Starting phenix.real_space_refine (version: dev) on Thu Apr 7 12:58:42 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v4j_21041/04_2022/6v4j_21041_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v4j_21041/04_2022/6v4j_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_21041/04_2022/6v4j_21041.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v4j_21041/04_2022/6v4j_21041.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v4j_21041/04_2022/6v4j_21041_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v4j_21041/04_2022/6v4j_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 Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral 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-4553/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: {'PTRANS': 5, 'CIS': 1, '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: 11.83, per 1000 atoms: 0.57 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: 9.34 Conformation dependent library (CDL) restraints added in 3.5 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: 1.11 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: 6.59 Time building geometry restraints manager: 10.05 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: 0.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.160 Construct map_model_manager: 0.010 Extract box with map and model: 4.510 Check model and map are aligned: 0.340 Convert atoms to be neutral: 0.200 Process input model: 55.190 Find NCS groups from input model: 1.840 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:13.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.710 ------------------------------------------------------------------------------- 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 : 16.38 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 : 2.468 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: 0.6754 time to fit residues: 576.1115 Evaluate side-chains 435 residues out of total 2193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 395 time to evaluate : 2.409 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 38 residues processed: 2 average time/residue: 0.1925 time to fit residues: 3.7853 ------------------------------------------------------------------------------- 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: 4.9990 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: 0.4822 moved from start: 0.3108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.069 21078 Z= 0.228 Angle : 0.803 31.739 28651 Z= 0.391 Chirality : 0.046 0.244 3441 Planarity : 0.005 0.082 3553 Dihedral : 5.466 26.191 2807 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 14.47 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.24 % Favored : 96.72 % Rotamer Outliers : 7.02 % 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: 1362 sheet: -0.27 (0.37), residues: 200 loop : -1.86 (0.18), residues: 1061 *********************** 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 606 residues out of total 2193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 453 time to evaluate : 2.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 153 outliers final: 68 residues processed: 554 average time/residue: 0.7957 time to fit residues: 536.9468 Evaluate side-chains 448 residues out of total 2193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 380 time to evaluate : 2.290 Switching outliers to nearest non-outliers outliers start: 68 outliers final: 50 residues processed: 18 average time/residue: 0.2546 time to fit residues: 10.5953 ------------------------------------------------------------------------------- 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: 2.9990 chunk 74 optimal weight: 5.9990 chunk 201 optimal weight: 0.0170 chunk 164 optimal weight: 0.3980 chunk 66 optimal weight: 5.9990 chunk 241 optimal weight: 10.0000 chunk 261 optimal weight: 1.9990 chunk 215 optimal weight: 0.7980 chunk 239 optimal weight: 7.9990 chunk 82 optimal weight: 7.9990 chunk 194 optimal weight: 6.9990 overall best weight: 1.2422 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 HIS ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4840 moved from start: 0.3744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.076 21078 Z= 0.207 Angle : 0.742 19.741 28651 Z= 0.362 Chirality : 0.044 0.293 3441 Planarity : 0.005 0.096 3553 Dihedral : 5.186 25.649 2807 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer Outliers : 7.47 % 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: -0.28 (0.13), residues: 1391 sheet: 0.43 (0.44), residues: 152 loop : -2.04 (0.17), residues: 1080 *********************** 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 580 residues out of total 2193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 417 time to evaluate : 2.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 163 outliers final: 92 residues processed: 518 average time/residue: 0.8122 time to fit residues: 507.5773 Evaluate side-chains 470 residues out of total 2193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 378 time to evaluate : 2.294 Switching outliers to nearest non-outliers outliers start: 92 outliers final: 68 residues processed: 24 average time/residue: 0.4423 time to fit residues: 17.7250 ------------------------------------------------------------------------------- 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: 0.3980 chunk 181 optimal weight: 5.9990 chunk 125 optimal weight: 7.9990 chunk 26 optimal weight: 5.9990 chunk 115 optimal weight: 5.9990 chunk 162 optimal weight: 1.9990 chunk 242 optimal weight: 0.0870 chunk 257 optimal weight: 5.9990 chunk 126 optimal weight: 2.9990 chunk 230 optimal weight: 9.9990 chunk 69 optimal weight: 3.9990 overall best weight: 1.8964 ------------------------------------------------------------------------------- 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 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4902 moved from start: 0.4151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.103 21078 Z= 0.257 Angle : 0.738 19.710 28651 Z= 0.366 Chirality : 0.044 0.241 3441 Planarity : 0.005 0.080 3553 Dihedral : 5.340 25.481 2807 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % 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: -1.73 (0.15), residues: 2623 helix: -0.58 (0.13), residues: 1395 sheet: -0.04 (0.41), residues: 176 loop : -2.06 (0.18), residues: 1052 *********************** 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 588 residues out of total 2193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 419 time to evaluate : 2.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 169 outliers final: 105 residues processed: 527 average time/residue: 0.8081 time to fit residues: 514.0192 Evaluate side-chains 476 residues out of total 2193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 371 time to evaluate : 2.262 Switching outliers to nearest non-outliers outliers start: 105 outliers final: 76 residues processed: 29 average time/residue: 0.2511 time to fit residues: 15.0696 ------------------------------------------------------------------------------- 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: 6.9990 chunk 145 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 191 optimal weight: 4.9990 chunk 106 optimal weight: 3.9990 chunk 219 optimal weight: 0.0030 chunk 177 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 131 optimal weight: 10.0000 chunk 230 optimal weight: 10.0000 chunk 64 optimal weight: 0.9980 overall best weight: 1.5594 ------------------------------------------------------------------------------- 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 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 G 253 GLN G 265 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4894 moved from start: 0.4455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.113 21078 Z= 0.238 Angle : 0.729 19.181 28651 Z= 0.356 Chirality : 0.043 0.220 3441 Planarity : 0.005 0.078 3553 Dihedral : 5.231 24.913 2807 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 15.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer Outliers : 7.70 % 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: -1.73 (0.15), residues: 2623 helix: -0.59 (0.13), residues: 1395 sheet: 0.09 (0.40), residues: 176 loop : -2.06 (0.18), residues: 1052 *********************** 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 576 residues out of total 2193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 408 time to evaluate : 2.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 168 outliers final: 102 residues processed: 519 average time/residue: 0.8148 time to fit residues: 508.6741 Evaluate side-chains 485 residues out of total 2193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 383 time to evaluate : 2.212 Switching outliers to nearest non-outliers outliers start: 102 outliers final: 77 residues processed: 25 average time/residue: 0.2488 time to fit residues: 13.1499 ------------------------------------------------------------------------------- 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: 5.9990 chunk 231 optimal weight: 6.9990 chunk 50 optimal weight: 1.9990 chunk 150 optimal weight: 7.9990 chunk 63 optimal weight: 0.7980 chunk 257 optimal weight: 3.9990 chunk 213 optimal weight: 3.9990 chunk 119 optimal weight: 0.6980 chunk 21 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 chunk 135 optimal weight: 0.8980 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 313 GLN B 448 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: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4879 moved from start: 0.4694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.153 21078 Z= 0.245 Angle : 0.742 18.880 28651 Z= 0.363 Chirality : 0.043 0.207 3441 Planarity : 0.005 0.083 3553 Dihedral : 5.073 23.947 2807 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer Outliers : 7.66 % 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: -1.61 (0.15), residues: 2623 helix: -0.50 (0.13), residues: 1403 sheet: 0.02 (0.39), residues: 188 loop : -2.02 (0.18), residues: 1032 *********************** 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 571 residues out of total 2193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 404 time to evaluate : 2.303 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 167 outliers final: 102 residues processed: 507 average time/residue: 0.8102 time to fit residues: 494.5158 Evaluate side-chains 478 residues out of total 2193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 376 time to evaluate : 2.164 Switching outliers to nearest non-outliers outliers start: 102 outliers final: 79 residues processed: 23 average time/residue: 0.2763 time to fit residues: 12.8162 ------------------------------------------------------------------------------- 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: 5.9990 chunk 29 optimal weight: 6.9990 chunk 146 optimal weight: 8.9990 chunk 187 optimal weight: 20.0000 chunk 145 optimal weight: 3.9990 chunk 216 optimal weight: 8.9990 chunk 143 optimal weight: 0.7980 chunk 256 optimal weight: 10.0000 chunk 160 optimal weight: 7.9990 chunk 156 optimal weight: 8.9990 chunk 118 optimal weight: 1.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 448 HIS B 213 HIS B 313 GLN B 448 HIS B 453 ASN 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 18 ASN F 84 GLN F 91 ASN F 253 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5038 moved from start: 0.5012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.242 21078 Z= 0.435 Angle : 0.934 20.090 28651 Z= 0.477 Chirality : 0.051 0.221 3441 Planarity : 0.007 0.118 3553 Dihedral : 6.152 31.632 2807 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 21.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer Outliers : 7.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.63 (0.15), residues: 2623 helix: -1.39 (0.12), residues: 1388 sheet: -0.57 (0.39), residues: 188 loop : -2.34 (0.17), residues: 1047 *********************** 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 598 residues out of total 2193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 424 time to evaluate : 2.319 Fit side-chains revert: symmetry clash outliers start: 174 outliers final: 102 residues processed: 540 average time/residue: 0.8327 time to fit residues: 541.5251 Evaluate side-chains 499 residues out of total 2193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 397 time to evaluate : 2.323 Switching outliers to nearest non-outliers outliers start: 102 outliers final: 78 residues processed: 24 average time/residue: 0.2895 time to fit residues: 14.0624 ------------------------------------------------------------------------------- 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: 6.9990 chunk 102 optimal weight: 0.8980 chunk 153 optimal weight: 0.4980 chunk 77 optimal weight: 0.8980 chunk 50 optimal weight: 0.4980 chunk 49 optimal weight: 3.9990 chunk 162 optimal weight: 1.9990 chunk 174 optimal weight: 10.0000 chunk 126 optimal weight: 0.8980 chunk 23 optimal weight: 0.0030 chunk 201 optimal weight: 10.0000 overall best weight: 0.5590 ------------------------------------------------------------------------------- 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 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 448 HIS ** C 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 453 ASN ** D 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 437 ASN D 453 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4873 moved from start: 0.5159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.496 21078 Z= 0.447 Angle : 0.928 55.241 28651 Z= 0.444 Chirality : 0.043 0.210 3441 Planarity : 0.006 0.093 3553 Dihedral : 5.197 24.388 2807 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 15.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer Outliers : 5.32 % 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: -1.86 (0.15), residues: 2623 helix: -0.77 (0.13), residues: 1396 sheet: 0.14 (0.42), residues: 164 loop : -2.01 (0.18), residues: 1063 *********************** 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 511 residues out of total 2193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 395 time to evaluate : 2.491 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 116 outliers final: 82 residues processed: 490 average time/residue: 0.8212 time to fit residues: 484.0350 Evaluate side-chains 457 residues out of total 2193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 375 time to evaluate : 2.404 Switching outliers to nearest non-outliers outliers start: 82 outliers final: 68 residues processed: 14 average time/residue: 0.2929 time to fit residues: 9.6928 ------------------------------------------------------------------------------- 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: 0.0000 chunk 245 optimal weight: 3.9990 chunk 224 optimal weight: 0.9980 chunk 238 optimal weight: 0.4980 chunk 143 optimal weight: 0.0040 chunk 104 optimal weight: 1.9990 chunk 187 optimal weight: 0.5980 chunk 73 optimal weight: 0.0970 chunk 215 optimal weight: 0.2980 chunk 225 optimal weight: 0.8980 chunk 156 optimal weight: 6.9990 overall best weight: 0.1794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 313 GLN 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 Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4868 moved from start: 0.5230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.717 21078 Z= 0.560 Angle : 1.018 73.899 28651 Z= 0.479 Chirality : 0.044 0.433 3441 Planarity : 0.006 0.102 3553 Dihedral : 5.156 24.193 2807 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 18.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer Outliers : 4.22 % 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: -1.78 (0.15), residues: 2623 helix: -0.71 (0.13), residues: 1399 sheet: 0.35 (0.41), residues: 168 loop : -2.01 (0.18), residues: 1056 *********************** 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 465 residues out of total 2193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 373 time to evaluate : 2.423 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 92 outliers final: 74 residues processed: 452 average time/residue: 0.9482 time to fit residues: 517.0935 Evaluate side-chains 436 residues out of total 2193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 362 time to evaluate : 2.354 Switching outliers to nearest non-outliers outliers start: 74 outliers final: 69 residues processed: 5 average time/residue: 0.6903 time to fit residues: 7.5934 ------------------------------------------------------------------------------- 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: 1.9990 chunk 154 optimal weight: 0.8980 chunk 119 optimal weight: 1.9990 chunk 175 optimal weight: 6.9990 chunk 265 optimal weight: 4.9990 chunk 243 optimal weight: 0.1980 chunk 211 optimal weight: 0.9990 chunk 21 optimal weight: 4.9990 chunk 163 optimal weight: 2.9990 chunk 129 optimal weight: 0.6980 chunk 167 optimal weight: 0.8980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4868 moved from start: 0.5240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.717 21078 Z= 0.626 Angle : 1.041 73.899 28651 Z= 0.499 Chirality : 0.044 0.433 3441 Planarity : 0.006 0.102 3553 Dihedral : 5.156 24.193 2807 Min Nonbonded Distance : 1.671 Molprobity Statistics. All-atom Clashscore : 19.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer Outliers : 3.26 % 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: -1.78 (0.15), residues: 2623 helix: -0.71 (0.13), residues: 1399 sheet: 0.35 (0.41), residues: 168 loop : -2.01 (0.18), residues: 1056 ********************** 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 434 residues out of total 2193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 363 time to evaluate : 2.396 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 71 outliers final: 69 residues processed: 434 average time/residue: 0.8774 time to fit residues: 453.6699 Evaluate side-chains 430 residues out of total 2193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 361 time to evaluate : 2.281 Switching outliers to nearest non-outliers outliers start: 69 outliers final: 69 residues processed: 0 time to fit residues: 3.0708 ------------------------------------------------------------------------------- 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: 0.8980 chunk 64 optimal weight: 6.9990 chunk 194 optimal weight: 8.9990 chunk 31 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 chunk 211 optimal weight: 0.6980 chunk 88 optimal weight: 2.9990 chunk 217 optimal weight: 6.9990 chunk 26 optimal weight: 0.9990 chunk 38 optimal weight: 6.9990 chunk 185 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4741 r_free = 0.4741 target = 0.233452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4628 r_free = 0.4628 target = 0.221649 restraints weight = 31762.584| |-----------------------------------------------------------------------------| r_work (start): 0.4627 rms_B_bonded: 1.03 r_work: 0.4602 rms_B_bonded: 1.16 restraints_weight: 0.5000 r_work: 0.4547 rms_B_bonded: 2.39 restraints_weight: 0.2500 r_work: 0.4455 rms_B_bonded: 4.86 restraints_weight: 0.1250 r_work (final): 0.4455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5199 moved from start: 0.5239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.717 21078 Z= 0.626 Angle : 1.041 73.899 28651 Z= 0.499 Chirality : 0.044 0.433 3441 Planarity : 0.006 0.102 3553 Dihedral : 5.156 24.193 2807 Min Nonbonded Distance : 1.671 Molprobity Statistics. All-atom Clashscore : 20.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer Outliers : 3.26 % 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: -1.78 (0.15), residues: 2623 helix: -0.71 (0.13), residues: 1399 sheet: 0.35 (0.41), residues: 168 loop : -2.01 (0.18), residues: 1056 =============================================================================== Job complete usr+sys time: 7152.68 seconds wall clock time: 127 minutes 49.62 seconds (7669.62 seconds total)