990 chunk 120 optimal weight: 5.9990 chunk 181 optimal weight: 8.9990 chunk 166 optimal weight: 0.9980 chunk 144 optimal weight: 0.0470 chunk 14 optimal weight: 5.9990 chunk 111 optimal weight: 0.6980 chunk 88 optimal weight: 0.9980 overall best weight: 0.9480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 219 HIS B 330 HIS B 512 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.3648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 15566 Z= 0.179 Angle : 0.543 8.791 21086 Z= 0.276 Chirality : 0.042 0.191 2370 Planarity : 0.004 0.051 2622 Dihedral : 8.416 87.994 2194 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.30 % Favored : 95.59 % Rotamer: Outliers : 3.30 % Allowed : 36.37 % Favored : 60.33 % 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: -0.40 (0.20), residues: 1836 helix: 0.46 (0.16), residues: 1078 sheet: 0.19 (0.53), residues: 88 loop : -1.47 (0.23), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 188 HIS 0.018 0.001 HIS B 330 PHE 0.026 0.001 PHE D 486 TYR 0.018 0.001 TYR A 283 ARG 0.006 0.000 ARG A 431 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 212 time to evaluate : 2.035 Fit side-chains revert: symmetry clash REVERT: A 47 ARG cc_start: 0.5144 (OUTLIER) cc_final: 0.4514 (ptt90) REVERT: A 55 HIS cc_start: 0.7355 (OUTLIER) cc_final: 0.7046 (m170) REVERT: A 106 MET cc_start: 0.7202 (tmm) cc_final: 0.6972 (tmm) REVERT: A 162 MET cc_start: 0.8825 (tpt) cc_final: 0.8383 (mmm) REVERT: A 182 ARG cc_start: 0.6894 (OUTLIER) cc_final: 0.6259 (mpp80) REVERT: A 465 MET cc_start: 0.7791 (OUTLIER) cc_final: 0.7503 (tpt) REVERT: B 68 GLU cc_start: 0.6899 (mm-30) cc_final: 0.6313 (tp30) REVERT: B 142 LEU cc_start: 0.8589 (tt) cc_final: 0.8361 (tt) REVERT: B 143 ASP cc_start: 0.7216 (OUTLIER) cc_final: 0.6738 (m-30) REVERT: B 237 TRP cc_start: 0.7858 (OUTLIER) cc_final: 0.7022 (t60) REVERT: B 418 LEU cc_start: 0.7709 (OUTLIER) cc_final: 0.7390 (mt) REVERT: B 421 GLN cc_start: 0.7800 (mp10) cc_final: 0.7552 (mp10) REVERT: B 426 TYR cc_start: 0.7988 (m-80) cc_final: 0.7742 (m-80) REVERT: B 519 ILE cc_start: 0.6990 (OUTLIER) cc_final: 0.6427 (pt) REVERT: C 47 ARG cc_start: 0.5342 (OUTLIER) cc_final: 0.4674 (mmp-170) REVERT: C 55 HIS cc_start: 0.7345 (OUTLIER) cc_final: 0.6980 (m170) REVERT: C 162 MET cc_start: 0.8845 (tpt) cc_final: 0.8393 (mmm) REVERT: C 182 ARG cc_start: 0.6865 (OUTLIER) cc_final: 0.6256 (mpp80) REVERT: C 343 GLN cc_start: 0.6108 (OUTLIER) cc_final: 0.5728 (tp-100) REVERT: D 319 TYR cc_start: 0.7875 (t80) cc_final: 0.7599 (t80) REVERT: D 394 GLN cc_start: 0.7601 (OUTLIER) cc_final: 0.7317 (tm-30) REVERT: D 418 LEU cc_start: 0.7698 (OUTLIER) cc_final: 0.7384 (mt) REVERT: D 489 ARG cc_start: 0.7213 (ttp80) cc_final: 0.6838 (ttp-170) REVERT: D 519 ILE cc_start: 0.6922 (OUTLIER) cc_final: 0.6391 (pt) outliers start: 54 outliers final: 32 residues processed: 257 average time/residue: 1.2630 time to fit residues: 359.9691 Evaluate side-chains 249 residues out of total 1636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 202 time to evaluate : 1.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ARG Chi-restraints excluded: chain A residue 55 HIS Chi-restraints excluded: chain A residue 182 ARG Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 383 GLN Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain B residue 143 ASP Chi-restraints excluded: chain B residue 237 TRP Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 324 MET Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 394 GLN Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain C residue 47 ARG Chi-restraints excluded: chain C residue 55 HIS Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 182 ARG Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 263 ASN Chi-restraints excluded: chain C residue 343 GLN Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 407 THR Chi-restraints excluded: chain C residue 474 ILE Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 324 MET Chi-restraints excluded: chain D residue 345 ILE Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 394 GLN Chi-restraints excluded: chain D residue 405 TYR Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 459 VAL Chi-restraints excluded: chain D residue 519 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 114 optimal weight: 0.6980 chunk 153 optimal weight: 0.8980 chunk 44 optimal weight: 0.3980 chunk 133 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 144 optimal weight: 0.4980 chunk 60 optimal weight: 2.9990 chunk 148 optimal weight: 9.9990 chunk 18 optimal weight: 0.7980 chunk 26 optimal weight: 7.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 342 GLN B 330 HIS B 484 GLN B 512 ASN D 219 HIS D 417 GLN D 512 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.212134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.149160 restraints weight = 16415.376| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 2.21 r_work: 0.3438 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3315 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.3732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.077 15566 Z= 0.155 Angle : 0.532 8.725 21086 Z= 0.269 Chirality : 0.041 0.212 2370 Planarity : 0.004 0.051 2622 Dihedral : 8.150 88.047 2194 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.98 % Favored : 95.92 % Rotamer: Outliers : 3.36 % Allowed : 36.67 % Favored : 59.96 % 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: -0.27 (0.20), residues: 1836 helix: 0.58 (0.16), residues: 1072 sheet: 0.19 (0.53), residues: 88 loop : -1.41 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 188 HIS 0.012 0.001 HIS B 330 PHE 0.017 0.001 PHE A 187 TYR 0.027 0.001 TYR B 405 ARG 0.006 0.000 ARG B 489 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6760.65 seconds wall clock time: 120 minutes 5.73 seconds (7205.73 seconds total)