Starting phenix.real_space_refine (version: dev) on Sun Feb 26 08:42:15 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v4j_21041/02_2023/6v4j_21041_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v4j_21041/02_2023/6v4j_21041.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v4j_21041/02_2023/6v4j_21041.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v4j_21041/02_2023/6v4j_21041.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v4j_21041/02_2023/6v4j_21041_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v4j_21041/02_2023/6v4j_21041_neut.pdb" } resolution = 2.97 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.001 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 7018 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "A PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 275": "OE1" <-> "OE2" Residue "B PHE 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 444": "OE1" <-> "OE2" Residue "B PHE 472": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 76": "OD1" <-> "OD2" Residue "E PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 283": "OD1" <-> "OD2" Residue "E GLU 293": "OE1" <-> "OE2" Residue "F ASP 76": "OD1" <-> "OD2" Residue "F PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 307": "OE1" <-> "OE2" Residue "F TYR 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 76": "OD1" <-> "OD2" Residue "G PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 76": "OD1" <-> "OD2" Residue "H PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 308": "OD1" <-> "OD2" Residue "H ARG 332": "NH1" <-> "NH2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 20637 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3450 Classifications: {'peptide': 447} Link IDs: {'PTRANS': 17, 'TRANS': 429} Chain breaks: 5 Chain: "B" Number of atoms: 3354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3354 Classifications: {'peptide': 434} Link IDs: {'PTRANS': 16, 'TRANS': 417} Chain breaks: 6 Chain: "C" Number of atoms: 3414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3414 Classifications: {'peptide': 442} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 17, 'TRANS': 424} Chain breaks: 5 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 3390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3390 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 17, 'TRANS': 420} Chain breaks: 5 Chain: "E" Number of atoms: 1748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1748 Classifications: {'peptide': 234} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 227} Chain breaks: 2 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "F" Number of atoms: 1767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1767 Classifications: {'peptide': 234} Link IDs: {'PTRANS': 5, 'TRANS': 228} Chain breaks: 2 Chain: "G" Number of atoms: 1753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1753 Classifications: {'peptide': 234} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 228} Chain breaks: 2 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "H" Number of atoms: 1761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1761 Classifications: {'peptide': 234} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 228} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 11.63, per 1000 atoms: 0.56 Number of scatterers: 20637 At special positions: 0 Unit cell: (120.474, 177.606, 109.296, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 105 16.00 O 3660 8.00 N 3346 7.00 C 13526 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 251 " - pdb=" SG CYS A 348 " distance=2.05 Simple disulfide: pdb=" SG CYS B 251 " - pdb=" SG CYS B 348 " distance=2.03 Simple disulfide: pdb=" SG CYS C 251 " - pdb=" SG CYS C 348 " distance=1.59 Simple disulfide: pdb=" SG CYS D 251 " - pdb=" SG CYS D 348 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.51 Conformation dependent library (CDL) restraints added in 3.0 seconds 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4974 Finding SS restraints... Secondary structure from input PDB file: 139 helices and 8 sheets defined 62.8% alpha, 4.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.14 Creating SS restraints... Processing helix chain 'A' and resid 2 through 20 removed outlier: 3.772A pdb=" N ILE A 6 " --> pdb=" O GLN A 2 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ARG A 8 " --> pdb=" O ARG A 4 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ILE A 9 " --> pdb=" O SER A 5 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N THR A 20 " --> pdb=" O LEU A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 22 No H-bonds generated for 'chain 'A' and resid 21 through 22' Processing helix chain 'A' and resid 23 through 27 removed outlier: 3.727A pdb=" N LEU A 26 " --> pdb=" O ALA A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 48 removed outlier: 3.781A pdb=" N LEU A 46 " --> pdb=" O THR A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 76 Processing helix chain 'A' and resid 77 through 79 No H-bonds generated for 'chain 'A' and resid 77 through 79' Processing helix chain 'A' and resid 85 through 89 removed outlier: 3.739A pdb=" N LEU A 89 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 109 Processing helix chain 'A' and resid 124 through 149 removed outlier: 3.731A pdb=" N MET A 140 " --> pdb=" O TRP A 136 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU A 145 " --> pdb=" O GLY A 141 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA A 146 " --> pdb=" O ILE A 142 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N VAL A 147 " --> pdb=" O ILE A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 202 removed outlier: 4.517A pdb=" N ALA A 184 " --> pdb=" O GLU A 180 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N TRP A 186 " --> pdb=" O ALA A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 217 Processing helix chain 'A' and resid 235 through 252 removed outlier: 3.968A pdb=" N CYS A 251 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ASN A 252 " --> pdb=" O ILE A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 261 removed outlier: 4.114A pdb=" N ALA A 258 " --> pdb=" O LEU A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 271 Processing helix chain 'A' and resid 273 through 298 removed outlier: 4.063A pdb=" N ARG A 277 " --> pdb=" O ASP A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 319 Processing helix chain 'A' and resid 333 through 345 removed outlier: 4.560A pdb=" N VAL A 337 " --> pdb=" O LEU A 333 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE A 345 " --> pdb=" O PHE A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 377 Processing helix chain 'A' and resid 392 through 420 removed outlier: 4.133A pdb=" N VAL A 396 " --> pdb=" O PRO A 392 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASP A 397 " --> pdb=" O GLN A 393 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA A 398 " --> pdb=" O ARG A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 435 Processing helix chain 'A' and resid 442 through 446 removed outlier: 4.107A pdb=" N ALA A 446 " --> pdb=" O GLY A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 469 Processing helix chain 'A' and resid 471 through 479 removed outlier: 4.152A pdb=" N LEU A 475 " --> pdb=" O ILE A 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 20 removed outlier: 3.594A pdb=" N ILE B 6 " --> pdb=" O GLN B 2 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N THR B 20 " --> pdb=" O LEU B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 22 No H-bonds generated for 'chain 'B' and resid 21 through 22' Processing helix chain 'B' and resid 23 through 27 removed outlier: 3.575A pdb=" N LEU B 26 " --> pdb=" O ALA B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 55 Processing helix chain 'B' and resid 69 through 77 Processing helix chain 'B' and resid 78 through 82 removed outlier: 4.099A pdb=" N GLY B 81 " --> pdb=" O THR B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 89 removed outlier: 3.688A pdb=" N LEU B 89 " --> pdb=" O LEU B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 110 Processing helix chain 'B' and resid 124 through 149 removed outlier: 3.652A pdb=" N ILE B 142 " --> pdb=" O GLY B 138 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ILE B 143 " --> pdb=" O GLY B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 203 removed outlier: 4.495A pdb=" N ALA B 184 " --> pdb=" O GLU B 180 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ALA B 203 " --> pdb=" O ALA B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 217 Processing helix chain 'B' and resid 235 through 251 removed outlier: 3.598A pdb=" N ALA B 250 " --> pdb=" O LEU B 246 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N CYS B 251 " --> pdb=" O LEU B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 261 removed outlier: 4.083A pdb=" N ALA B 258 " --> pdb=" O LEU B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 298 Processing helix chain 'B' and resid 302 through 319 removed outlier: 3.520A pdb=" N ALA B 306 " --> pdb=" O SER B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 345 removed outlier: 3.731A pdb=" N ILE B 345 " --> pdb=" O PHE B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 377 Processing helix chain 'B' and resid 392 through 420 removed outlier: 4.105A pdb=" N VAL B 396 " --> pdb=" O PRO B 392 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ASP B 397 " --> pdb=" O GLN B 393 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ALA B 398 " --> pdb=" O ARG B 394 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL B 399 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N TRP B 400 " --> pdb=" O VAL B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 437 Processing helix chain 'B' and resid 453 through 469 Processing helix chain 'B' and resid 471 through 479 removed outlier: 3.651A pdb=" N LEU B 475 " --> pdb=" O ILE B 471 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N LEU B 477 " --> pdb=" O THR B 473 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU B 478 " --> pdb=" O LEU B 474 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 20 removed outlier: 3.738A pdb=" N ILE C 6 " --> pdb=" O GLN C 2 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ARG C 8 " --> pdb=" O ARG C 4 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ILE C 9 " --> pdb=" O SER C 5 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N THR C 20 " --> pdb=" O LEU C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 27 removed outlier: 3.722A pdb=" N LEU C 26 " --> pdb=" O ALA C 23 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 53 Processing helix chain 'C' and resid 69 through 80 removed outlier: 3.818A pdb=" N LEU C 80 " --> pdb=" O PHE C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 89 removed outlier: 3.720A pdb=" N LEU C 89 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 111 removed outlier: 3.896A pdb=" N THR C 111 " --> pdb=" O SER C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 145 removed outlier: 3.732A pdb=" N ILE C 143 " --> pdb=" O GLY C 139 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU C 145 " --> pdb=" O GLY C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 203 removed outlier: 4.409A pdb=" N ALA C 184 " --> pdb=" O GLU C 180 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N TRP C 186 " --> pdb=" O ALA C 182 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE C 188 " --> pdb=" O ALA C 184 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ALA C 203 " --> pdb=" O ALA C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 217 Processing helix chain 'C' and resid 235 through 251 removed outlier: 4.070A pdb=" N CYS C 251 " --> pdb=" O LEU C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 258 removed outlier: 4.147A pdb=" N ALA C 258 " --> pdb=" O LEU C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 267 No H-bonds generated for 'chain 'C' and resid 265 through 267' Processing helix chain 'C' and resid 268 through 273 Processing helix chain 'C' and resid 273 through 298 removed outlier: 3.941A pdb=" N ARG C 277 " --> pdb=" O ASP C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 319 removed outlier: 3.724A pdb=" N ALA C 306 " --> pdb=" O SER C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 345 removed outlier: 3.710A pdb=" N ILE C 345 " --> pdb=" O PHE C 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 375 removed outlier: 3.584A pdb=" N LEU C 375 " --> pdb=" O GLU C 371 " (cutoff:3.500A) Processing helix chain 'C' and resid 392 through 420 removed outlier: 4.163A pdb=" N VAL C 396 " --> pdb=" O PRO C 392 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ASP C 397 " --> pdb=" O GLN C 393 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ALA C 398 " --> pdb=" O ARG C 394 " (cutoff:3.500A) Processing helix chain 'C' and resid 424 through 437 Processing helix chain 'C' and resid 453 through 469 Processing helix chain 'C' and resid 470 through 473 Processing helix chain 'C' and resid 474 through 479 removed outlier: 4.277A pdb=" N LEU C 478 " --> pdb=" O LEU C 474 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N THR C 479 " --> pdb=" O LEU C 475 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 474 through 479' Processing helix chain 'D' and resid 2 through 20 removed outlier: 3.727A pdb=" N ILE D 6 " --> pdb=" O GLN D 2 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG D 8 " --> pdb=" O ARG D 4 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N THR D 20 " --> pdb=" O LEU D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 27 removed outlier: 3.673A pdb=" N LEU D 26 " --> pdb=" O ALA D 23 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 55 Processing helix chain 'D' and resid 69 through 82 Processing helix chain 'D' and resid 85 through 89 removed outlier: 3.682A pdb=" N PHE D 88 " --> pdb=" O SER D 85 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU D 89 " --> pdb=" O LEU D 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 85 through 89' Processing helix chain 'D' and resid 97 through 109 Processing helix chain 'D' and resid 110 through 112 No H-bonds generated for 'chain 'D' and resid 110 through 112' Processing helix chain 'D' and resid 124 through 143 removed outlier: 3.713A pdb=" N ILE D 143 " --> pdb=" O GLY D 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 202 removed outlier: 4.493A pdb=" N ALA D 184 " --> pdb=" O GLU D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 217 Processing helix chain 'D' and resid 235 through 251 removed outlier: 3.600A pdb=" N ALA D 250 " --> pdb=" O LEU D 246 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N CYS D 251 " --> pdb=" O LEU D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 261 removed outlier: 4.034A pdb=" N ALA D 258 " --> pdb=" O LEU D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 271 removed outlier: 3.585A pdb=" N TYR D 270 " --> pdb=" O PRO D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 298 Processing helix chain 'D' and resid 302 through 319 removed outlier: 3.561A pdb=" N ALA D 306 " --> pdb=" O SER D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 333 through 345 removed outlier: 3.731A pdb=" N ILE D 345 " --> pdb=" O PHE D 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 357 through 377 Processing helix chain 'D' and resid 392 through 420 removed outlier: 4.110A pdb=" N VAL D 396 " --> pdb=" O PRO D 392 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASP D 397 " --> pdb=" O GLN D 393 " (cutoff:3.500A) Processing helix chain 'D' and resid 423 through 437 removed outlier: 3.572A pdb=" N ALA D 427 " --> pdb=" O ASP D 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 453 through 469 Processing helix chain 'D' and resid 471 through 479 removed outlier: 4.201A pdb=" N LEU D 475 " --> pdb=" O ILE D 471 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU D 477 " --> pdb=" O THR D 473 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N THR D 479 " --> pdb=" O LEU D 475 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 20 Processing helix chain 'E' and resid 54 through 61 Processing helix chain 'E' and resid 75 through 91 Processing helix chain 'E' and resid 101 through 106 Processing helix chain 'E' and resid 107 through 112 Processing helix chain 'E' and resid 241 through 252 Processing helix chain 'E' and resid 264 through 271 removed outlier: 3.906A pdb=" N LYS E 269 " --> pdb=" O GLN E 265 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU E 270 " --> pdb=" O ARG E 266 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 291 removed outlier: 3.879A pdb=" N LEU E 290 " --> pdb=" O ASP E 286 " (cutoff:3.500A) Processing helix chain 'E' and resid 294 through 298 removed outlier: 3.668A pdb=" N VAL E 298 " --> pdb=" O ILE E 295 " (cutoff:3.500A) Processing helix chain 'E' and resid 307 through 322 removed outlier: 3.833A pdb=" N ASN E 311 " --> pdb=" O GLU E 307 " (cutoff:3.500A) Processing helix chain 'E' and resid 332 through 334 No H-bonds generated for 'chain 'E' and resid 332 through 334' Processing helix chain 'E' and resid 335 through 340 Processing helix chain 'E' and resid 350 through 355 Processing helix chain 'E' and resid 355 through 360 Processing helix chain 'F' and resid 9 through 20 Processing helix chain 'F' and resid 54 through 61 Processing helix chain 'F' and resid 75 through 91 Processing helix chain 'F' and resid 101 through 106 Processing helix chain 'F' and resid 107 through 112 Processing helix chain 'F' and resid 243 through 252 Processing helix chain 'F' and resid 264 through 274 Processing helix chain 'F' and resid 286 through 291 removed outlier: 4.286A pdb=" N LEU F 290 " --> pdb=" O ASP F 286 " (cutoff:3.500A) Processing helix chain 'F' and resid 294 through 298 removed outlier: 3.711A pdb=" N VAL F 298 " --> pdb=" O ILE F 295 " (cutoff:3.500A) Processing helix chain 'F' and resid 307 through 321 Processing helix chain 'F' and resid 335 through 340 Processing helix chain 'F' and resid 349 through 360 removed outlier: 4.359A pdb=" N ALA F 353 " --> pdb=" O SER F 349 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N THR F 354 " --> pdb=" O PRO F 350 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 20 Processing helix chain 'G' and resid 54 through 61 Processing helix chain 'G' and resid 75 through 91 Processing helix chain 'G' and resid 101 through 106 Processing helix chain 'G' and resid 107 through 112 Processing helix chain 'G' and resid 241 through 252 Processing helix chain 'G' and resid 264 through 274 Processing helix chain 'G' and resid 286 through 291 removed outlier: 4.307A pdb=" N LEU G 290 " --> pdb=" O ASP G 286 " (cutoff:3.500A) Processing helix chain 'G' and resid 294 through 298 removed outlier: 3.722A pdb=" N VAL G 298 " --> pdb=" O ILE G 295 " (cutoff:3.500A) Processing helix chain 'G' and resid 309 through 321 Processing helix chain 'G' and resid 335 through 340 Processing helix chain 'G' and resid 350 through 355 Processing helix chain 'G' and resid 355 through 360 Processing helix chain 'H' and resid 9 through 20 Processing helix chain 'H' and resid 54 through 61 Processing helix chain 'H' and resid 75 through 91 Processing helix chain 'H' and resid 101 through 106 Processing helix chain 'H' and resid 107 through 112 Processing helix chain 'H' and resid 243 through 252 Processing helix chain 'H' and resid 264 through 274 Processing helix chain 'H' and resid 286 through 291 removed outlier: 4.277A pdb=" N LEU H 290 " --> pdb=" O ASP H 286 " (cutoff:3.500A) Processing helix chain 'H' and resid 294 through 298 removed outlier: 3.746A pdb=" N VAL H 298 " --> pdb=" O ILE H 295 " (cutoff:3.500A) Processing helix chain 'H' and resid 309 through 321 Processing helix chain 'H' and resid 335 through 340 Processing helix chain 'H' and resid 350 through 355 Processing helix chain 'H' and resid 355 through 360 Processing sheet with id=AA1, first strand: chain 'E' and resid 48 through 49 removed outlier: 8.139A pdb=" N VAL E 48 " --> pdb=" O ILE E 26 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ILE E 28 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 278 through 281 removed outlier: 6.382A pdb=" N PHE E 301 " --> pdb=" O MET E 327 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N LEU E 329 " --> pdb=" O PHE E 301 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N ALA E 303 " --> pdb=" O LEU E 329 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N ILE E 348 " --> pdb=" O VAL E 326 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N VAL E 328 " --> pdb=" O ILE E 348 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 48 through 49 removed outlier: 8.139A pdb=" N VAL F 48 " --> pdb=" O ILE F 26 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ILE F 28 " --> pdb=" O VAL F 48 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 278 through 281 removed outlier: 5.933A pdb=" N VAL F 257 " --> pdb=" O ILE F 278 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N PHE F 280 " --> pdb=" O VAL F 257 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N LEU F 259 " --> pdb=" O PHE F 280 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N PHE F 301 " --> pdb=" O MET F 327 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N LEU F 329 " --> pdb=" O PHE F 301 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N ALA F 303 " --> pdb=" O LEU F 329 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N VAL F 326 " --> pdb=" O VAL F 346 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N ILE F 348 " --> pdb=" O VAL F 326 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N VAL F 328 " --> pdb=" O ILE F 348 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 48 through 49 removed outlier: 8.139A pdb=" N VAL G 48 " --> pdb=" O ILE G 26 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ILE G 28 " --> pdb=" O VAL G 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 278 through 281 removed outlier: 5.966A pdb=" N VAL G 257 " --> pdb=" O ILE G 278 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N PHE G 280 " --> pdb=" O VAL G 257 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N LEU G 259 " --> pdb=" O PHE G 280 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N ILE G 348 " --> pdb=" O VAL G 326 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N VAL G 328 " --> pdb=" O ILE G 348 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 48 through 49 removed outlier: 8.139A pdb=" N VAL H 48 " --> pdb=" O ILE H 26 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ILE H 28 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N LYS H 2 " --> pdb=" O MET H 68 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N VAL H 70 " --> pdb=" O LYS H 2 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N ILE H 4 " --> pdb=" O VAL H 70 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N LEU H 69 " --> pdb=" O VAL H 96 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 278 through 281 removed outlier: 5.826A pdb=" N VAL H 257 " --> pdb=" O ILE H 278 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N PHE H 280 " --> pdb=" O VAL H 257 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N LEU H 259 " --> pdb=" O PHE H 280 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N ILE H 348 " --> pdb=" O VAL H 326 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N VAL H 328 " --> pdb=" O ILE H 348 " (cutoff:3.500A) 1128 hydrogen bonds defined for protein. 3270 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: 6.55 Time building geometry restraints manager: 9.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.71 - 0.94: 1 0.94 - 1.17: 1 1.17 - 1.40: 8552 1.40 - 1.63: 12350 1.63 - 1.86: 174 Bond restraints: 21078 Sorted by residual: bond pdb=" C LEU E 69 " pdb=" N VAL E 70 " ideal model delta sigma weight residual 1.332 0.705 0.627 1.23e-02 6.61e+03 2.60e+03 bond pdb=" C MET E 68 " pdb=" N LEU E 69 " ideal model delta sigma weight residual 1.329 1.567 -0.238 1.40e-02 5.10e+03 2.88e+02 bond pdb=" C ASN E 18 " pdb=" N LEU E 19 " ideal model delta sigma weight residual 1.333 1.130 0.203 1.43e-02 4.89e+03 2.02e+02 bond pdb=" C LEU E 19 " pdb=" N VAL E 20 " ideal model delta sigma weight residual 1.332 1.488 -0.156 1.36e-02 5.41e+03 1.31e+02 bond pdb=" CA SER F 314 " pdb=" C SER F 314 " ideal model delta sigma weight residual 1.524 1.481 0.043 1.29e-02 6.01e+03 1.09e+01 ... (remaining 21073 not shown) Histogram of bond angle deviations from ideal: 77.04 - 94.22: 2 94.22 - 111.41: 8531 111.41 - 128.59: 19911 128.59 - 145.78: 205 145.78 - 162.96: 2 Bond angle restraints: 28651 Sorted by residual: angle pdb=" O MET E 68 " pdb=" C MET E 68 " pdb=" N LEU E 69 " ideal model delta sigma weight residual 123.25 77.04 46.21 1.14e+00 7.69e-01 1.64e+03 angle pdb=" CA MET E 68 " pdb=" C MET E 68 " pdb=" N LEU E 69 " ideal model delta sigma weight residual 115.36 161.19 -45.83 1.48e+00 4.57e-01 9.59e+02 angle pdb=" C ASN E 18 " pdb=" N LEU E 19 " pdb=" CA LEU E 19 " ideal model delta sigma weight residual 121.92 86.82 35.10 1.73e+00 3.34e-01 4.12e+02 angle pdb=" CA ASN E 18 " pdb=" C ASN E 18 " pdb=" N LEU E 19 " ideal model delta sigma weight residual 118.17 96.79 21.38 1.33e+00 5.65e-01 2.58e+02 angle pdb=" O ASN E 18 " pdb=" C ASN E 18 " pdb=" N LEU E 19 " ideal model delta sigma weight residual 122.46 143.51 -21.05 1.38e+00 5.25e-01 2.33e+02 ... (remaining 28646 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.74: 11046 16.74 - 33.48: 951 33.48 - 50.22: 165 50.22 - 66.96: 32 66.96 - 83.69: 18 Dihedral angle restraints: 12212 sinusoidal: 4518 harmonic: 7694 Sorted by residual: dihedral pdb=" CA CYS C 251 " pdb=" C CYS C 251 " pdb=" N ASN C 252 " pdb=" CA ASN C 252 " ideal model delta harmonic sigma weight residual 180.00 -96.39 -83.61 0 5.00e+00 4.00e-02 2.80e+02 dihedral pdb=" CA GLU B 275 " pdb=" C GLU B 275 " pdb=" N PHE B 276 " pdb=" CA PHE B 276 " ideal model delta harmonic sigma weight residual 180.00 -130.51 -49.49 0 5.00e+00 4.00e-02 9.80e+01 dihedral pdb=" CA VAL C 118 " pdb=" C VAL C 118 " pdb=" N GLY C 119 " pdb=" CA GLY C 119 " ideal model delta harmonic sigma weight residual -180.00 -139.24 -40.76 0 5.00e+00 4.00e-02 6.65e+01 ... (remaining 12209 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.123: 2930 0.123 - 0.246: 424 0.246 - 0.369: 70 0.369 - 0.492: 11 0.492 - 0.615: 6 Chirality restraints: 3441 Sorted by residual: chirality pdb=" CB VAL D 445 " pdb=" CA VAL D 445 " pdb=" CG1 VAL D 445 " pdb=" CG2 VAL D 445 " both_signs ideal model delta sigma weight residual False -2.63 -2.01 -0.62 2.00e-01 2.50e+01 9.47e+00 chirality pdb=" CB ILE B 220 " pdb=" CA ILE B 220 " pdb=" CG1 ILE B 220 " pdb=" CG2 ILE B 220 " both_signs ideal model delta sigma weight residual False 2.64 2.06 0.59 2.00e-01 2.50e+01 8.68e+00 chirality pdb=" CA ASP H 308 " pdb=" N ASP H 308 " pdb=" C ASP H 308 " pdb=" CB ASP H 308 " both_signs ideal model delta sigma weight residual False 2.51 1.95 0.56 2.00e-01 2.50e+01 7.90e+00 ... (remaining 3438 not shown) Planarity restraints: 3553 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 55 " -0.102 5.00e-02 4.00e+02 1.49e-01 3.53e+01 pdb=" N PRO B 56 " 0.257 5.00e-02 4.00e+02 pdb=" CA PRO B 56 " -0.076 5.00e-02 4.00e+02 pdb=" CD PRO B 56 " -0.079 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU E 19 " -0.035 2.00e-02 2.50e+03 5.89e-02 3.47e+01 pdb=" C LEU E 19 " 0.102 2.00e-02 2.50e+03 pdb=" O LEU E 19 " -0.034 2.00e-02 2.50e+03 pdb=" N VAL E 20 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE C 466 " -0.026 2.00e-02 2.50e+03 5.15e-02 2.66e+01 pdb=" C PHE C 466 " 0.089 2.00e-02 2.50e+03 pdb=" O PHE C 466 " -0.033 2.00e-02 2.50e+03 pdb=" N GLY C 467 " -0.030 2.00e-02 2.50e+03 ... (remaining 3550 not shown) Histogram of nonbonded interaction distances: 0.24 - 1.18: 11 1.18 - 2.11: 78 2.11 - 3.04: 12770 3.04 - 3.97: 52828 3.97 - 4.90: 91129 Warning: very small nonbonded interaction distances. Nonbonded interactions: 156816 Sorted by model distance: nonbonded pdb=" CD GLU F 77 " pdb=" CD GLU H 77 " model vdw 0.244 3.500 nonbonded pdb=" SD MET F 68 " pdb=" CG LEU F 358 " model vdw 1.061 3.830 nonbonded pdb=" OE2 GLU F 107 " pdb=" CE1 HIS H 54 " model vdw 1.082 3.260 nonbonded pdb=" CE1 HIS F 54 " pdb=" OE2 GLU H 107 " model vdw 1.090 3.260 nonbonded pdb=" OD1 ASP G 308 " pdb=" NE2 GLN G 331 " model vdw 1.096 2.520 ... (remaining 156811 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 1 through 28 or resid 37 through 89 or resid 94 through 11 \ 7 or resid 124 through 153 or resid 178 through 267 or (resid 268 and (name N or \ name CA or name C or name O or name CB )) or resid 269 through 270 or resid 275 \ through 483)) selection = (chain 'B' and (resid 1 through 28 or resid 37 through 61 or resid 68 through 11 \ 7 or resid 124 through 267 or (resid 268 and (name N or name CA or name C or nam \ e O or name CB )) or resid 269 through 483)) selection = (chain 'C' and (resid 1 through 28 or resid 37 through 89 or resid 94 through 11 \ 7 or resid 124 through 270 or resid 275 through 483)) selection = (chain 'D' and (resid 1 through 28 or resid 37 through 89 or resid 94 through 11 \ 7 or resid 124 through 267 or (resid 268 and (name N or name CA or name C or nam \ e O or name CB )) or resid 269 through 270 or resid 275 through 483)) } ncs_group { reference = (chain 'E' and (resid 1 through 308 or (resid 309 and (name N or name CA or name \ C or name O or name CB )) or resid 310 through 360)) selection = (chain 'F' and (resid 1 through 17 or (resid 18 and (name N or name CA or name C \ or name O or name CB )) or resid 19 through 67 or (resid 68 and (name N or name \ CA or name C or name O or name CB )) or resid 69 through 76 or (resid 77 and (n \ ame N or name CA or name C or name O or name CB )) or resid 78 through 308 or (r \ esid 309 and (name N or name CA or name C or name O or name CB )) or resid 310 t \ hrough 331 or (resid 332 and (name N or name CA or name C or name O or name CB ) \ ) or resid 333 through 357 or (resid 358 and (name N or name CA or name C or nam \ e O or name CB )) or resid 359 through 360)) selection = (chain 'G' and (resid 1 through 17 or (resid 18 and (name N or name CA or name C \ or name O or name CB )) or resid 19 through 331 or (resid 332 and (name N or na \ me CA or name C or name O or name CB )) or resid 333 through 360)) selection = (chain 'H' and (resid 1 through 17 or (resid 18 and (name N or name CA or name C \ or name O or name CB )) or resid 19 through 76 or (resid 77 and (name N or name \ CA or name C or name O or name CB )) or resid 78 through 308 or (resid 309 and \ (name N or name CA or name C or name O or name CB )) or resid 310 through 331 or \ (resid 332 and (name N or name CA or name C or name O or name CB )) or resid 33 \ 3 through 360)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 105 5.16 5 C 13526 2.51 5 N 3346 2.21 5 O 3660 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 0.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.170 Construct map_model_manager: 0.010 Extract box with map and model: 4.360 Check model and map are aligned: 0.310 Process input model: 52.570 Find NCS groups from input model: 1.570 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Set scattering table: 0.190 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4829 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 : 0.010 0.627 21078 Z= 0.661 Angle : 1.789 46.214 28651 Z= 1.023 Chirality : 0.094 0.615 3441 Planarity : 0.011 0.149 3553 Dihedral : 13.199 83.694 7226 Min Nonbonded Distance : 0.244 Molprobity Statistics. All-atom Clashscore : 16.47 Ramachandran Plot: Outliers : 0.34 % Allowed : 4.00 % Favored : 95.65 % Rotamer Outliers : 5.36 % Cbeta Deviations : 0.32 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -0.54 (0.15), residues: 2623 helix: 0.95 (0.13), residues: 1393 sheet: -0.70 (0.41), residues: 180 loop : -2.17 (0.16), residues: 1050 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 713 residues out of total 2193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 596 time to evaluate : 2.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 117 outliers final: 40 residues processed: 691 average time/residue: 0.7241 time to fit residues: 613.5879 Evaluate side-chains 439 residues out of total 2193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 399 time to evaluate : 2.215 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 38 residues processed: 2 average time/residue: 0.1944 time to fit residues: 3.8308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 224 optimal weight: 3.9990 chunk 201 optimal weight: 5.9990 chunk 111 optimal weight: 3.9990 chunk 68 optimal weight: 7.9990 chunk 135 optimal weight: 3.9990 chunk 107 optimal weight: 0.9980 chunk 208 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 126 optimal weight: 0.8980 chunk 155 optimal weight: 0.9990 chunk 241 optimal weight: 5.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 HIS A 436 ASN A 448 HIS A 453 ASN B 57 ASN ** B 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 HIS B 266 HIS B 367 GLN B 448 HIS ** C 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 213 HIS ** C 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 377 HIS C 448 HIS C 453 ASN ** D 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 213 HIS ** D 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 377 HIS D 448 HIS ** E 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 311 ASN G 91 ASN G 121 HIS H 91 ASN ** H 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4824 moved from start: 0.3074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 21078 Z= 0.213 Angle : 0.795 32.997 28651 Z= 0.386 Chirality : 0.046 0.244 3441 Planarity : 0.005 0.083 3553 Dihedral : 5.454 27.575 2807 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 14.95 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.43 % Favored : 96.53 % Rotamer Outliers : 7.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % 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: -1.17 (0.15), residues: 2623 helix: -0.01 (0.13), residues: 1365 sheet: -0.25 (0.37), residues: 200 loop : -1.86 (0.18), residues: 1058 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 610 residues out of total 2193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 453 time to evaluate : 2.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 157 outliers final: 72 residues processed: 555 average time/residue: 0.8318 time to fit residues: 554.6425 Evaluate side-chains 464 residues out of total 2193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 392 time to evaluate : 2.225 Switching outliers to nearest non-outliers outliers start: 72 outliers final: 52 residues processed: 20 average time/residue: 0.3207 time to fit residues: 12.7637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 134 optimal weight: 6.9990 chunk 74 optimal weight: 4.9990 chunk 201 optimal weight: 0.0370 chunk 164 optimal weight: 0.9990 chunk 66 optimal weight: 0.0000 chunk 241 optimal weight: 10.0000 chunk 261 optimal weight: 0.9980 chunk 215 optimal weight: 0.9980 chunk 239 optimal weight: 6.9990 chunk 82 optimal weight: 8.9990 chunk 194 optimal weight: 1.9990 overall best weight: 0.6064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 HIS A 313 GLN ** B 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 HIS B 313 GLN ** C 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 213 HIS ** C 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 437 ASN C 453 ASN D 213 HIS ** D 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 453 ASN E 91 ASN E 311 ASN F 91 ASN G 18 ASN ** H 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4775 moved from start: 0.3825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.044 21078 Z= 0.159 Angle : 0.670 19.677 28651 Z= 0.322 Chirality : 0.043 0.298 3441 Planarity : 0.004 0.072 3553 Dihedral : 4.956 25.312 2807 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer Outliers : 6.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % 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: -1.08 (0.15), residues: 2623 helix: 0.01 (0.13), residues: 1394 sheet: 0.72 (0.44), residues: 156 loop : -1.89 (0.18), residues: 1073 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 573 residues out of total 2193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 425 time to evaluate : 2.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 148 outliers final: 69 residues processed: 525 average time/residue: 0.8804 time to fit residues: 552.8256 Evaluate side-chains 449 residues out of total 2193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 380 time to evaluate : 2.190 Switching outliers to nearest non-outliers outliers start: 69 outliers final: 55 residues processed: 14 average time/residue: 0.4767 time to fit residues: 12.1476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 239 optimal weight: 2.9990 chunk 181 optimal weight: 0.2980 chunk 125 optimal weight: 5.9990 chunk 26 optimal weight: 0.0980 chunk 115 optimal weight: 8.9990 chunk 162 optimal weight: 1.9990 chunk 242 optimal weight: 4.9990 chunk 257 optimal weight: 5.9990 chunk 126 optimal weight: 0.4980 chunk 230 optimal weight: 0.6980 chunk 69 optimal weight: 8.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 HIS A 313 GLN B 57 ASN B 213 HIS B 313 GLN C 213 HIS C 313 GLN C 393 GLN C 453 ASN D 213 HIS ** D 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 91 ASN F 18 ASN F 91 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4780 moved from start: 0.4210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.063 21078 Z= 0.161 Angle : 0.638 19.330 28651 Z= 0.309 Chirality : 0.042 0.239 3441 Planarity : 0.004 0.073 3553 Dihedral : 4.813 24.441 2807 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer Outliers : 6.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % 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 (0.15), residues: 2623 helix: 0.07 (0.13), residues: 1396 sheet: 0.87 (0.43), residues: 156 loop : -1.80 (0.18), residues: 1071 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 543 residues out of total 2193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 409 time to evaluate : 2.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 134 outliers final: 85 residues processed: 501 average time/residue: 0.9085 time to fit residues: 541.7449 Evaluate side-chains 455 residues out of total 2193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 370 time to evaluate : 2.326 Switching outliers to nearest non-outliers outliers start: 85 outliers final: 66 residues processed: 19 average time/residue: 0.4786 time to fit residues: 15.7635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 214 optimal weight: 3.9990 chunk 145 optimal weight: 4.9990 chunk 3 optimal weight: 0.1980 chunk 191 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 chunk 219 optimal weight: 0.9990 chunk 177 optimal weight: 10.0000 chunk 0 optimal weight: 10.9990 chunk 131 optimal weight: 9.9990 chunk 230 optimal weight: 3.9990 chunk 64 optimal weight: 7.9990 overall best weight: 2.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 HIS A 313 GLN A 437 ASN B 213 HIS B 313 GLN B 448 HIS C 213 HIS C 313 GLN C 393 GLN C 453 ASN D 213 HIS ** D 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 453 ASN E 91 ASN F 91 ASN G 253 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4948 moved from start: 0.4457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.053 21078 Z= 0.280 Angle : 0.770 19.566 28651 Z= 0.386 Chirality : 0.047 0.215 3441 Planarity : 0.005 0.074 3553 Dihedral : 5.556 27.968 2807 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 18.15 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.88 % Favored : 95.08 % Rotamer Outliers : 7.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % 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: -1.85 (0.15), residues: 2623 helix: -0.70 (0.13), residues: 1387 sheet: 0.11 (0.41), residues: 176 loop : -2.10 (0.18), residues: 1060 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 586 residues out of total 2193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 417 time to evaluate : 2.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 169 outliers final: 97 residues processed: 527 average time/residue: 0.8916 time to fit residues: 560.7113 Evaluate side-chains 485 residues out of total 2193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 388 time to evaluate : 2.257 Switching outliers to nearest non-outliers outliers start: 97 outliers final: 71 residues processed: 26 average time/residue: 0.4646 time to fit residues: 19.5292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 86 optimal weight: 0.8980 chunk 231 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 150 optimal weight: 2.9990 chunk 63 optimal weight: 6.9990 chunk 257 optimal weight: 5.9990 chunk 213 optimal weight: 0.9990 chunk 119 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 135 optimal weight: 4.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 HIS A 313 GLN B 213 HIS B 448 HIS C 213 HIS C 313 GLN C 453 ASN D 213 HIS ** D 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 453 ASN E 91 ASN F 91 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4872 moved from start: 0.4736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 21078 Z= 0.182 Angle : 0.712 18.885 28651 Z= 0.338 Chirality : 0.043 0.220 3441 Planarity : 0.004 0.077 3553 Dihedral : 5.099 24.378 2807 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 15.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer Outliers : 6.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % 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: -1.55 (0.15), residues: 2623 helix: -0.49 (0.13), residues: 1398 sheet: 0.34 (0.41), residues: 164 loop : -1.91 (0.18), residues: 1061 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 547 residues out of total 2193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 408 time to evaluate : 2.155 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 139 outliers final: 85 residues processed: 503 average time/residue: 0.8761 time to fit residues: 527.9959 Evaluate side-chains 473 residues out of total 2193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 388 time to evaluate : 2.243 Switching outliers to nearest non-outliers outliers start: 85 outliers final: 66 residues processed: 19 average time/residue: 0.4374 time to fit residues: 14.8184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 248 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 146 optimal weight: 6.9990 chunk 187 optimal weight: 0.8980 chunk 145 optimal weight: 0.9980 chunk 216 optimal weight: 0.0870 chunk 143 optimal weight: 0.9980 chunk 256 optimal weight: 4.9990 chunk 160 optimal weight: 0.7980 chunk 156 optimal weight: 0.0670 chunk 118 optimal weight: 0.0570 overall best weight: 0.3814 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 HIS A 436 ASN B 213 HIS C 213 HIS C 453 ASN D 213 HIS ** D 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 453 ASN E 91 ASN F 91 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4782 moved from start: 0.5097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 21078 Z= 0.151 Angle : 0.682 18.096 28651 Z= 0.320 Chirality : 0.042 0.193 3441 Planarity : 0.004 0.074 3553 Dihedral : 4.707 23.030 2807 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer Outliers : 5.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % 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: -1.19 (0.16), residues: 2623 helix: -0.16 (0.13), residues: 1421 sheet: 0.62 (0.41), residues: 172 loop : -1.87 (0.18), residues: 1030 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 2193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 424 time to evaluate : 2.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 121 outliers final: 73 residues processed: 508 average time/residue: 0.8700 time to fit residues: 530.1591 Evaluate side-chains 453 residues out of total 2193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 380 time to evaluate : 2.107 Switching outliers to nearest non-outliers outliers start: 73 outliers final: 63 residues processed: 10 average time/residue: 0.2270 time to fit residues: 7.0094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 158 optimal weight: 0.9990 chunk 102 optimal weight: 2.9990 chunk 153 optimal weight: 0.9980 chunk 77 optimal weight: 4.9990 chunk 50 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 162 optimal weight: 0.9980 chunk 174 optimal weight: 9.9990 chunk 126 optimal weight: 5.9990 chunk 23 optimal weight: 0.7980 chunk 201 optimal weight: 9.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 HIS A 436 ASN B 213 HIS B 448 HIS C 213 HIS ** C 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 453 ASN D 213 HIS ** D 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 453 ASN F 91 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4817 moved from start: 0.5235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 21078 Z= 0.176 Angle : 0.726 18.944 28651 Z= 0.340 Chirality : 0.043 0.217 3441 Planarity : 0.004 0.074 3553 Dihedral : 4.711 22.000 2807 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer Outliers : 4.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % 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: -1.12 (0.16), residues: 2623 helix: -0.15 (0.13), residues: 1399 sheet: 0.70 (0.41), residues: 172 loop : -1.77 (0.18), residues: 1052 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 2193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 394 time to evaluate : 2.257 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 99 outliers final: 68 residues processed: 472 average time/residue: 0.8945 time to fit residues: 503.4122 Evaluate side-chains 446 residues out of total 2193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 378 time to evaluate : 2.282 Switching outliers to nearest non-outliers outliers start: 68 outliers final: 57 residues processed: 11 average time/residue: 0.3769 time to fit residues: 9.0591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 233 optimal weight: 1.9990 chunk 245 optimal weight: 8.9990 chunk 224 optimal weight: 1.9990 chunk 238 optimal weight: 0.8980 chunk 143 optimal weight: 0.0870 chunk 104 optimal weight: 6.9990 chunk 187 optimal weight: 5.9990 chunk 73 optimal weight: 3.9990 chunk 215 optimal weight: 0.0980 chunk 225 optimal weight: 0.8980 chunk 156 optimal weight: 0.0970 overall best weight: 0.4156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 313 GLN A 436 ASN B 213 HIS B 448 HIS C 213 HIS ** C 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 453 ASN D 213 HIS ** D 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 453 ASN E 84 GLN F 91 ASN G 265 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4758 moved from start: 0.5468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.048 21078 Z= 0.160 Angle : 0.719 18.146 28651 Z= 0.331 Chirality : 0.042 0.182 3441 Planarity : 0.004 0.076 3553 Dihedral : 4.582 21.369 2807 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer Outliers : 4.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % 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: -0.98 (0.16), residues: 2623 helix: -0.01 (0.13), residues: 1410 sheet: 0.77 (0.41), residues: 172 loop : -1.76 (0.18), residues: 1041 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 2193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 383 time to evaluate : 2.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 88 outliers final: 59 residues processed: 454 average time/residue: 0.9284 time to fit residues: 505.5493 Evaluate side-chains 422 residues out of total 2193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 363 time to evaluate : 2.233 Switching outliers to nearest non-outliers outliers start: 59 outliers final: 55 residues processed: 4 average time/residue: 0.7812 time to fit residues: 7.1353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 252 optimal weight: 0.7980 chunk 154 optimal weight: 1.9990 chunk 119 optimal weight: 0.6980 chunk 175 optimal weight: 0.9990 chunk 265 optimal weight: 2.9990 chunk 243 optimal weight: 0.9980 chunk 211 optimal weight: 0.4980 chunk 21 optimal weight: 5.9990 chunk 163 optimal weight: 0.7980 chunk 129 optimal weight: 0.4980 chunk 167 optimal weight: 0.9990 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 213 HIS A 313 GLN A 436 ASN B 213 HIS B 266 HIS B 436 ASN B 448 HIS C 213 HIS ** C 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 453 ASN D 213 HIS ** D 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4769 moved from start: 0.5574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 21078 Z= 0.168 Angle : 0.735 19.269 28651 Z= 0.338 Chirality : 0.042 0.186 3441 Planarity : 0.004 0.075 3553 Dihedral : 4.562 21.659 2807 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer Outliers : 3.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % 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: -0.93 (0.16), residues: 2623 helix: 0.02 (0.13), residues: 1413 sheet: 0.77 (0.41), residues: 172 loop : -1.72 (0.18), residues: 1038 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 2193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 372 time to evaluate : 2.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 72 outliers final: 58 residues processed: 434 average time/residue: 0.9568 time to fit residues: 492.9416 Evaluate side-chains 416 residues out of total 2193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 358 time to evaluate : 2.319 Switching outliers to nearest non-outliers outliers start: 58 outliers final: 53 residues processed: 5 average time/residue: 0.2253 time to fit residues: 5.2351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 224 optimal weight: 0.1980 chunk 64 optimal weight: 0.9980 chunk 194 optimal weight: 1.9990 chunk 31 optimal weight: 9.9990 chunk 58 optimal weight: 1.9990 chunk 211 optimal weight: 8.9990 chunk 88 optimal weight: 6.9990 chunk 217 optimal weight: 4.9990 chunk 26 optimal weight: 9.9990 chunk 38 optimal weight: 8.9990 chunk 185 optimal weight: 7.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 HIS A 313 GLN A 436 ASN A 448 HIS B 213 HIS B 448 HIS C 213 HIS ** C 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 453 ASN D 213 HIS ** D 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 453 ASN F 84 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4742 r_free = 0.4742 target = 0.233982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4644 r_free = 0.4644 target = 0.223823 restraints weight = 31231.742| |-----------------------------------------------------------------------------| r_work (start): 0.4639 rms_B_bonded: 0.86 r_work: 0.4562 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.4485 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.4485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5242 moved from start: 0.5468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.082 21078 Z= 0.250 Angle : 0.813 19.153 28651 Z= 0.386 Chirality : 0.046 0.215 3441 Planarity : 0.005 0.075 3553 Dihedral : 5.138 23.713 2807 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 16.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer Outliers : 3.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % 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: -1.44 (0.15), residues: 2623 helix: -0.39 (0.13), residues: 1388 sheet: 0.38 (0.39), residues: 192 loop : -1.93 (0.18), residues: 1043 =============================================================================== Job complete usr+sys time: 7778.58 seconds wall clock time: 139 minutes 20.52 seconds (8360.52 seconds total)