Starting phenix.real_space_refine (version: dev) on Sun May 15 07:31:45 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bbm_7076/05_2022/6bbm_7076_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bbm_7076/05_2022/6bbm_7076.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bbm_7076/05_2022/6bbm_7076.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bbm_7076/05_2022/6bbm_7076.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bbm_7076/05_2022/6bbm_7076_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bbm_7076/05_2022/6bbm_7076_updated.pdb" } resolution = 4.1 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= 0.000 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 ARG 47": "NH1" <-> "NH2" Residue "A ARG 63": "NH1" <-> "NH2" Residue "A ARG 66": "NH1" <-> "NH2" Residue "A ARG 74": "NH1" <-> "NH2" Residue "A ARG 127": "NH1" <-> "NH2" Residue "A ARG 129": "NH1" <-> "NH2" Residue "A ARG 152": "NH1" <-> "NH2" Residue "A ASP 159": "OD1" <-> "OD2" Residue "A GLU 162": "OE1" <-> "OE2" Residue "A ARG 164": "NH1" <-> "NH2" Residue "A ARG 278": "NH1" <-> "NH2" Residue "A ARG 285": "NH1" <-> "NH2" Residue "A ASP 291": "OD1" <-> "OD2" Residue "A ARG 296": "NH1" <-> "NH2" Residue "A GLU 306": "OE1" <-> "OE2" Residue "A ARG 308": "NH1" <-> "NH2" Residue "A ARG 324": "NH1" <-> "NH2" Residue "A ARG 326": "NH1" <-> "NH2" Residue "A ARG 329": "NH1" <-> "NH2" Residue "A ARG 332": "NH1" <-> "NH2" Residue "A ARG 349": "NH1" <-> "NH2" Residue "A GLU 360": "OE1" <-> "OE2" Residue "A GLU 404": "OE1" <-> "OE2" Residue "A ARG 450": "NH1" <-> "NH2" Residue "A ARG 459": "NH1" <-> "NH2" Residue "A ASP 461": "OD1" <-> "OD2" Residue "B GLU 32": "OE1" <-> "OE2" Residue "B ARG 47": "NH1" <-> "NH2" Residue "B ARG 63": "NH1" <-> "NH2" Residue "B ARG 66": "NH1" <-> "NH2" Residue "B ARG 74": "NH1" <-> "NH2" Residue "B ARG 127": "NH1" <-> "NH2" Residue "B ARG 129": "NH1" <-> "NH2" Residue "B ARG 152": "NH1" <-> "NH2" Residue "B ASP 156": "OD1" <-> "OD2" Residue "B ARG 164": "NH1" <-> "NH2" Residue "B GLU 266": "OE1" <-> "OE2" Residue "B ARG 278": "NH1" <-> "NH2" Residue "B ARG 285": "NH1" <-> "NH2" Residue "B ASP 291": "OD1" <-> "OD2" Residue "B ARG 296": "NH1" <-> "NH2" Residue "B GLU 306": "OE1" <-> "OE2" Residue "B ARG 308": "NH1" <-> "NH2" Residue "B ARG 324": "NH1" <-> "NH2" Residue "B ARG 326": "NH1" <-> "NH2" Residue "B ARG 329": "NH1" <-> "NH2" Residue "B ARG 332": "NH1" <-> "NH2" Residue "B ARG 349": "NH1" <-> "NH2" Residue "B ARG 450": "NH1" <-> "NH2" Residue "B ARG 459": "NH1" <-> "NH2" Residue "C ARG 47": "NH1" <-> "NH2" Residue "C ARG 63": "NH1" <-> "NH2" Residue "C ARG 66": "NH1" <-> "NH2" Residue "C ARG 74": "NH1" <-> "NH2" Residue "C ARG 127": "NH1" <-> "NH2" Residue "C ARG 129": "NH1" <-> "NH2" Residue "C ARG 152": "NH1" <-> "NH2" Residue "C ASP 156": "OD1" <-> "OD2" Residue "C ASP 159": "OD1" <-> "OD2" Residue "C ARG 164": "NH1" <-> "NH2" Residue "C ARG 192": "NH1" <-> "NH2" Residue "C GLU 194": "OE1" <-> "OE2" Residue "C ASP 253": "OD1" <-> "OD2" Residue "C GLU 266": "OE1" <-> "OE2" Residue "C ARG 278": "NH1" <-> "NH2" Residue "C ARG 285": "NH1" <-> "NH2" Residue "C GLU 292": "OE1" <-> "OE2" Residue "C ARG 296": "NH1" <-> "NH2" Residue "C ARG 308": "NH1" <-> "NH2" Residue "C ARG 324": "NH1" <-> "NH2" Residue "C ARG 329": "NH1" <-> "NH2" Residue "C ARG 332": "NH1" <-> "NH2" Residue "C ARG 349": "NH1" <-> "NH2" Residue "C ARG 459": "NH1" <-> "NH2" Residue "C ASP 469": "OD1" <-> "OD2" Residue "D GLU 46": "OE1" <-> "OE2" Residue "D ARG 47": "NH1" <-> "NH2" Residue "D ASP 58": "OD1" <-> "OD2" Residue "D ARG 63": "NH1" <-> "NH2" Residue "D ARG 66": "NH1" <-> "NH2" Residue "D ARG 74": "NH1" <-> "NH2" Residue "D GLU 77": "OE1" <-> "OE2" Residue "D PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 127": "NH1" <-> "NH2" Residue "D ARG 129": "NH1" <-> "NH2" Residue "D ARG 152": "NH1" <-> "NH2" Residue "D ARG 164": "NH1" <-> "NH2" Residue "D ARG 192": "NH1" <-> "NH2" Residue "D ASP 225": "OD1" <-> "OD2" Residue "D PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 280": "OD1" <-> "OD2" Residue "D ARG 285": "NH1" <-> "NH2" Residue "D ARG 296": "NH1" <-> "NH2" Residue "D ARG 308": "NH1" <-> "NH2" Residue "D ARG 324": "NH1" <-> "NH2" Residue "D ARG 326": "NH1" <-> "NH2" Residue "D ARG 332": "NH1" <-> "NH2" Residue "D ARG 349": "NH1" <-> "NH2" Residue "D ASP 421": "OD1" <-> "OD2" Residue "D ARG 450": "NH1" <-> "NH2" Residue "D ASP 461": "OD1" <-> "OD2" Residue "D GLU 471": "OE1" <-> "OE2" Residue "E ARG 47": "NH1" <-> "NH2" Residue "E ARG 63": "NH1" <-> "NH2" Residue "E ARG 66": "NH1" <-> "NH2" Residue "E ARG 74": "NH1" <-> "NH2" Residue "E TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 127": "NH1" <-> "NH2" Residue "E GLU 128": "OE1" <-> "OE2" Residue "E ARG 129": "NH1" <-> "NH2" Residue "E ARG 152": "NH1" <-> "NH2" Residue "E ARG 164": "NH1" <-> "NH2" Residue "E GLU 170": "OE1" <-> "OE2" Residue "E ARG 192": "NH1" <-> "NH2" Residue "E ASP 212": "OD1" <-> "OD2" Residue "E GLU 246": "OE1" <-> "OE2" Residue "E ARG 278": "NH1" <-> "NH2" Residue "E ARG 285": "NH1" <-> "NH2" Residue "E ARG 296": "NH1" <-> "NH2" Residue "E ARG 308": "NH1" <-> "NH2" Residue "E ARG 326": "NH1" <-> "NH2" Residue "E ARG 329": "NH1" <-> "NH2" Residue "E ARG 332": "NH1" <-> "NH2" Residue "E ARG 366": "NH1" <-> "NH2" Residue "E GLU 374": "OE1" <-> "OE2" Residue "E ASP 421": "OD1" <-> "OD2" Residue "E ARG 450": "NH1" <-> "NH2" Residue "E ARG 459": "NH1" <-> "NH2" Residue "E TYR 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 469": "OD1" <-> "OD2" Residue "E ASP 470": "OD1" <-> "OD2" Residue "F GLU 46": "OE1" <-> "OE2" Residue "F ARG 47": "NH1" <-> "NH2" Residue "F ASP 50": "OD1" <-> "OD2" Residue "F ARG 63": "NH1" <-> "NH2" Residue "F ARG 66": "NH1" <-> "NH2" Residue "F ARG 74": "NH1" <-> "NH2" Residue "F GLU 92": "OE1" <-> "OE2" Residue "F ARG 127": "NH1" <-> "NH2" Residue "F ARG 129": "NH1" <-> "NH2" Residue "F ASP 148": "OD1" <-> "OD2" Residue "F ARG 152": "NH1" <-> "NH2" Residue "F GLU 155": "OE1" <-> "OE2" Residue "F ASP 156": "OD1" <-> "OD2" Residue "F ARG 164": "NH1" <-> "NH2" Residue "F ASP 176": "OD1" <-> "OD2" Residue "F ARG 192": "NH1" <-> "NH2" Residue "F ASP 202": "OD1" <-> "OD2" Residue "F ARG 278": "NH1" <-> "NH2" Residue "F ARG 285": "NH1" <-> "NH2" Residue "F ARG 296": "NH1" <-> "NH2" Residue "F ARG 308": "NH1" <-> "NH2" Residue "F ARG 324": "NH1" <-> "NH2" Residue "F ARG 326": "NH1" <-> "NH2" Residue "F ARG 329": "NH1" <-> "NH2" Residue "F ARG 332": "NH1" <-> "NH2" Residue "F ASP 355": "OD1" <-> "OD2" Residue "F GLU 360": "OE1" <-> "OE2" Residue "F GLU 363": "OE1" <-> "OE2" Residue "F GLU 374": "OE1" <-> "OE2" Residue "F ARG 450": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 23956 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 3164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3164 Classifications: {'peptide': 405} Link IDs: {'PTRANS': 15, 'TRANS': 389} Chain breaks: 1 Chain: "B" Number of atoms: 3482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3482 Classifications: {'peptide': 447} Link IDs: {'PTRANS': 18, 'TRANS': 428} Chain breaks: 1 Chain: "C" Number of atoms: 3526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3526 Classifications: {'peptide': 453} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 18, 'TRANS': 434} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 3550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 455, 3550 Classifications: {'peptide': 455} Link IDs: {'PTRANS': 19, 'TRANS': 435} Chain: "E" Number of atoms: 3539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3539 Classifications: {'peptide': 454} Link IDs: {'PTRANS': 19, 'TRANS': 434} Chain breaks: 2 Chain: "F" Number of atoms: 3490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3490 Classifications: {'peptide': 448} Link IDs: {'PTRANS': 18, 'TRANS': 429} Chain breaks: 1 Chain: "V" Number of atoms: 621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 621 Classifications: {'peptide': 125} Incomplete info: {'backbone_only': 4, 'truncation_to_alanine': 121} Link IDs: {'TRANS': 124} Unresolved non-hydrogen bonds: 254 Unresolved non-hydrogen angles: 383 Unresolved non-hydrogen dihedrals: 125 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'UNK:plan-1': 125} Unresolved non-hydrogen planarities: 125 Chain: "W" Number of atoms: 621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 621 Classifications: {'peptide': 125} Incomplete info: {'backbone_only': 4, 'truncation_to_alanine': 121} Link IDs: {'TRANS': 124} Chain breaks: 2 Unresolved non-hydrogen bonds: 254 Unresolved non-hydrogen angles: 383 Unresolved non-hydrogen dihedrals: 125 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'UNK:plan-1': 125} Unresolved non-hydrogen planarities: 125 Chain: "X" Number of atoms: 601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 601 Classifications: {'peptide': 121} Incomplete info: {'backbone_only': 4, 'truncation_to_alanine': 117} Link IDs: {'TRANS': 120} Unresolved non-hydrogen bonds: 246 Unresolved non-hydrogen angles: 371 Unresolved non-hydrogen dihedrals: 121 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'UNK:plan-1': 121} Unresolved non-hydrogen planarities: 121 Chain: "Y" Number of atoms: 616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 616 Classifications: {'peptide': 124} Incomplete info: {'backbone_only': 4, 'truncation_to_alanine': 120} Link IDs: {'TRANS': 123} Unresolved non-hydrogen bonds: 252 Unresolved non-hydrogen angles: 380 Unresolved non-hydrogen dihedrals: 124 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'UNK:plan-1': 124} Unresolved non-hydrogen planarities: 124 Chain: "Z" Number of atoms: 611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 611 Classifications: {'peptide': 123} Incomplete info: {'backbone_only': 4, 'truncation_to_alanine': 119} Link IDs: {'TRANS': 122} Unresolved non-hydrogen bonds: 250 Unresolved non-hydrogen angles: 377 Unresolved non-hydrogen dihedrals: 123 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'UNK:plan-1': 123} Unresolved non-hydrogen planarities: 123 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "W" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 13.06, per 1000 atoms: 0.55 Number of scatterers: 23956 At special positions: 0 Unit cell: (157.29, 131.61, 145.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 78 16.00 P 10 15.00 O 4761 8.00 N 4344 7.00 C 14763 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 10.36 Conformation dependent library (CDL) restraints added in 3.4 seconds 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6178 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 155 helices and 15 sheets defined 45.1% alpha, 5.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.71 Creating SS restraints... Processing helix chain 'A' and resid 32 through 41 removed outlier: 3.965A pdb=" N VAL A 37 " --> pdb=" O ALA A 33 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N GLY A 40 " --> pdb=" O SER A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 54 removed outlier: 3.503A pdb=" N VAL A 51 " --> pdb=" O TRP A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 67 No H-bonds generated for 'chain 'A' and resid 64 through 67' Processing helix chain 'A' and resid 72 through 78 removed outlier: 3.853A pdb=" N GLN A 76 " --> pdb=" O MET A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 90 Processing helix chain 'A' and resid 102 through 104 No H-bonds generated for 'chain 'A' and resid 102 through 104' Processing helix chain 'A' and resid 120 through 129 removed outlier: 3.578A pdb=" N ASP A 124 " --> pdb=" O SER A 120 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N ILE A 125 " --> pdb=" O ALA A 121 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N VAL A 126 " --> pdb=" O TYR A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 139 removed outlier: 3.785A pdb=" N ILE A 136 " --> pdb=" O VAL A 132 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N SER A 137 " --> pdb=" O ARG A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 145 No H-bonds generated for 'chain 'A' and resid 142 through 145' Processing helix chain 'A' and resid 154 through 158 Processing helix chain 'A' and resid 212 through 218 removed outlier: 3.909A pdb=" N LYS A 217 " --> pdb=" O ASP A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 247 Processing helix chain 'A' and resid 265 through 276 removed outlier: 3.562A pdb=" N MET A 269 " --> pdb=" O SER A 265 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG A 271 " --> pdb=" O GLN A 267 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N ALA A 274 " --> pdb=" O MET A 270 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N SER A 275 " --> pdb=" O ARG A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 306 removed outlier: 3.528A pdb=" N GLU A 306 " --> pdb=" O GLY A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 330 removed outlier: 3.735A pdb=" N ARG A 329 " --> pdb=" O SER A 325 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ILE A 330 " --> pdb=" O ARG A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 347 No H-bonds generated for 'chain 'A' and resid 345 through 347' Processing helix chain 'A' and resid 357 through 372 removed outlier: 3.900A pdb=" N ARG A 366 " --> pdb=" O ALA A 362 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N SER A 367 " --> pdb=" O GLU A 363 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ALA A 370 " --> pdb=" O ARG A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 391 No H-bonds generated for 'chain 'A' and resid 389 through 391' Processing helix chain 'A' and resid 399 through 401 No H-bonds generated for 'chain 'A' and resid 399 through 401' Processing helix chain 'A' and resid 421 through 424 No H-bonds generated for 'chain 'A' and resid 421 through 424' Processing helix chain 'B' and resid 31 through 35 Processing helix chain 'B' and resid 38 through 43 removed outlier: 3.531A pdb=" N MET B 42 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU B 43 " --> pdb=" O GLY B 39 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 38 through 43' Processing helix chain 'B' and resid 45 through 54 removed outlier: 3.636A pdb=" N TRP B 48 " --> pdb=" O ASN B 45 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N ASP B 49 " --> pdb=" O GLU B 46 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N VAL B 51 " --> pdb=" O TRP B 48 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N ALA B 52 " --> pdb=" O ASP B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 71 removed outlier: 3.651A pdb=" N HIS B 67 " --> pdb=" O ARG B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 94 Processing helix chain 'B' and resid 104 through 110 Processing helix chain 'B' and resid 119 through 128 removed outlier: 3.981A pdb=" N ASP B 124 " --> pdb=" O SER B 120 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ILE B 125 " --> pdb=" O ALA B 121 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL B 126 " --> pdb=" O TYR B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 141 removed outlier: 4.091A pdb=" N ILE B 136 " --> pdb=" O VAL B 132 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N SER B 137 " --> pdb=" O ARG B 133 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ALA B 139 " --> pdb=" O MET B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 147 Processing helix chain 'B' and resid 154 through 165 removed outlier: 4.102A pdb=" N ASP B 159 " --> pdb=" O GLU B 155 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU B 162 " --> pdb=" O LEU B 158 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N SER B 163 " --> pdb=" O ASP B 159 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL B 165 " --> pdb=" O ALA B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 192 removed outlier: 3.692A pdb=" N THR B 189 " --> pdb=" O VAL B 185 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG B 192 " --> pdb=" O ALA B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 216 No H-bonds generated for 'chain 'B' and resid 214 through 216' Processing helix chain 'B' and resid 237 through 248 removed outlier: 4.332A pdb=" N ALA B 241 " --> pdb=" O LYS B 237 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLU B 246 " --> pdb=" O MET B 242 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASN B 247 " --> pdb=" O ASN B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 274 Processing helix chain 'B' and resid 281 through 283 No H-bonds generated for 'chain 'B' and resid 281 through 283' Processing helix chain 'B' and resid 294 through 299 Processing helix chain 'B' and resid 302 through 304 No H-bonds generated for 'chain 'B' and resid 302 through 304' Processing helix chain 'B' and resid 322 through 333 removed outlier: 3.853A pdb=" N ARG B 328 " --> pdb=" O ARG B 324 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG B 329 " --> pdb=" O SER B 325 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N GLU B 333 " --> pdb=" O ARG B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 347 No H-bonds generated for 'chain 'B' and resid 345 through 347' Processing helix chain 'B' and resid 357 through 374 removed outlier: 3.555A pdb=" N ILE B 361 " --> pdb=" O THR B 358 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N ALA B 362 " --> pdb=" O LEU B 359 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N GLU B 363 " --> pdb=" O GLU B 360 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER B 365 " --> pdb=" O ALA B 362 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG B 366 " --> pdb=" O GLU B 363 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LEU B 368 " --> pdb=" O SER B 365 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N LYS B 369 " --> pdb=" O ARG B 366 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLU B 374 " --> pdb=" O LEU B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 391 removed outlier: 3.550A pdb=" N GLN B 391 " --> pdb=" O SER B 388 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 388 through 391' Processing helix chain 'B' and resid 409 through 411 No H-bonds generated for 'chain 'B' and resid 409 through 411' Processing helix chain 'C' and resid 32 through 43 removed outlier: 3.567A pdb=" N LEU C 38 " --> pdb=" O GLU C 34 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLY C 39 " --> pdb=" O GLN C 35 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY C 40 " --> pdb=" O SER C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 51 removed outlier: 4.070A pdb=" N VAL C 51 " --> pdb=" O TRP C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 77 removed outlier: 3.913A pdb=" N HIS C 67 " --> pdb=" O ARG C 63 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLN C 76 " --> pdb=" O MET C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 93 removed outlier: 3.721A pdb=" N SER C 90 " --> pdb=" O THR C 86 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU C 91 " --> pdb=" O LEU C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 100 No H-bonds generated for 'chain 'C' and resid 97 through 100' Processing helix chain 'C' and resid 102 through 106 removed outlier: 3.566A pdb=" N TYR C 105 " --> pdb=" O GLY C 102 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU C 106 " --> pdb=" O PHE C 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 102 through 106' Processing helix chain 'C' and resid 119 through 131 removed outlier: 3.743A pdb=" N VAL C 126 " --> pdb=" O TYR C 122 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARG C 127 " --> pdb=" O ALA C 123 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA C 130 " --> pdb=" O VAL C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 135 No H-bonds generated for 'chain 'C' and resid 133 through 135' Processing helix chain 'C' and resid 155 through 163 removed outlier: 3.717A pdb=" N LEU C 160 " --> pdb=" O ASP C 156 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER C 163 " --> pdb=" O ASP C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 192 removed outlier: 4.383A pdb=" N ALA C 188 " --> pdb=" O ASP C 184 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG C 192 " --> pdb=" O ALA C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 246 Processing helix chain 'C' and resid 265 through 276 removed outlier: 3.561A pdb=" N MET C 269 " --> pdb=" O SER C 265 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA C 274 " --> pdb=" O MET C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 303 removed outlier: 4.105A pdb=" N GLY C 302 " --> pdb=" O SER C 298 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE C 303 " --> pdb=" O GLY C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 332 removed outlier: 4.293A pdb=" N ARG C 326 " --> pdb=" O GLU C 322 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N ARG C 329 " --> pdb=" O SER C 325 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE C 330 " --> pdb=" O ARG C 326 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA C 331 " --> pdb=" O ALA C 327 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 347 No H-bonds generated for 'chain 'C' and resid 345 through 347' Processing helix chain 'C' and resid 357 through 363 removed outlier: 4.291A pdb=" N ILE C 361 " --> pdb=" O ARG C 357 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ALA C 362 " --> pdb=" O THR C 358 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU C 363 " --> pdb=" O LEU C 359 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 357 through 363' Processing helix chain 'C' and resid 365 through 368 No H-bonds generated for 'chain 'C' and resid 365 through 368' Processing helix chain 'C' and resid 387 through 391 removed outlier: 3.701A pdb=" N GLN C 391 " --> pdb=" O SER C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 401 No H-bonds generated for 'chain 'C' and resid 399 through 401' Processing helix chain 'D' and resid 32 through 42 removed outlier: 4.018A pdb=" N SER D 36 " --> pdb=" O GLU D 32 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N VAL D 37 " --> pdb=" O ALA D 33 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N GLY D 40 " --> pdb=" O SER D 36 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU D 41 " --> pdb=" O VAL D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 54 removed outlier: 4.201A pdb=" N ASP D 49 " --> pdb=" O GLU D 46 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ASP D 50 " --> pdb=" O ARG D 47 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N VAL D 51 " --> pdb=" O TRP D 48 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N ALA D 52 " --> pdb=" O ASP D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 71 removed outlier: 3.746A pdb=" N HIS D 67 " --> pdb=" O ARG D 63 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ILE D 68 " --> pdb=" O PRO D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 78 Processing helix chain 'D' and resid 85 through 92 removed outlier: 3.558A pdb=" N SER D 90 " --> pdb=" O THR D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 111 Processing helix chain 'D' and resid 122 through 127 removed outlier: 3.711A pdb=" N VAL D 126 " --> pdb=" O TYR D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 139 removed outlier: 3.614A pdb=" N SER D 137 " --> pdb=" O ARG D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 164 removed outlier: 3.647A pdb=" N GLU D 162 " --> pdb=" O LEU D 158 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 191 removed outlier: 4.515A pdb=" N ALA D 188 " --> pdb=" O ASP D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 214 through 216 No H-bonds generated for 'chain 'D' and resid 214 through 216' Processing helix chain 'D' and resid 238 through 247 removed outlier: 4.189A pdb=" N VAL D 245 " --> pdb=" O ALA D 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 276 removed outlier: 3.738A pdb=" N MET D 269 " --> pdb=" O SER D 265 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N MET D 270 " --> pdb=" O GLU D 266 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ARG D 271 " --> pdb=" O GLN D 267 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N ALA D 274 " --> pdb=" O MET D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 285 removed outlier: 3.953A pdb=" N ARG D 285 " --> pdb=" O THR D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 306 removed outlier: 3.815A pdb=" N THR D 300 " --> pdb=" O ARG D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 331 removed outlier: 4.741A pdb=" N ARG D 329 " --> pdb=" O SER D 325 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ALA D 331 " --> pdb=" O ALA D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 357 through 368 removed outlier: 4.967A pdb=" N ALA D 362 " --> pdb=" O THR D 358 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ILE D 364 " --> pdb=" O GLU D 360 " (cutoff:3.500A) Processing helix chain 'D' and resid 387 through 391 Processing helix chain 'D' and resid 399 through 401 No H-bonds generated for 'chain 'D' and resid 399 through 401' Processing helix chain 'D' and resid 407 through 411 removed outlier: 4.161A pdb=" N ASP D 411 " --> pdb=" O ILE D 408 " (cutoff:3.500A) Processing helix chain 'D' and resid 421 through 424 No H-bonds generated for 'chain 'D' and resid 421 through 424' Processing helix chain 'D' and resid 455 through 457 No H-bonds generated for 'chain 'D' and resid 455 through 457' Processing helix chain 'E' and resid 31 through 42 removed outlier: 3.965A pdb=" N LEU E 38 " --> pdb=" O GLU E 34 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLY E 39 " --> pdb=" O GLN E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 53 removed outlier: 4.441A pdb=" N GLU E 53 " --> pdb=" O ASP E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 78 removed outlier: 3.777A pdb=" N GLU E 71 " --> pdb=" O HIS E 67 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA E 73 " --> pdb=" O PHE E 69 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU E 77 " --> pdb=" O ALA E 73 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER E 78 " --> pdb=" O ARG E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 84 through 93 removed outlier: 4.200A pdb=" N GLU E 92 " --> pdb=" O ALA E 88 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG E 93 " --> pdb=" O GLU E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 108 No H-bonds generated for 'chain 'E' and resid 106 through 108' Processing helix chain 'E' and resid 123 through 143 removed outlier: 4.041A pdb=" N VAL E 131 " --> pdb=" O ARG E 127 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL E 132 " --> pdb=" O GLU E 128 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ARG E 133 " --> pdb=" O ARG E 129 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N SER E 137 " --> pdb=" O ARG E 133 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N VAL E 138 " --> pdb=" O GLU E 134 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N GLU E 141 " --> pdb=" O SER E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 169 removed outlier: 3.930A pdb=" N LEU E 158 " --> pdb=" O SER E 154 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU E 160 " --> pdb=" O ASP E 156 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ALA E 161 " --> pdb=" O LEU E 157 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N SER E 163 " --> pdb=" O ASP E 159 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ARG E 164 " --> pdb=" O LEU E 160 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL E 165 " --> pdb=" O ALA E 161 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N LYS E 167 " --> pdb=" O SER E 163 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ILE E 168 " --> pdb=" O ARG E 164 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA E 169 " --> pdb=" O VAL E 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 192 removed outlier: 4.112A pdb=" N ASP E 187 " --> pdb=" O ALA E 183 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N ALA E 188 " --> pdb=" O ASP E 184 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA E 191 " --> pdb=" O ASP E 187 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ARG E 192 " --> pdb=" O ALA E 188 " (cutoff:3.500A) Processing helix chain 'E' and resid 214 through 217 No H-bonds generated for 'chain 'E' and resid 214 through 217' Processing helix chain 'E' and resid 237 through 246 removed outlier: 4.242A pdb=" N ALA E 241 " --> pdb=" O LYS E 237 " (cutoff:3.500A) Processing helix chain 'E' and resid 265 through 272 Processing helix chain 'E' and resid 282 through 285 No H-bonds generated for 'chain 'E' and resid 282 through 285' Processing helix chain 'E' and resid 292 through 304 Processing helix chain 'E' and resid 324 through 333 removed outlier: 3.663A pdb=" N ARG E 329 " --> pdb=" O SER E 325 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ALA E 331 " --> pdb=" O ALA E 327 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU E 333 " --> pdb=" O ARG E 329 " (cutoff:3.500A) Processing helix chain 'E' and resid 357 through 360 No H-bonds generated for 'chain 'E' and resid 357 through 360' Processing helix chain 'E' and resid 369 through 375 removed outlier: 3.573A pdb=" N LYS E 373 " --> pdb=" O LYS E 369 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLU E 374 " --> pdb=" O ALA E 370 " (cutoff:3.500A) Processing helix chain 'E' and resid 387 through 390 Processing helix chain 'E' and resid 399 through 401 No H-bonds generated for 'chain 'E' and resid 399 through 401' Processing helix chain 'E' and resid 408 through 411 No H-bonds generated for 'chain 'E' and resid 408 through 411' Processing helix chain 'E' and resid 421 through 423 No H-bonds generated for 'chain 'E' and resid 421 through 423' Processing helix chain 'F' and resid 31 through 40 removed outlier: 3.764A pdb=" N SER F 36 " --> pdb=" O GLU F 32 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LEU F 38 " --> pdb=" O GLU F 34 " (cutoff:3.500A) Processing helix chain 'F' and resid 46 through 52 removed outlier: 4.418A pdb=" N ASP F 49 " --> pdb=" O GLU F 46 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ASP F 50 " --> pdb=" O ARG F 47 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL F 51 " --> pdb=" O TRP F 48 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA F 52 " --> pdb=" O ASP F 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 46 through 52' Processing helix chain 'F' and resid 63 through 77 removed outlier: 3.648A pdb=" N HIS F 67 " --> pdb=" O ARG F 63 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ILE F 68 " --> pdb=" O PRO F 64 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N PHE F 69 " --> pdb=" O HIS F 65 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA F 73 " --> pdb=" O PHE F 69 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ARG F 74 " --> pdb=" O THR F 70 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU F 75 " --> pdb=" O GLU F 71 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLN F 76 " --> pdb=" O MET F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 94 Processing helix chain 'F' and resid 105 through 111 removed outlier: 3.876A pdb=" N LEU F 109 " --> pdb=" O TYR F 105 " (cutoff:3.500A) Processing helix chain 'F' and resid 120 through 128 removed outlier: 3.992A pdb=" N ASP F 124 " --> pdb=" O SER F 120 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE F 125 " --> pdb=" O ALA F 121 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N VAL F 126 " --> pdb=" O TYR F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 130 through 146 removed outlier: 3.657A pdb=" N ILE F 136 " --> pdb=" O VAL F 132 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER F 137 " --> pdb=" O ARG F 133 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLU F 141 " --> pdb=" O SER F 137 " (cutoff:3.500A) Processing helix chain 'F' and resid 157 through 169 removed outlier: 4.220A pdb=" N ARG F 164 " --> pdb=" O LEU F 160 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N PHE F 166 " --> pdb=" O GLU F 162 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N LYS F 167 " --> pdb=" O SER F 163 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ILE F 168 " --> pdb=" O ARG F 164 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ALA F 169 " --> pdb=" O VAL F 165 " (cutoff:3.500A) Processing helix chain 'F' and resid 184 through 193 Processing helix chain 'F' and resid 215 through 218 No H-bonds generated for 'chain 'F' and resid 215 through 218' Processing helix chain 'F' and resid 239 through 249 removed outlier: 3.721A pdb=" N VAL F 245 " --> pdb=" O ALA F 241 " (cutoff:3.500A) Processing helix chain 'F' and resid 265 through 272 removed outlier: 4.014A pdb=" N MET F 269 " --> pdb=" O SER F 265 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ARG F 271 " --> pdb=" O GLN F 267 " (cutoff:3.500A) Processing helix chain 'F' and resid 281 through 285 Processing helix chain 'F' and resid 294 through 304 Processing helix chain 'F' and resid 321 through 333 removed outlier: 4.304A pdb=" N ARG F 326 " --> pdb=" O GLU F 322 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG F 328 " --> pdb=" O ARG F 324 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N ARG F 329 " --> pdb=" O SER F 325 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ILE F 330 " --> pdb=" O ARG F 326 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA F 331 " --> pdb=" O ALA F 327 " (cutoff:3.500A) Processing helix chain 'F' and resid 345 through 347 No H-bonds generated for 'chain 'F' and resid 345 through 347' Processing helix chain 'F' and resid 357 through 364 removed outlier: 3.808A pdb=" N ALA F 362 " --> pdb=" O THR F 358 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU F 363 " --> pdb=" O LEU F 359 " (cutoff:3.500A) Processing helix chain 'F' and resid 369 through 372 No H-bonds generated for 'chain 'F' and resid 369 through 372' Processing helix chain 'F' and resid 387 through 391 removed outlier: 3.622A pdb=" N GLU F 390 " --> pdb=" O ARG F 387 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLN F 391 " --> pdb=" O SER F 388 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 387 through 391' Processing helix chain 'F' and resid 399 through 401 No H-bonds generated for 'chain 'F' and resid 399 through 401' Processing helix chain 'F' and resid 421 through 423 No H-bonds generated for 'chain 'F' and resid 421 through 423' Processing helix chain 'V' and resid 118 through 128 removed outlier: 3.664A pdb=" N UNK V 122 " --> pdb=" O UNK V 118 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N UNK V 123 " --> pdb=" O UNK V 119 " (cutoff:3.500A) Processing helix chain 'V' and resid 141 through 147 Processing helix chain 'V' and resid 155 through 162 removed outlier: 3.987A pdb=" N UNK V 161 " --> pdb=" O UNK V 157 " (cutoff:3.500A) Processing helix chain 'V' and resid 177 through 185 Processing helix chain 'V' and resid 222 through 227 removed outlier: 3.512A pdb=" N UNK V 227 " --> pdb=" O UNK V 223 " (cutoff:3.500A) Processing helix chain 'W' and resid 121 through 127 Processing helix chain 'W' and resid 142 through 149 removed outlier: 3.553A pdb=" N UNK W 148 " --> pdb=" O UNK W 144 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N UNK W 149 " --> pdb=" O UNK W 145 " (cutoff:3.500A) Processing helix chain 'W' and resid 153 through 162 removed outlier: 4.256A pdb=" N UNK W 158 " --> pdb=" O UNK W 155 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N UNK W 159 " --> pdb=" O UNK W 156 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N UNK W 161 " --> pdb=" O UNK W 158 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N UNK W 162 " --> pdb=" O UNK W 159 " (cutoff:3.500A) Processing helix chain 'W' and resid 177 through 186 removed outlier: 4.338A pdb=" N UNK W 180 " --> pdb=" O UNK W 177 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N UNK W 185 " --> pdb=" O UNK W 182 " (cutoff:3.500A) Processing helix chain 'W' and resid 201 through 204 No H-bonds generated for 'chain 'W' and resid 201 through 204' Processing helix chain 'W' and resid 223 through 231 removed outlier: 3.684A pdb=" N UNK W 229 " --> pdb=" O UNK W 225 " (cutoff:3.500A) Processing helix chain 'X' and resid 123 through 133 removed outlier: 4.189A pdb=" N UNK X 128 " --> pdb=" O UNK X 125 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N UNK X 131 " --> pdb=" O UNK X 128 " (cutoff:3.500A) Processing helix chain 'X' and resid 141 through 143 No H-bonds generated for 'chain 'X' and resid 141 through 143' Processing helix chain 'X' and resid 146 through 153 removed outlier: 3.754A pdb=" N UNK X 151 " --> pdb=" O UNK X 147 " (cutoff:3.500A) Processing helix chain 'X' and resid 158 through 166 removed outlier: 3.701A pdb=" N UNK X 162 " --> pdb=" O UNK X 158 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N UNK X 164 " --> pdb=" O UNK X 160 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N UNK X 166 " --> pdb=" O UNK X 162 " (cutoff:3.500A) Processing helix chain 'X' and resid 178 through 182 removed outlier: 3.886A pdb=" N UNK X 181 " --> pdb=" O UNK X 178 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N UNK X 182 " --> pdb=" O UNK X 179 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 178 through 182' Processing helix chain 'X' and resid 184 through 187 No H-bonds generated for 'chain 'X' and resid 184 through 187' Processing helix chain 'X' and resid 227 through 229 No H-bonds generated for 'chain 'X' and resid 227 through 229' Processing helix chain 'Y' and resid 121 through 130 removed outlier: 4.183A pdb=" N UNK Y 130 " --> pdb=" O UNK Y 126 " (cutoff:3.500A) Processing helix chain 'Y' and resid 144 through 147 No H-bonds generated for 'chain 'Y' and resid 144 through 147' Processing helix chain 'Y' and resid 154 through 157 No H-bonds generated for 'chain 'Y' and resid 154 through 157' Processing helix chain 'Y' and resid 181 through 188 removed outlier: 4.381A pdb=" N UNK Y 186 " --> pdb=" O UNK Y 182 " (cutoff:3.500A) Processing helix chain 'Y' and resid 201 through 204 No H-bonds generated for 'chain 'Y' and resid 201 through 204' Processing helix chain 'Y' and resid 222 through 231 Processing helix chain 'Z' and resid 120 through 130 Processing helix chain 'Z' and resid 141 through 147 removed outlier: 3.646A pdb=" N UNK Z 147 " --> pdb=" O UNK Z 143 " (cutoff:3.500A) Processing helix chain 'Z' and resid 154 through 156 No H-bonds generated for 'chain 'Z' and resid 154 through 156' Processing helix chain 'Z' and resid 167 through 170 No H-bonds generated for 'chain 'Z' and resid 167 through 170' Processing helix chain 'Z' and resid 181 through 189 removed outlier: 3.623A pdb=" N UNK Z 185 " --> pdb=" O UNK Z 181 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N UNK Z 186 " --> pdb=" O UNK Z 182 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N UNK Z 188 " --> pdb=" O UNK Z 184 " (cutoff:3.500A) Processing helix chain 'Z' and resid 203 through 206 No H-bonds generated for 'chain 'Z' and resid 203 through 206' Processing helix chain 'Z' and resid 222 through 232 removed outlier: 3.898A pdb=" N UNK Z 232 " --> pdb=" O UNK Z 228 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 227 through 229 removed outlier: 5.865A pdb=" N LEU A 414 " --> pdb=" O ILE A 228 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LYS A 440 " --> pdb=" O ILE A 415 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N PHE A 417 " --> pdb=" O ILE A 438 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N ILE A 438 " --> pdb=" O PHE A 417 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N TYR A 419 " --> pdb=" O ILE A 436 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N ILE A 436 " --> pdb=" O TYR A 419 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 310 through 313 removed outlier: 6.369A pdb=" N VAL A 256 " --> pdb=" O TYR A 311 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N ASP A 313 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ILE A 258 " --> pdb=" O ASP A 313 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 448 through 452 removed outlier: 6.424A pdb=" N ILE B 415 " --> pdb=" O GLY B 439 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU B 414 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA B 230 " --> pdb=" O MET B 416 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N VAL B 379 " --> pdb=" O ILE B 227 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N VAL B 229 " --> pdb=" O VAL B 379 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N ALA B 381 " --> pdb=" O VAL B 229 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N ILE B 340 " --> pdb=" O VAL B 380 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N LEU B 382 " --> pdb=" O ILE B 340 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ILE B 342 " --> pdb=" O LEU B 382 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 379 through 383 removed outlier: 6.357A pdb=" N LEU C 414 " --> pdb=" O ILE C 228 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N ALA C 230 " --> pdb=" O LEU C 414 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N MET C 416 " --> pdb=" O ALA C 230 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR C 419 " --> pdb=" O GLU C 435 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 257 through 259 removed outlier: 6.449A pdb=" N TYR C 311 " --> pdb=" O ILE C 258 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'D' and resid 414 through 418 removed outlier: 6.185A pdb=" N ALA D 381 " --> pdb=" O VAL D 229 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N ALA D 231 " --> pdb=" O ALA D 381 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N SER D 383 " --> pdb=" O ALA D 231 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 258 through 260 removed outlier: 6.884A pdb=" N MET D 341 " --> pdb=" O PHE D 259 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'D' and resid 451 through 454 Processing sheet with id= I, first strand: chain 'E' and resid 227 through 231 removed outlier: 6.449A pdb=" N LEU E 414 " --> pdb=" O ILE E 228 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N ALA E 230 " --> pdb=" O LEU E 414 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N MET E 416 " --> pdb=" O ALA E 230 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'E' and resid 257 through 259 Processing sheet with id= K, first strand: chain 'E' and resid 435 through 438 removed outlier: 3.740A pdb=" N ILE E 438 " --> pdb=" O GLY E 447 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N GLY E 447 " --> pdb=" O ILE E 438 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 452 through 454 removed outlier: 3.737A pdb=" N ARG E 459 " --> pdb=" O ASN E 454 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'F' and resid 228 through 230 removed outlier: 3.767A pdb=" N LYS F 440 " --> pdb=" O ILE F 415 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N PHE F 417 " --> pdb=" O ILE F 438 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N ILE F 438 " --> pdb=" O PHE F 417 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'F' and resid 257 through 259 removed outlier: 6.690A pdb=" N TYR F 311 " --> pdb=" O ILE F 258 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'F' and resid 433 through 436 472 hydrogen bonds defined for protein. 1287 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: 6.69 Time building geometry restraints manager: 11.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 7871 1.33 - 1.45: 3135 1.45 - 1.57: 13075 1.57 - 1.69: 15 1.69 - 1.81: 156 Bond restraints: 24252 Sorted by residual: bond pdb=" C VAL F 379 " pdb=" N VAL F 380 " ideal model delta sigma weight residual 1.335 1.290 0.045 1.16e-02 7.43e+03 1.49e+01 bond pdb=" N GLU E 170 " pdb=" CA GLU E 170 " ideal model delta sigma weight residual 1.463 1.505 -0.042 1.24e-02 6.50e+03 1.14e+01 bond pdb=" C LEU A 318 " pdb=" N THR A 319 " ideal model delta sigma weight residual 1.330 1.285 0.046 1.37e-02 5.33e+03 1.11e+01 bond pdb=" N GLY A 465 " pdb=" CA GLY A 465 " ideal model delta sigma weight residual 1.443 1.485 -0.043 1.37e-02 5.33e+03 9.75e+00 bond pdb=" N GLU D 170 " pdb=" CA GLU D 170 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.25e-02 6.40e+03 7.61e+00 ... (remaining 24247 not shown) Histogram of bond angle deviations from ideal: 97.56 - 105.48: 499 105.48 - 113.40: 13511 113.40 - 121.32: 12564 121.32 - 129.23: 6265 129.23 - 137.15: 101 Bond angle restraints: 32940 Sorted by residual: angle pdb=" N VAL C 138 " pdb=" CA VAL C 138 " pdb=" C VAL C 138 " ideal model delta sigma weight residual 112.12 106.89 5.23 8.40e-01 1.42e+00 3.88e+01 angle pdb=" C UNK X 169 " pdb=" N UNK X 170 " pdb=" CA UNK X 170 " ideal model delta sigma weight residual 121.70 131.91 -10.21 1.80e+00 3.09e-01 3.21e+01 angle pdb=" C ARG C 152 " pdb=" N THR C 153 " pdb=" CA THR C 153 " ideal model delta sigma weight residual 122.41 134.13 -11.72 2.09e+00 2.29e-01 3.14e+01 angle pdb=" N VAL E 165 " pdb=" CA VAL E 165 " pdb=" C VAL E 165 " ideal model delta sigma weight residual 113.22 106.78 6.44 1.23e+00 6.61e-01 2.74e+01 angle pdb=" C ARG C 54 " pdb=" N VAL C 55 " pdb=" CA VAL C 55 " ideal model delta sigma weight residual 121.97 131.34 -9.37 1.80e+00 3.09e-01 2.71e+01 ... (remaining 32935 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.04: 14532 35.04 - 70.08: 324 70.08 - 105.12: 32 105.12 - 140.17: 5 140.17 - 175.21: 4 Dihedral angle restraints: 14897 sinusoidal: 5398 harmonic: 9499 Sorted by residual: dihedral pdb=" CA ALA B 169 " pdb=" C ALA B 169 " pdb=" N GLU B 170 " pdb=" CA GLU B 170 " ideal model delta harmonic sigma weight residual 180.00 93.00 87.00 0 5.00e+00 4.00e-02 3.03e+02 dihedral pdb=" CA LYS F 180 " pdb=" C LYS F 180 " pdb=" N ASN F 181 " pdb=" CA ASN F 181 " ideal model delta harmonic sigma weight residual 180.00 116.20 63.80 0 5.00e+00 4.00e-02 1.63e+02 dihedral pdb=" CA PRO D 27 " pdb=" C PRO D 27 " pdb=" N PRO D 28 " pdb=" CA PRO D 28 " ideal model delta harmonic sigma weight residual 180.00 123.12 56.88 0 5.00e+00 4.00e-02 1.29e+02 ... (remaining 14894 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 2450 0.054 - 0.107: 1109 0.107 - 0.161: 239 0.161 - 0.214: 42 0.214 - 0.268: 8 Chirality restraints: 3848 Sorted by residual: chirality pdb=" CB ILE D 227 " pdb=" CA ILE D 227 " pdb=" CG1 ILE D 227 " pdb=" CG2 ILE D 227 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" CB ILE B 193 " pdb=" CA ILE B 193 " pdb=" CG1 ILE B 193 " pdb=" CG2 ILE B 193 " both_signs ideal model delta sigma weight residual False 2.64 2.91 -0.27 2.00e-01 2.50e+01 1.78e+00 chirality pdb=" CB ILE B 227 " pdb=" CA ILE B 227 " pdb=" CG1 ILE B 227 " pdb=" CG2 ILE B 227 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.68e+00 ... (remaining 3845 not shown) Planarity restraints: 4404 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA D 169 " 0.034 2.00e-02 2.50e+03 6.81e-02 4.63e+01 pdb=" C ALA D 169 " -0.118 2.00e-02 2.50e+03 pdb=" O ALA D 169 " 0.046 2.00e-02 2.50e+03 pdb=" N GLU D 170 " 0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA C 169 " 0.033 2.00e-02 2.50e+03 6.52e-02 4.26e+01 pdb=" C ALA C 169 " -0.113 2.00e-02 2.50e+03 pdb=" O ALA C 169 " 0.044 2.00e-02 2.50e+03 pdb=" N GLU C 170 " 0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA E 464 " 0.031 2.00e-02 2.50e+03 6.14e-02 3.77e+01 pdb=" C ALA E 464 " -0.106 2.00e-02 2.50e+03 pdb=" O ALA E 464 " 0.041 2.00e-02 2.50e+03 pdb=" N GLY E 465 " 0.035 2.00e-02 2.50e+03 ... (remaining 4401 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 5134 2.76 - 3.30: 22809 3.30 - 3.83: 39126 3.83 - 4.37: 45500 4.37 - 4.90: 73277 Nonbonded interactions: 185846 Sorted by model distance: nonbonded pdb=" O ARG C 74 " pdb=" OG SER C 78 " model vdw 2.231 2.440 nonbonded pdb=" O LEU B 109 " pdb=" OG1 THR B 113 " model vdw 2.236 2.440 nonbonded pdb=" OD1 ASN D 140 " pdb=" OG SER F 115 " model vdw 2.238 2.440 nonbonded pdb=" OG SER D 224 " pdb=" O ALA D 372 " model vdw 2.250 2.440 nonbonded pdb=" OH TYR A 344 " pdb=" OD1 ASP F 411 " model vdw 2.252 2.440 ... (remaining 185841 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 27 through 464) selection = (chain 'B' and (resid 27 through 166 or resid 204 through 464)) selection = (chain 'C' and (resid 27 through 166 or resid 204 through 464)) selection = (chain 'D' and (resid 27 through 166 or resid 204 through 464)) selection = (chain 'E' and (resid 27 through 166 or resid 204 through 464)) selection = (chain 'F' and (resid 27 through 166 or resid 204 through 464)) } ncs_group { reference = (chain 'V' and ((resid 113 through 121 and (name N or name CA or name C or name \ O )) or resid 122 through 232)) selection = (chain 'W' and ((resid 114 through 122 and (name N or name CA or name C or name \ O )) or resid 123 through 233)) selection = (chain 'X' and ((resid 113 through 121 and (name N or name CA or name C or name \ O )) or resid 122 through 232)) selection = (chain 'Y' and ((resid 113 through 121 and (name N or name CA or name C or name \ O )) or resid 122 through 232)) selection = (chain 'Z' and ((resid 113 through 121 and (name N or name CA or name C or name \ O )) or resid 122 through 232)) } 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: 5 Type Number sf(0) Gaussians P 10 5.49 5 S 78 5.16 5 C 14763 2.51 5 N 4344 2.21 5 O 4761 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 group one per residue 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: 1.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 6.140 Check model and map are aligned: 0.410 Convert atoms to be neutral: 0.230 Process input model: 59.420 Find NCS groups from input model: 1.950 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Set scattering table: 0.020 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:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 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 : 0.008 0.064 24252 Z= 0.527 Angle : 1.201 15.089 32940 Z= 0.654 Chirality : 0.061 0.268 3848 Planarity : 0.008 0.123 4404 Dihedral : 16.696 175.208 8719 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.19 % Allowed : 13.75 % Favored : 86.06 % Rotamer Outliers : 0.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.83 % 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: -5.97 (0.12), residues: 2640 helix: -4.57 (0.07), residues: 1104 sheet: -3.68 (0.26), residues: 257 loop : -3.39 (0.15), residues: 1279 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 367 time to evaluate : 2.571 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 5 residues processed: 380 average time/residue: 0.4235 time to fit residues: 234.8236 Evaluate side-chains 230 residues out of total 2252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 225 time to evaluate : 2.719 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2529 time to fit residues: 6.6209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 272 optimal weight: 30.0000 chunk 244 optimal weight: 5.9990 chunk 135 optimal weight: 6.9990 chunk 83 optimal weight: 9.9990 chunk 165 optimal weight: 1.9990 chunk 130 optimal weight: 0.5980 chunk 253 optimal weight: 3.9990 chunk 97 optimal weight: 8.9990 chunk 153 optimal weight: 0.8980 chunk 188 optimal weight: 0.9980 chunk 293 optimal weight: 9.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 GLN ** A 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 441 GLN A 456 GLN B 198 GLN B 243 ASN ** B 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 29 HIS C 45 ASN C 112 ASN ** C 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 174 ASN ** C 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 399 ASN C 441 GLN D 76 GLN D 243 ASN D 247 ASN D 410 GLN ** E 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 425 HIS E 427 ASN F 118 ASN F 208 ASN F 267 GLN F 391 GLN F 399 ASN ** F 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 24252 Z= 0.204 Angle : 0.760 11.940 32940 Z= 0.372 Chirality : 0.045 0.197 3848 Planarity : 0.005 0.109 4404 Dihedral : 10.897 174.358 3585 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 15.62 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.68 % Favored : 89.17 % Rotamer Outliers : 0.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.39 % 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: -5.25 (0.13), residues: 2640 helix: -3.69 (0.10), residues: 1166 sheet: -3.32 (0.27), residues: 255 loop : -3.20 (0.16), residues: 1219 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 337 time to evaluate : 2.762 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 337 average time/residue: 0.4016 time to fit residues: 203.6296 Evaluate side-chains 226 residues out of total 2252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 225 time to evaluate : 2.814 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2278 time to fit residues: 4.3567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 163 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 chunk 244 optimal weight: 7.9990 chunk 199 optimal weight: 5.9990 chunk 80 optimal weight: 10.0000 chunk 293 optimal weight: 10.0000 chunk 317 optimal weight: 10.0000 chunk 261 optimal weight: 0.0020 chunk 291 optimal weight: 10.0000 chunk 100 optimal weight: 4.9990 chunk 235 optimal weight: 0.2980 overall best weight: 2.0594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 GLN ** B 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 288 GLN ** B 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 140 ASN C 243 ASN C 384 GLN ** D 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 410 GLN ** E 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 112 ASN ** E 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 267 GLN E 410 GLN E 456 GLN F 281 GLN F 399 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.2824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 24252 Z= 0.202 Angle : 0.699 11.998 32940 Z= 0.341 Chirality : 0.044 0.196 3848 Planarity : 0.005 0.102 4404 Dihedral : 10.222 177.347 3585 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.11 % Allowed : 11.25 % Favored : 88.64 % Rotamer Outliers : 0.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.31 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.65 (0.14), residues: 2640 helix: -3.02 (0.12), residues: 1180 sheet: -3.14 (0.26), residues: 267 loop : -3.05 (0.17), residues: 1193 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 324 time to evaluate : 2.984 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: 1 outliers final: 0 residues processed: 324 average time/residue: 0.3797 time to fit residues: 189.4032 Evaluate side-chains 227 residues out of total 2252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 227 time to evaluate : 3.023 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.8321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 290 optimal weight: 10.0000 chunk 220 optimal weight: 6.9990 chunk 152 optimal weight: 5.9990 chunk 32 optimal weight: 7.9990 chunk 140 optimal weight: 0.2980 chunk 197 optimal weight: 2.9990 chunk 294 optimal weight: 20.0000 chunk 312 optimal weight: 10.0000 chunk 154 optimal weight: 0.0980 chunk 279 optimal weight: 20.0000 chunk 84 optimal weight: 0.0040 overall best weight: 1.8796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 HIS A 384 GLN A 456 GLN ** B 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 29 HIS ** C 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 456 GLN F 76 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.3252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 24252 Z= 0.193 Angle : 0.680 11.330 32940 Z= 0.329 Chirality : 0.043 0.197 3848 Planarity : 0.005 0.097 4404 Dihedral : 9.898 179.867 3585 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 15.22 Ramachandran Plot: Outliers : 0.04 % Allowed : 11.10 % Favored : 88.86 % Rotamer Outliers : 0.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.28 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.22 (0.15), residues: 2640 helix: -2.62 (0.13), residues: 1177 sheet: -2.92 (0.27), residues: 272 loop : -2.85 (0.17), residues: 1191 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 323 time to evaluate : 3.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 324 average time/residue: 0.3659 time to fit residues: 185.5540 Evaluate side-chains 219 residues out of total 2252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 219 time to evaluate : 2.803 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.5485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 260 optimal weight: 1.9990 chunk 177 optimal weight: 1.9990 chunk 4 optimal weight: 50.0000 chunk 232 optimal weight: 4.9990 chunk 128 optimal weight: 0.0980 chunk 266 optimal weight: 30.0000 chunk 215 optimal weight: 6.9990 chunk 0 optimal weight: 30.0000 chunk 159 optimal weight: 7.9990 chunk 280 optimal weight: 20.0000 chunk 78 optimal weight: 0.0770 overall best weight: 1.8344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 ASN A 252 GLN A 281 GLN A 334 HIS B 399 ASN ** B 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 243 ASN ** C 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 45 ASN ** D 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 76 GLN F 399 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.3577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 24252 Z= 0.185 Angle : 0.668 10.809 32940 Z= 0.322 Chirality : 0.043 0.200 3848 Planarity : 0.005 0.092 4404 Dihedral : 9.586 174.168 3585 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 15.00 Ramachandran Plot: Outliers : 0.04 % Allowed : 11.06 % Favored : 88.90 % Rotamer Outliers : 0.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.28 % 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: -3.95 (0.15), residues: 2640 helix: -2.34 (0.13), residues: 1186 sheet: -2.69 (0.28), residues: 273 loop : -2.82 (0.17), residues: 1181 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 296 time to evaluate : 2.798 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 revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 297 average time/residue: 0.3439 time to fit residues: 163.2898 Evaluate side-chains 215 residues out of total 2252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 215 time to evaluate : 2.789 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.5829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 105 optimal weight: 10.0000 chunk 281 optimal weight: 10.0000 chunk 61 optimal weight: 4.9990 chunk 183 optimal weight: 0.5980 chunk 77 optimal weight: 0.7980 chunk 312 optimal weight: 10.0000 chunk 259 optimal weight: 2.9990 chunk 144 optimal weight: 0.1980 chunk 25 optimal weight: 8.9990 chunk 103 optimal weight: 9.9990 chunk 164 optimal weight: 3.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 HIS B 243 ASN C 281 GLN ** D 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 410 GLN ** E 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 35 GLN ** F 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 0.3798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 24252 Z= 0.180 Angle : 0.667 12.395 32940 Z= 0.318 Chirality : 0.043 0.193 3848 Planarity : 0.004 0.085 4404 Dihedral : 9.352 169.639 3585 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 14.71 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.61 % Favored : 89.36 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.20 % 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: -3.66 (0.15), residues: 2640 helix: -2.06 (0.14), residues: 1180 sheet: -2.53 (0.29), residues: 273 loop : -2.71 (0.17), residues: 1187 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 296 time to evaluate : 2.940 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: 0 outliers final: 0 residues processed: 296 average time/residue: 0.3653 time to fit residues: 170.6902 Evaluate side-chains 221 residues out of total 2252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 221 time to evaluate : 2.839 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.7641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 301 optimal weight: 10.0000 chunk 35 optimal weight: 6.9990 chunk 178 optimal weight: 3.9990 chunk 228 optimal weight: 9.9990 chunk 176 optimal weight: 6.9990 chunk 263 optimal weight: 30.0000 chunk 174 optimal weight: 20.0000 chunk 311 optimal weight: 40.0000 chunk 194 optimal weight: 0.9990 chunk 189 optimal weight: 0.0970 chunk 143 optimal weight: 5.9990 overall best weight: 3.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 HIS A 456 GLN B 243 ASN ** B 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 425 HIS ** D 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 441 GLN D 456 GLN ** E 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 334 HIS ** E 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 410 GLN F 425 HIS ** F 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.3837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 24252 Z= 0.272 Angle : 0.724 11.166 32940 Z= 0.350 Chirality : 0.045 0.205 3848 Planarity : 0.005 0.081 4404 Dihedral : 9.552 170.503 3585 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 17.31 Ramachandran Plot: Outliers : 0.04 % Allowed : 12.65 % Favored : 87.31 % Rotamer Outliers : 0.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.28 % 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: -3.67 (0.15), residues: 2640 helix: -2.06 (0.14), residues: 1184 sheet: -2.69 (0.28), residues: 274 loop : -2.68 (0.18), residues: 1182 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 278 time to evaluate : 3.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 279 average time/residue: 0.3484 time to fit residues: 155.9120 Evaluate side-chains 207 residues out of total 2252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 207 time to evaluate : 2.831 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.7700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 192 optimal weight: 3.9990 chunk 124 optimal weight: 7.9990 chunk 185 optimal weight: 0.8980 chunk 93 optimal weight: 0.1980 chunk 61 optimal weight: 6.9990 chunk 60 optimal weight: 0.9980 chunk 197 optimal weight: 4.9990 chunk 212 optimal weight: 0.9990 chunk 153 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 244 optimal weight: 10.0000 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 334 HIS ** B 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 399 ASN D 201 HIS ** D 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 441 GLN ** E 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 252 GLN ** E 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.4157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.092 24252 Z= 0.166 Angle : 0.658 11.464 32940 Z= 0.315 Chirality : 0.042 0.179 3848 Planarity : 0.005 0.112 4404 Dihedral : 9.176 169.483 3585 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.96 % Favored : 90.00 % Rotamer Outliers : 0.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.20 % 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: -3.41 (0.16), residues: 2640 helix: -1.84 (0.14), residues: 1199 sheet: -2.43 (0.29), residues: 278 loop : -2.58 (0.18), residues: 1163 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 290 time to evaluate : 2.764 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 revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 291 average time/residue: 0.3444 time to fit residues: 161.5388 Evaluate side-chains 214 residues out of total 2252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 214 time to evaluate : 3.000 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.6270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 283 optimal weight: 40.0000 chunk 298 optimal weight: 20.0000 chunk 272 optimal weight: 30.0000 chunk 290 optimal weight: 10.0000 chunk 174 optimal weight: 30.0000 chunk 126 optimal weight: 9.9990 chunk 227 optimal weight: 9.9990 chunk 89 optimal weight: 1.9990 chunk 262 optimal weight: 6.9990 chunk 274 optimal weight: 30.0000 chunk 289 optimal weight: 9.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 HIS A 76 GLN A 150 GLN ** A 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 334 HIS A 456 GLN ** B 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 376 ASN B 441 GLN ** B 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 425 HIS D 456 GLN E 76 GLN ** E 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 243 ASN ** F 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.4096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.077 24252 Z= 0.518 Angle : 0.937 10.589 32940 Z= 0.461 Chirality : 0.051 0.230 3848 Planarity : 0.006 0.093 4404 Dihedral : 10.277 175.833 3585 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 23.55 Ramachandran Plot: Outliers : 0.08 % Allowed : 15.04 % Favored : 84.89 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.24 % 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: -3.97 (0.15), residues: 2640 helix: -2.28 (0.13), residues: 1183 sheet: -3.08 (0.27), residues: 269 loop : -2.81 (0.17), residues: 1188 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 240 time to evaluate : 2.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 240 average time/residue: 0.3375 time to fit residues: 130.5665 Evaluate side-chains 191 residues out of total 2252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 191 time to evaluate : 2.609 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.3380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 190 optimal weight: 4.9990 chunk 306 optimal weight: 20.0000 chunk 187 optimal weight: 3.9990 chunk 145 optimal weight: 0.6980 chunk 213 optimal weight: 1.9990 chunk 321 optimal weight: 20.0000 chunk 296 optimal weight: 20.0000 chunk 256 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 197 optimal weight: 0.0470 chunk 157 optimal weight: 6.9990 overall best weight: 2.1484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 ASN A 334 HIS B 243 ASN ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 441 GLN ** D 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 427 ASN ** E 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 247 ASN F 346 GLN ** F 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.4267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.060 24252 Z= 0.217 Angle : 0.720 11.423 32940 Z= 0.345 Chirality : 0.044 0.180 3848 Planarity : 0.005 0.086 4404 Dihedral : 9.713 179.758 3585 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 16.76 Ramachandran Plot: Outliers : 0.08 % Allowed : 11.25 % Favored : 88.67 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -3.55 (0.15), residues: 2640 helix: -1.88 (0.14), residues: 1182 sheet: -2.73 (0.29), residues: 268 loop : -2.70 (0.17), residues: 1190 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 2252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 267 time to evaluate : 3.088 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: 0 outliers final: 0 residues processed: 267 average time/residue: 0.3539 time to fit residues: 153.0984 Evaluate side-chains 203 residues out of total 2252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 203 time to evaluate : 2.955 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.9439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 203 optimal weight: 0.8980 chunk 272 optimal weight: 30.0000 chunk 78 optimal weight: 9.9990 chunk 236 optimal weight: 8.9990 chunk 37 optimal weight: 9.9990 chunk 71 optimal weight: 7.9990 chunk 256 optimal weight: 10.0000 chunk 107 optimal weight: 6.9990 chunk 263 optimal weight: 40.0000 chunk 32 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 ASN A 334 HIS A 456 GLN B 243 ASN ** B 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 456 GLN ** E 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.114715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.097858 restraints weight = 65473.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.097548 restraints weight = 60747.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.098447 restraints weight = 59378.228| |-----------------------------------------------------------------------------| r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.4322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.055 24252 Z= 0.306 Angle : 0.767 11.053 32940 Z= 0.372 Chirality : 0.046 0.176 3848 Planarity : 0.005 0.084 4404 Dihedral : 9.794 178.986 3585 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 18.66 Ramachandran Plot: Outliers : 0.04 % Allowed : 13.98 % Favored : 85.98 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -3.60 (0.15), residues: 2640 helix: -1.85 (0.14), residues: 1187 sheet: -2.81 (0.29), residues: 267 loop : -2.80 (0.17), residues: 1186 =============================================================================== Job complete usr+sys time: 4007.75 seconds wall clock time: 74 minutes 21.71 seconds (4461.71 seconds total)