Starting phenix.real_space_refine on Wed Dec 13 06:29:05 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bbm_7076/12_2023/6bbm_7076_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bbm_7076/12_2023/6bbm_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_7076/12_2023/6bbm_7076.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bbm_7076/12_2023/6bbm_7076.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bbm_7076/12_2023/6bbm_7076_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bbm_7076/12_2023/6bbm_7076_updated.pdb" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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 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. 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: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 12.93, per 1000 atoms: 0.54 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: 10.26 Conformation dependent library (CDL) restraints added in 3.9 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: 4.93 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: 6.90 Time building geometry restraints manager: 10.88 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 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: 1.180 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: 5.300 Check model and map are aligned: 0.390 Set scattering table: 0.230 Process input model: 61.880 Find NCS groups from input model: 2.000 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 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 : 9.86 Ramachandran Plot: Outliers : 0.19 % Allowed : 13.75 % Favored : 86.06 % Rotamer: Outliers : 0.58 % Allowed : 11.95 % Favored : 87.47 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP D 457 HIS 0.009 0.002 HIS A 29 PHE 0.031 0.003 PHE D 259 TYR 0.029 0.002 TYR D 344 ARG 0.012 0.001 ARG B 152 *********************** 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 : 2.775 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: 0.4522 time to fit residues: 250.4131 Evaluate side-chains 232 residues out of total 2252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 227 time to evaluate : 2.689 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2211 time to fit residues: 5.7547 ------------------------------------------------------------------------------- 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 ** 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 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 243 ASN D 247 ASN D 410 GLN D 441 GLN ** E 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 425 HIS 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: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 24252 Z= 0.195 Angle : 0.740 11.651 32940 Z= 0.361 Chirality : 0.044 0.181 3848 Planarity : 0.005 0.108 4404 Dihedral : 10.593 170.482 3585 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 15.44 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.85 % Favored : 90.00 % Rotamer: Outliers : 0.09 % Allowed : 5.86 % Favored : 94.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.35 % 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: -5.17 (0.13), residues: 2640 helix: -3.60 (0.10), residues: 1167 sheet: -3.37 (0.26), residues: 265 loop : -3.15 (0.16), residues: 1208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 294 HIS 0.005 0.001 HIS E 425 PHE 0.019 0.001 PHE C 460 TYR 0.025 0.001 TYR D 344 ARG 0.005 0.001 ARG D 129 *********************** 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 337 residues out of total 2252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 335 time to evaluate : 2.823 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: 2 outliers final: 1 residues processed: 336 average time/residue: 0.4301 time to fit residues: 216.6440 Evaluate side-chains 222 residues out of total 2252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 221 time to evaluate : 2.643 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.2297 time to fit residues: 3.8627 ------------------------------------------------------------------------------- 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: 4.9990 chunk 91 optimal weight: 10.0000 chunk 244 optimal weight: 4.9990 chunk 199 optimal weight: 5.9990 chunk 80 optimal weight: 9.9990 chunk 293 optimal weight: 10.0000 chunk 317 optimal weight: 10.0000 chunk 261 optimal weight: 10.0000 chunk 291 optimal weight: 10.0000 chunk 100 optimal weight: 6.9990 chunk 235 optimal weight: 6.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN ** A 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 456 GLN B 288 GLN B 399 ASN ** B 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 425 HIS C 441 GLN D 198 GLN ** D 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 441 GLN E 112 ASN E 334 HIS E 410 GLN ** E 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 425 HIS F 441 GLN ** F 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 24252 Z= 0.410 Angle : 0.856 11.781 32940 Z= 0.423 Chirality : 0.048 0.194 3848 Planarity : 0.006 0.103 4404 Dihedral : 10.876 179.626 3585 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 20.97 Ramachandran Plot: Outliers : 0.15 % Allowed : 14.05 % Favored : 85.80 % Rotamer: Outliers : 0.18 % Allowed : 6.71 % Favored : 93.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.35 % 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: -4.83 (0.14), residues: 2640 helix: -3.15 (0.12), residues: 1168 sheet: -3.32 (0.28), residues: 257 loop : -3.15 (0.16), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 294 HIS 0.009 0.002 HIS B 67 PHE 0.023 0.002 PHE C 460 TYR 0.026 0.002 TYR C 344 ARG 0.010 0.001 ARG F 93 *********************** 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 283 residues out of total 2252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 279 time to evaluate : 3.056 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 282 average time/residue: 0.3907 time to fit residues: 169.8809 Evaluate side-chains 213 residues out of total 2252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 212 time to evaluate : 2.515 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2074 time to fit residues: 3.8572 ------------------------------------------------------------------------------- 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: 3.9990 chunk 152 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 chunk 140 optimal weight: 5.9990 chunk 197 optimal weight: 6.9990 chunk 294 optimal weight: 20.0000 chunk 312 optimal weight: 10.0000 chunk 154 optimal weight: 7.9990 chunk 279 optimal weight: 20.0000 chunk 84 optimal weight: 0.0870 overall best weight: 4.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 334 HIS A 456 GLN ** B 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 45 ASN ** D 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 441 GLN D 456 GLN ** E 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 252 GLN ** E 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 76 GLN F 399 ASN ** F 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.3151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 24252 Z= 0.314 Angle : 0.785 12.036 32940 Z= 0.384 Chirality : 0.047 0.237 3848 Planarity : 0.005 0.099 4404 Dihedral : 10.552 178.806 3585 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 18.48 Ramachandran Plot: Outliers : 0.11 % Allowed : 12.69 % Favored : 87.20 % Rotamer: Outliers : 0.09 % Allowed : 4.93 % Favored : 94.98 % 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: -4.48 (0.14), residues: 2640 helix: -2.81 (0.13), residues: 1153 sheet: -3.19 (0.28), residues: 258 loop : -3.02 (0.17), residues: 1229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP F 48 HIS 0.005 0.001 HIS E 67 PHE 0.027 0.002 PHE D 259 TYR 0.025 0.002 TYR D 344 ARG 0.010 0.001 ARG B 366 *********************** 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 287 residues out of total 2252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 285 time to evaluate : 2.805 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: 2 outliers final: 0 residues processed: 286 average time/residue: 0.3784 time to fit residues: 171.6175 Evaluate side-chains 198 residues out of total 2252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 198 time to evaluate : 2.599 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.4523 ------------------------------------------------------------------------------- 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: 0.6980 chunk 177 optimal weight: 7.9990 chunk 4 optimal weight: 30.0000 chunk 232 optimal weight: 10.0000 chunk 128 optimal weight: 6.9990 chunk 266 optimal weight: 30.0000 chunk 215 optimal weight: 0.0050 chunk 0 optimal weight: 40.0000 chunk 159 optimal weight: 0.0030 chunk 280 optimal weight: 20.0000 chunk 78 optimal weight: 0.0060 overall best weight: 1.5422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 ASN A 243 ASN A 281 GLN A 334 HIS A 410 GLN ** B 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 243 ASN ** C 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 441 GLN ** D 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 410 GLN ** E 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 456 GLN F 247 ASN F 281 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.3533 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= 0.176 Angle : 0.689 12.237 32940 Z= 0.332 Chirality : 0.043 0.195 3848 Planarity : 0.005 0.095 4404 Dihedral : 9.929 179.215 3585 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 14.91 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.87 % Favored : 89.09 % Rotamer: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % 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: -2.29 (0.14), residues: 1138 sheet: -2.98 (0.28), residues: 264 loop : -2.81 (0.17), residues: 1238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP D 48 HIS 0.004 0.001 HIS C 201 PHE 0.019 0.001 PHE D 259 TYR 0.020 0.001 TYR A 105 ARG 0.007 0.001 ARG A 349 *********************** 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 311 residues out of total 2252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 311 time to evaluate : 2.612 Fit side-chains 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: 311 average time/residue: 0.3697 time to fit residues: 179.7988 Evaluate side-chains 220 residues out of total 2252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 220 time to evaluate : 2.694 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.5811 ------------------------------------------------------------------------------- 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: 9.9990 chunk 61 optimal weight: 7.9990 chunk 183 optimal weight: 10.0000 chunk 77 optimal weight: 7.9990 chunk 312 optimal weight: 10.0000 chunk 259 optimal weight: 0.0070 chunk 144 optimal weight: 9.9990 chunk 25 optimal weight: 0.8980 chunk 103 optimal weight: 9.9990 chunk 164 optimal weight: 9.9990 overall best weight: 5.3804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 ASN ** A 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 334 HIS A 456 GLN ** B 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 243 ASN C 386 ASN ** D 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 118 ASN F 243 ASN ** 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: 0.7443 moved from start: 0.3649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 24252 Z= 0.374 Angle : 0.816 11.591 32940 Z= 0.399 Chirality : 0.048 0.252 3848 Planarity : 0.005 0.092 4404 Dihedral : 10.312 178.261 3585 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 20.35 Ramachandran Plot: Outliers : 0.11 % Allowed : 14.32 % Favored : 85.57 % Rotamer: Outliers : 0.09 % Allowed : 3.60 % Favored : 96.31 % 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: -4.13 (0.15), residues: 2640 helix: -2.42 (0.14), residues: 1163 sheet: -3.23 (0.27), residues: 267 loop : -2.88 (0.17), residues: 1210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP F 457 HIS 0.007 0.001 HIS C 29 PHE 0.021 0.002 PHE B 166 TYR 0.022 0.002 TYR E 344 ARG 0.008 0.001 ARG C 172 *********************** 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 272 residues out of total 2252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 270 time to evaluate : 2.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 271 average time/residue: 0.3391 time to fit residues: 150.1141 Evaluate side-chains 203 residues out of total 2252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 203 time to evaluate : 2.504 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.2636 ------------------------------------------------------------------------------- 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: 9.9990 chunk 35 optimal weight: 1.9990 chunk 178 optimal weight: 2.9990 chunk 228 optimal weight: 7.9990 chunk 176 optimal weight: 0.6980 chunk 263 optimal weight: 30.0000 chunk 174 optimal weight: 0.8980 chunk 311 optimal weight: 30.0000 chunk 194 optimal weight: 2.9990 chunk 189 optimal weight: 6.9990 chunk 143 optimal weight: 0.6980 overall best weight: 1.4584 ------------------------------------------------------------------------------- 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** ** B 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 243 ASN ** C 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 399 ASN ** E 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 252 GLN ** E 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 386 ASN ** E 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7287 moved from start: 0.3939 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= 0.178 Angle : 0.691 11.687 32940 Z= 0.332 Chirality : 0.044 0.285 3848 Planarity : 0.004 0.087 4404 Dihedral : 9.741 179.313 3585 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 15.59 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.27 % Favored : 89.66 % Rotamer: Outliers : 0.04 % Allowed : 1.55 % Favored : 98.40 % 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: -3.63 (0.15), residues: 2640 helix: -1.97 (0.15), residues: 1131 sheet: -2.85 (0.29), residues: 264 loop : -2.67 (0.17), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP F 457 HIS 0.004 0.001 HIS B 29 PHE 0.018 0.001 PHE D 259 TYR 0.021 0.001 TYR A 105 ARG 0.005 0.000 ARG D 366 *********************** 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 301 residues out of total 2252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 300 time to evaluate : 2.611 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: 301 average time/residue: 0.3623 time to fit residues: 175.0896 Evaluate side-chains 216 residues out of total 2252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 216 time to evaluate : 2.468 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.2486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 61.3032 > 50: distance: 36 - 40: 28.355 distance: 40 - 41: 26.864 distance: 41 - 42: 8.896 distance: 41 - 44: 26.123 distance: 42 - 43: 25.867 distance: 42 - 49: 23.685 distance: 44 - 45: 13.437 distance: 45 - 46: 9.979 distance: 46 - 47: 16.822 distance: 47 - 48: 15.139 distance: 49 - 50: 13.670 distance: 50 - 51: 18.619 distance: 50 - 53: 16.254 distance: 51 - 52: 38.062 distance: 51 - 56: 30.418 distance: 53 - 54: 14.759 distance: 53 - 55: 23.804 distance: 56 - 57: 29.397 distance: 57 - 58: 13.928 distance: 57 - 60: 14.024 distance: 58 - 59: 34.471 distance: 58 - 61: 33.828 distance: 61 - 62: 40.190 distance: 62 - 63: 14.131 distance: 63 - 64: 8.793 distance: 63 - 65: 25.625 distance: 65 - 66: 40.660 distance: 66 - 67: 37.298 distance: 66 - 69: 41.511 distance: 67 - 68: 44.098 distance: 67 - 73: 45.896 distance: 69 - 70: 42.918 distance: 70 - 71: 28.434 distance: 70 - 72: 21.770 distance: 73 - 74: 4.205 distance: 74 - 75: 10.130 distance: 74 - 77: 42.963 distance: 75 - 76: 45.596 distance: 75 - 82: 24.116 distance: 77 - 78: 39.970 distance: 78 - 79: 8.821 distance: 79 - 80: 20.290 distance: 79 - 81: 18.690 distance: 82 - 83: 11.305 distance: 82 - 88: 11.739 distance: 83 - 84: 37.949 distance: 83 - 86: 17.601 distance: 84 - 85: 31.101 distance: 84 - 89: 9.717 distance: 86 - 87: 28.721 distance: 87 - 88: 14.822 distance: 89 - 90: 32.207 distance: 90 - 91: 14.704 distance: 90 - 93: 22.414 distance: 91 - 92: 15.768 distance: 91 - 95: 21.863 distance: 93 - 94: 9.985 distance: 95 - 96: 18.913 distance: 96 - 97: 18.861 distance: 96 - 99: 30.612 distance: 97 - 98: 21.504 distance: 97 - 103: 17.779 distance: 99 - 100: 9.666 distance: 100 - 101: 19.505 distance: 100 - 102: 25.962 distance: 103 - 104: 13.458 distance: 104 - 105: 17.780 distance: 104 - 107: 11.265 distance: 105 - 106: 13.024 distance: 105 - 111: 7.895 distance: 107 - 108: 15.996 distance: 108 - 109: 33.847 distance: 108 - 110: 3.005 distance: 119 - 180: 3.512