Starting phenix.real_space_refine on Mon Feb 19 15:38:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vfg_31952/02_2024/7vfg_31952.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vfg_31952/02_2024/7vfg_31952.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vfg_31952/02_2024/7vfg_31952.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vfg_31952/02_2024/7vfg_31952.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vfg_31952/02_2024/7vfg_31952.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vfg_31952/02_2024/7vfg_31952.pdb" } resolution = 3.87 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= 1.000 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: 4 Type Number sf(0) Gaussians S 78 5.16 5 C 16032 2.51 5 N 4074 2.21 5 O 4860 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E ASP 25": "OD1" <-> "OD2" Residue "E GLU 77": "OE1" <-> "OE2" Residue "E GLU 109": "OE1" <-> "OE2" Residue "E TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 311": "OE1" <-> "OE2" Residue "E GLU 314": "OE1" <-> "OE2" Residue "E GLU 444": "OE1" <-> "OE2" Residue "E GLU 465": "OE1" <-> "OE2" Residue "E TYR 519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 520": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 57": "OE1" <-> "OE2" Residue "F GLU 109": "OE1" <-> "OE2" Residue "F GLU 114": "OE1" <-> "OE2" Residue "F GLU 200": "OE1" <-> "OE2" Residue "F GLU 205": "OE1" <-> "OE2" Residue "F GLU 230": "OE1" <-> "OE2" Residue "F GLU 465": "OE1" <-> "OE2" Residue "F TYR 519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 150": "OE1" <-> "OE2" Residue "D GLU 165": "OE1" <-> "OE2" Residue "D GLU 248": "OE1" <-> "OE2" Residue "D GLU 314": "OE1" <-> "OE2" Residue "D GLU 465": "OE1" <-> "OE2" Residue "C GLU 77": "OE1" <-> "OE2" Residue "C GLU 109": "OE1" <-> "OE2" Residue "C TYR 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 311": "OE1" <-> "OE2" Residue "C GLU 314": "OE1" <-> "OE2" Residue "C GLU 444": "OE1" <-> "OE2" Residue "C GLU 465": "OE1" <-> "OE2" Residue "C TYR 519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 520": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 57": "OE1" <-> "OE2" Residue "A GLU 109": "OE1" <-> "OE2" Residue "A GLU 114": "OE1" <-> "OE2" Residue "A GLU 200": "OE1" <-> "OE2" Residue "A GLU 205": "OE1" <-> "OE2" Residue "A GLU 230": "OE1" <-> "OE2" Residue "A GLU 465": "OE1" <-> "OE2" Residue "A TYR 519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 150": "OE1" <-> "OE2" Residue "B GLU 165": "OE1" <-> "OE2" Residue "B GLU 248": "OE1" <-> "OE2" Residue "B GLU 314": "OE1" <-> "OE2" Residue "B GLU 465": "OE1" <-> "OE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 25044 Number of models: 1 Model: "" Number of chains: 6 Chain: "E" Number of atoms: 4174 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 527, 4160 Classifications: {'peptide': 527} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 25, 'TRANS': 501} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'GLN:plan1': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 28 Conformer: "B" Number of residues, atoms: 527, 4168 Classifications: {'peptide': 527} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 25, 'TRANS': 501} Chain breaks: 1 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 21 bond proxies already assigned to first conformer: 4243 Chain: "F" Number of atoms: 4174 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 527, 4160 Classifications: {'peptide': 527} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 25, 'TRANS': 501} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'GLN:plan1': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 28 Conformer: "B" Number of residues, atoms: 527, 4168 Classifications: {'peptide': 527} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 25, 'TRANS': 501} Chain breaks: 1 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 21 bond proxies already assigned to first conformer: 4243 Chain: "D" Number of atoms: 4174 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 527, 4160 Classifications: {'peptide': 527} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 25, 'TRANS': 501} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'GLN:plan1': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 28 Conformer: "B" Number of residues, atoms: 527, 4168 Classifications: {'peptide': 527} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 25, 'TRANS': 501} Chain breaks: 1 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 21 bond proxies already assigned to first conformer: 4243 Chain: "C" Number of atoms: 4174 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 527, 4160 Classifications: {'peptide': 527} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 25, 'TRANS': 501} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'GLN:plan1': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 28 Conformer: "B" Number of residues, atoms: 527, 4168 Classifications: {'peptide': 527} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 25, 'TRANS': 501} Chain breaks: 1 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 21 bond proxies already assigned to first conformer: 4243 Chain: "A" Number of atoms: 4174 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 527, 4160 Classifications: {'peptide': 527} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 25, 'TRANS': 501} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'GLN:plan1': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 28 Conformer: "B" Number of residues, atoms: 527, 4168 Classifications: {'peptide': 527} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 25, 'TRANS': 501} Chain breaks: 1 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 21 bond proxies already assigned to first conformer: 4243 Chain: "B" Number of atoms: 4174 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 527, 4160 Classifications: {'peptide': 527} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 25, 'TRANS': 501} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'GLN:plan1': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 28 Conformer: "B" Number of residues, atoms: 527, 4168 Classifications: {'peptide': 527} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 25, 'TRANS': 501} Chain breaks: 1 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 21 bond proxies already assigned to first conformer: 4243 Residues with excluded nonbonded symmetry interactions: 6 residue: pdb=" N ACYS E 94 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS E 94 " occ=0.50 residue: pdb=" N ACYS F 94 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS F 94 " occ=0.50 residue: pdb=" N ACYS D 94 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS D 94 " occ=0.50 residue: pdb=" N ACYS C 94 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS C 94 " occ=0.50 residue: pdb=" N ACYS A 94 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS A 94 " occ=0.50 residue: pdb=" N ACYS B 94 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS B 94 " occ=0.50 Time building chain proxies: 25.61, per 1000 atoms: 1.02 Number of scatterers: 25044 At special positions: 0 Unit cell: (178.08, 110.88, 106.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 78 16.00 O 4860 8.00 N 4074 7.00 C 16032 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.84 Conformation dependent library (CDL) restraints added in 9.6 seconds 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6036 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 72 sheets defined 19.8% alpha, 42.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.35 Creating SS restraints... Processing helix chain 'E' and resid 89 through 94 Processing helix chain 'E' and resid 112 through 119 Processing helix chain 'E' and resid 122 through 129 Processing helix chain 'E' and resid 132 through 137 Processing helix chain 'E' and resid 160 through 164 removed outlier: 3.553A pdb=" N ASP E 163 " --> pdb=" O THR E 160 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N VAL E 164 " --> pdb=" O PRO E 161 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 160 through 164' Processing helix chain 'E' and resid 165 through 170 removed outlier: 3.621A pdb=" N SER E 170 " --> pdb=" O THR E 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 186 through 189 Processing helix chain 'E' and resid 198 through 206 Processing helix chain 'E' and resid 279 through 295 removed outlier: 4.037A pdb=" N ASP E 293 " --> pdb=" O SER E 289 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ASP E 294 " --> pdb=" O ARG E 290 " (cutoff:3.500A) Processing helix chain 'E' and resid 389 through 394 removed outlier: 3.797A pdb=" N THR E 393 " --> pdb=" O ASN E 389 " (cutoff:3.500A) Processing helix chain 'E' and resid 396 through 401 removed outlier: 4.042A pdb=" N TRP E 400 " --> pdb=" O PRO E 396 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N THR E 401 " --> pdb=" O VAL E 397 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 396 through 401' Processing helix chain 'E' and resid 413 through 418 Processing helix chain 'E' and resid 458 through 469 Processing helix chain 'E' and resid 495 through 499 Processing helix chain 'E' and resid 516 through 521 Processing helix chain 'F' and resid 89 through 94 Processing helix chain 'F' and resid 112 through 119 Processing helix chain 'F' and resid 122 through 129 Processing helix chain 'F' and resid 132 through 137 Processing helix chain 'F' and resid 160 through 164 removed outlier: 3.894A pdb=" N VAL F 164 " --> pdb=" O PRO F 161 " (cutoff:3.500A) Processing helix chain 'F' and resid 186 through 189 Processing helix chain 'F' and resid 198 through 206 Processing helix chain 'F' and resid 279 through 295 removed outlier: 4.162A pdb=" N ASP F 293 " --> pdb=" O SER F 289 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ASP F 294 " --> pdb=" O ARG F 290 " (cutoff:3.500A) Processing helix chain 'F' and resid 389 through 394 removed outlier: 3.821A pdb=" N THR F 393 " --> pdb=" O ASN F 389 " (cutoff:3.500A) Processing helix chain 'F' and resid 396 through 401 removed outlier: 4.161A pdb=" N TRP F 400 " --> pdb=" O PRO F 396 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N THR F 401 " --> pdb=" O VAL F 397 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 396 through 401' Processing helix chain 'F' and resid 413 through 418 Processing helix chain 'F' and resid 458 through 469 Processing helix chain 'F' and resid 516 through 521 Processing helix chain 'D' and resid 89 through 94 Processing helix chain 'D' and resid 112 through 119 Processing helix chain 'D' and resid 122 through 129 Processing helix chain 'D' and resid 132 through 137 Processing helix chain 'D' and resid 160 through 164 removed outlier: 3.882A pdb=" N VAL D 164 " --> pdb=" O PRO D 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 186 through 189 Processing helix chain 'D' and resid 198 through 206 Processing helix chain 'D' and resid 279 through 295 removed outlier: 4.271A pdb=" N ASP D 293 " --> pdb=" O SER D 289 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N ASP D 294 " --> pdb=" O ARG D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 394 removed outlier: 3.871A pdb=" N THR D 393 " --> pdb=" O ASN D 389 " (cutoff:3.500A) Processing helix chain 'D' and resid 396 through 401 removed outlier: 4.108A pdb=" N TRP D 400 " --> pdb=" O PRO D 396 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N THR D 401 " --> pdb=" O VAL D 397 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 396 through 401' Processing helix chain 'D' and resid 413 through 418 Processing helix chain 'D' and resid 458 through 469 Processing helix chain 'D' and resid 495 through 499 Processing helix chain 'D' and resid 516 through 521 Processing helix chain 'C' and resid 89 through 94 Processing helix chain 'C' and resid 112 through 119 Processing helix chain 'C' and resid 122 through 129 Processing helix chain 'C' and resid 132 through 137 Processing helix chain 'C' and resid 160 through 164 removed outlier: 3.553A pdb=" N ASP C 163 " --> pdb=" O THR C 160 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N VAL C 164 " --> pdb=" O PRO C 161 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 160 through 164' Processing helix chain 'C' and resid 165 through 170 removed outlier: 3.616A pdb=" N SER C 170 " --> pdb=" O THR C 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 189 Processing helix chain 'C' and resid 198 through 206 Processing helix chain 'C' and resid 279 through 295 removed outlier: 4.038A pdb=" N ASP C 293 " --> pdb=" O SER C 289 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N ASP C 294 " --> pdb=" O ARG C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 389 through 394 removed outlier: 3.795A pdb=" N THR C 393 " --> pdb=" O ASN C 389 " (cutoff:3.500A) Processing helix chain 'C' and resid 396 through 401 removed outlier: 4.040A pdb=" N TRP C 400 " --> pdb=" O PRO C 396 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N THR C 401 " --> pdb=" O VAL C 397 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 396 through 401' Processing helix chain 'C' and resid 413 through 418 Processing helix chain 'C' and resid 458 through 469 Processing helix chain 'C' and resid 495 through 499 Processing helix chain 'C' and resid 516 through 521 Processing helix chain 'A' and resid 89 through 94 Processing helix chain 'A' and resid 112 through 119 Processing helix chain 'A' and resid 122 through 129 Processing helix chain 'A' and resid 132 through 137 Processing helix chain 'A' and resid 160 through 164 removed outlier: 3.896A pdb=" N VAL A 164 " --> pdb=" O PRO A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 189 Processing helix chain 'A' and resid 198 through 206 Processing helix chain 'A' and resid 279 through 295 removed outlier: 4.164A pdb=" N ASP A 293 " --> pdb=" O SER A 289 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N ASP A 294 " --> pdb=" O ARG A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 394 removed outlier: 3.819A pdb=" N THR A 393 " --> pdb=" O ASN A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 401 removed outlier: 4.161A pdb=" N TRP A 400 " --> pdb=" O PRO A 396 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N THR A 401 " --> pdb=" O VAL A 397 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 396 through 401' Processing helix chain 'A' and resid 413 through 418 Processing helix chain 'A' and resid 458 through 469 Processing helix chain 'A' and resid 516 through 521 Processing helix chain 'B' and resid 89 through 94 Processing helix chain 'B' and resid 112 through 119 Processing helix chain 'B' and resid 122 through 129 Processing helix chain 'B' and resid 132 through 137 Processing helix chain 'B' and resid 160 through 164 removed outlier: 3.882A pdb=" N VAL B 164 " --> pdb=" O PRO B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 189 Processing helix chain 'B' and resid 198 through 206 Processing helix chain 'B' and resid 279 through 295 removed outlier: 4.268A pdb=" N ASP B 293 " --> pdb=" O SER B 289 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N ASP B 294 " --> pdb=" O ARG B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 394 removed outlier: 3.869A pdb=" N THR B 393 " --> pdb=" O ASN B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 401 removed outlier: 4.106A pdb=" N TRP B 400 " --> pdb=" O PRO B 396 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N THR B 401 " --> pdb=" O VAL B 397 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 396 through 401' Processing helix chain 'B' and resid 413 through 418 Processing helix chain 'B' and resid 458 through 469 Processing helix chain 'B' and resid 495 through 499 Processing helix chain 'B' and resid 516 through 521 Processing sheet with id=AA1, first strand: chain 'E' and resid 32 through 40 removed outlier: 4.231A pdb=" N ILE E 215 " --> pdb=" O HIS E 68 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N HIS E 68 " --> pdb=" O ILE E 215 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N TYR E 217 " --> pdb=" O LEU E 66 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N LEU E 66 " --> pdb=" O TYR E 217 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N LEU E 69 " --> pdb=" O ILE E 158 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER E 152 " --> pdb=" O LEU E 75 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 32 through 40 removed outlier: 4.231A pdb=" N ILE E 215 " --> pdb=" O HIS E 68 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N HIS E 68 " --> pdb=" O ILE E 215 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N TYR E 217 " --> pdb=" O LEU E 66 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N LEU E 66 " --> pdb=" O TYR E 217 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 42 through 44 removed outlier: 6.285A pdb=" N SER E 102 " --> pdb=" O VAL E 106 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N VAL E 106 " --> pdb=" O SER E 102 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 78 through 79 removed outlier: 6.805A pdb=" N VAL E 78 " --> pdb=" O ILE E 148 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 139 through 141 removed outlier: 3.845A pdb=" N GLY E 82 " --> pdb=" O GLY E 141 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 227 through 236 removed outlier: 4.489A pdb=" N GLN E 522 " --> pdb=" O TYR E 262 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASN E 530 " --> pdb=" O SER E 254 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N SER E 254 " --> pdb=" O ASN E 530 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N LEU E 532 " --> pdb=" O ALA E 252 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N ALA E 252 " --> pdb=" O LEU E 532 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA E 252 " --> pdb=" O ILE E 492 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE E 492 " --> pdb=" O ALA E 252 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 475 through 478 removed outlier: 3.827A pdb=" N ARG E 475 " --> pdb=" O VAL E 257 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N ALA E 252 " --> pdb=" O LEU E 532 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N LEU E 532 " --> pdb=" O ALA E 252 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N SER E 254 " --> pdb=" O ASN E 530 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASN E 530 " --> pdb=" O SER E 254 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N GLN E 522 " --> pdb=" O TYR E 262 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 243 through 246 removed outlier: 3.669A pdb=" N ARG E 442 " --> pdb=" O VAL E 508 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TYR E 453 " --> pdb=" O VAL E 445 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N PHE E 447 " --> pdb=" O VAL E 451 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N VAL E 451 " --> pdb=" O PHE E 447 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 269 through 270 Processing sheet with id=AB1, first strand: chain 'E' and resid 296 through 299 removed outlier: 3.542A pdb=" N SER E 299 " --> pdb=" O SER E 340 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER E 340 " --> pdb=" O SER E 299 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 320 through 323 removed outlier: 5.066A pdb=" N SER E 366 " --> pdb=" O ASP E 327 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N PHE E 365 " --> pdb=" O HIS E 386 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N HIS E 386 " --> pdb=" O PHE E 365 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ALA E 367 " --> pdb=" O ILE E 384 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N ILE E 384 " --> pdb=" O ALA E 367 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N THR E 369 " --> pdb=" O ALA E 382 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG E 378 " --> pdb=" O SER E 373 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 349 through 350 Processing sheet with id=AB4, first strand: chain 'F' and resid 32 through 40 removed outlier: 4.258A pdb=" N ILE F 215 " --> pdb=" O HIS F 68 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N HIS F 68 " --> pdb=" O ILE F 215 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N TYR F 217 " --> pdb=" O LEU F 66 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N LEU F 66 " --> pdb=" O TYR F 217 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N LEU F 69 " --> pdb=" O ILE F 158 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER F 152 " --> pdb=" O LEU F 75 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 32 through 40 removed outlier: 4.258A pdb=" N ILE F 215 " --> pdb=" O HIS F 68 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N HIS F 68 " --> pdb=" O ILE F 215 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N TYR F 217 " --> pdb=" O LEU F 66 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N LEU F 66 " --> pdb=" O TYR F 217 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 42 through 44 removed outlier: 7.228A pdb=" N ASN F 96 " --> pdb=" O GLU F 111 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N GLU F 111 " --> pdb=" O ASN F 96 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N VAL F 98 " --> pdb=" O GLU F 109 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N GLU F 109 " --> pdb=" O VAL F 98 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ILE F 100 " --> pdb=" O ILE F 107 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 78 through 79 removed outlier: 6.924A pdb=" N VAL F 78 " --> pdb=" O ILE F 148 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 139 through 141 removed outlier: 3.757A pdb=" N GLY F 82 " --> pdb=" O GLY F 141 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 227 through 236 removed outlier: 3.543A pdb=" N SER F 227 " --> pdb=" O VAL F 535 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL F 535 " --> pdb=" O SER F 227 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASN F 530 " --> pdb=" O SER F 254 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N SER F 254 " --> pdb=" O ASN F 530 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N LEU F 532 " --> pdb=" O ALA F 252 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N ALA F 252 " --> pdb=" O LEU F 532 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 475 through 478 removed outlier: 3.900A pdb=" N ARG F 475 " --> pdb=" O VAL F 257 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N ALA F 252 " --> pdb=" O LEU F 532 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N LEU F 532 " --> pdb=" O ALA F 252 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N SER F 254 " --> pdb=" O ASN F 530 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASN F 530 " --> pdb=" O SER F 254 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 243 through 246 removed outlier: 3.591A pdb=" N ARG F 442 " --> pdb=" O VAL F 508 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU F 443 " --> pdb=" O GLU F 455 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TYR F 453 " --> pdb=" O VAL F 445 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N PHE F 447 " --> pdb=" O VAL F 451 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N VAL F 451 " --> pdb=" O PHE F 447 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 269 through 270 Processing sheet with id=AC4, first strand: chain 'F' and resid 296 through 299 removed outlier: 3.704A pdb=" N SER F 299 " --> pdb=" O SER F 340 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N SER F 340 " --> pdb=" O SER F 299 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 320 through 323 removed outlier: 6.554A pdb=" N ASP F 327 " --> pdb=" O SER F 366 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N ILE F 368 " --> pdb=" O ASP F 327 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N TYR F 329 " --> pdb=" O ILE F 368 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N GLY F 370 " --> pdb=" O TYR F 329 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N LYS F 331 " --> pdb=" O GLY F 370 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N TYR F 372 " --> pdb=" O LYS F 331 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N ASP F 333 " --> pdb=" O TYR F 372 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N PHE F 365 " --> pdb=" O HIS F 386 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N HIS F 386 " --> pdb=" O PHE F 365 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N ALA F 367 " --> pdb=" O ILE F 384 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N ILE F 384 " --> pdb=" O ALA F 367 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N THR F 369 " --> pdb=" O ALA F 382 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ARG F 378 " --> pdb=" O SER F 373 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 349 through 350 Processing sheet with id=AC7, first strand: chain 'D' and resid 32 through 40 removed outlier: 4.441A pdb=" N ILE D 215 " --> pdb=" O HIS D 68 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N HIS D 68 " --> pdb=" O ILE D 215 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N TYR D 217 " --> pdb=" O LEU D 66 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N LEU D 66 " --> pdb=" O TYR D 217 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N LEU D 69 " --> pdb=" O ILE D 158 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N SER D 152 " --> pdb=" O LEU D 75 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 32 through 40 removed outlier: 4.441A pdb=" N ILE D 215 " --> pdb=" O HIS D 68 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N HIS D 68 " --> pdb=" O ILE D 215 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N TYR D 217 " --> pdb=" O LEU D 66 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N LEU D 66 " --> pdb=" O TYR D 217 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 42 through 44 removed outlier: 3.663A pdb=" N ILE D 178 " --> pdb=" O ILE D 58 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ASN D 96 " --> pdb=" O GLU D 111 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N GLU D 111 " --> pdb=" O ASN D 96 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N VAL D 98 " --> pdb=" O GLU D 109 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLU D 109 " --> pdb=" O VAL D 98 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ILE D 100 " --> pdb=" O ILE D 107 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 78 through 79 removed outlier: 6.777A pdb=" N VAL D 78 " --> pdb=" O ILE D 148 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 139 through 141 Processing sheet with id=AD3, first strand: chain 'D' and resid 227 through 236 removed outlier: 3.600A pdb=" N SER D 227 " --> pdb=" O VAL D 535 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASN D 530 " --> pdb=" O SER D 254 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N SER D 254 " --> pdb=" O ASN D 530 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N LEU D 532 " --> pdb=" O ALA D 252 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N ALA D 252 " --> pdb=" O LEU D 532 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA D 252 " --> pdb=" O ILE D 492 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 475 through 478 removed outlier: 3.865A pdb=" N ARG D 475 " --> pdb=" O VAL D 257 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N ALA D 252 " --> pdb=" O LEU D 532 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N LEU D 532 " --> pdb=" O ALA D 252 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N SER D 254 " --> pdb=" O ASN D 530 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASN D 530 " --> pdb=" O SER D 254 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 243 through 246 removed outlier: 3.864A pdb=" N ARG D 442 " --> pdb=" O VAL D 508 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TYR D 453 " --> pdb=" O VAL D 445 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N PHE D 447 " --> pdb=" O VAL D 451 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N VAL D 451 " --> pdb=" O PHE D 447 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 269 through 270 Processing sheet with id=AD7, first strand: chain 'D' and resid 296 through 299 removed outlier: 3.636A pdb=" N SER D 299 " --> pdb=" O SER D 340 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 320 through 323 removed outlier: 6.314A pdb=" N ASP D 327 " --> pdb=" O SER D 366 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N ILE D 368 " --> pdb=" O ASP D 327 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N TYR D 329 " --> pdb=" O ILE D 368 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N GLY D 370 " --> pdb=" O TYR D 329 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LYS D 331 " --> pdb=" O GLY D 370 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N TYR D 372 " --> pdb=" O LYS D 331 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ASP D 333 " --> pdb=" O TYR D 372 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N PHE D 365 " --> pdb=" O HIS D 386 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N HIS D 386 " --> pdb=" O PHE D 365 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N ALA D 367 " --> pdb=" O ILE D 384 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N ILE D 384 " --> pdb=" O ALA D 367 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N THR D 369 " --> pdb=" O ALA D 382 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 349 through 350 Processing sheet with id=AE1, first strand: chain 'C' and resid 32 through 40 removed outlier: 4.234A pdb=" N ILE C 215 " --> pdb=" O HIS C 68 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N HIS C 68 " --> pdb=" O ILE C 215 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N TYR C 217 " --> pdb=" O LEU C 66 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N LEU C 66 " --> pdb=" O TYR C 217 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N LEU C 69 " --> pdb=" O ILE C 158 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SER C 152 " --> pdb=" O LEU C 75 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 32 through 40 removed outlier: 4.234A pdb=" N ILE C 215 " --> pdb=" O HIS C 68 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N HIS C 68 " --> pdb=" O ILE C 215 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N TYR C 217 " --> pdb=" O LEU C 66 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N LEU C 66 " --> pdb=" O TYR C 217 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 42 through 44 removed outlier: 6.285A pdb=" N SER C 102 " --> pdb=" O VAL C 106 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N VAL C 106 " --> pdb=" O SER C 102 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 78 through 79 removed outlier: 6.803A pdb=" N VAL C 78 " --> pdb=" O ILE C 148 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 139 through 141 removed outlier: 3.839A pdb=" N GLY C 82 " --> pdb=" O GLY C 141 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 227 through 236 removed outlier: 4.491A pdb=" N GLN C 522 " --> pdb=" O TYR C 262 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASN C 530 " --> pdb=" O SER C 254 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N SER C 254 " --> pdb=" O ASN C 530 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N LEU C 532 " --> pdb=" O ALA C 252 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N ALA C 252 " --> pdb=" O LEU C 532 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA C 252 " --> pdb=" O ILE C 492 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE C 492 " --> pdb=" O ALA C 252 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 475 through 478 removed outlier: 3.828A pdb=" N ARG C 475 " --> pdb=" O VAL C 257 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N ALA C 252 " --> pdb=" O LEU C 532 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N LEU C 532 " --> pdb=" O ALA C 252 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N SER C 254 " --> pdb=" O ASN C 530 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASN C 530 " --> pdb=" O SER C 254 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N GLN C 522 " --> pdb=" O TYR C 262 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 243 through 246 removed outlier: 3.666A pdb=" N ARG C 442 " --> pdb=" O VAL C 508 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TYR C 453 " --> pdb=" O VAL C 445 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N PHE C 447 " --> pdb=" O VAL C 451 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N VAL C 451 " --> pdb=" O PHE C 447 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 269 through 270 Processing sheet with id=AF1, first strand: chain 'C' and resid 296 through 299 removed outlier: 3.538A pdb=" N SER C 299 " --> pdb=" O SER C 340 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER C 340 " --> pdb=" O SER C 299 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 320 through 323 removed outlier: 5.062A pdb=" N SER C 366 " --> pdb=" O ASP C 327 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N PHE C 365 " --> pdb=" O HIS C 386 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N HIS C 386 " --> pdb=" O PHE C 365 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ALA C 367 " --> pdb=" O ILE C 384 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N ILE C 384 " --> pdb=" O ALA C 367 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N THR C 369 " --> pdb=" O ALA C 382 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG C 378 " --> pdb=" O SER C 373 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 349 through 350 Processing sheet with id=AF4, first strand: chain 'A' and resid 32 through 40 removed outlier: 4.258A pdb=" N ILE A 215 " --> pdb=" O HIS A 68 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N HIS A 68 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N TYR A 217 " --> pdb=" O LEU A 66 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N LEU A 66 " --> pdb=" O TYR A 217 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N LEU A 69 " --> pdb=" O ILE A 158 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER A 152 " --> pdb=" O LEU A 75 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'A' and resid 32 through 40 removed outlier: 4.258A pdb=" N ILE A 215 " --> pdb=" O HIS A 68 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N HIS A 68 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N TYR A 217 " --> pdb=" O LEU A 66 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N LEU A 66 " --> pdb=" O TYR A 217 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'A' and resid 42 through 44 removed outlier: 7.224A pdb=" N ASN A 96 " --> pdb=" O GLU A 111 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N GLU A 111 " --> pdb=" O ASN A 96 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N VAL A 98 " --> pdb=" O GLU A 109 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N GLU A 109 " --> pdb=" O VAL A 98 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ILE A 100 " --> pdb=" O ILE A 107 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'A' and resid 78 through 79 removed outlier: 6.923A pdb=" N VAL A 78 " --> pdb=" O ILE A 148 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'A' and resid 139 through 141 removed outlier: 3.761A pdb=" N GLY A 82 " --> pdb=" O GLY A 141 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'A' and resid 227 through 236 removed outlier: 3.539A pdb=" N SER A 227 " --> pdb=" O VAL A 535 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL A 535 " --> pdb=" O SER A 227 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASN A 530 " --> pdb=" O SER A 254 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N SER A 254 " --> pdb=" O ASN A 530 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N LEU A 532 " --> pdb=" O ALA A 252 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N ALA A 252 " --> pdb=" O LEU A 532 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'A' and resid 475 through 478 removed outlier: 3.900A pdb=" N ARG A 475 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N ALA A 252 " --> pdb=" O LEU A 532 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N LEU A 532 " --> pdb=" O ALA A 252 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N SER A 254 " --> pdb=" O ASN A 530 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASN A 530 " --> pdb=" O SER A 254 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'A' and resid 243 through 246 removed outlier: 3.590A pdb=" N ARG A 442 " --> pdb=" O VAL A 508 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU A 443 " --> pdb=" O GLU A 455 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR A 453 " --> pdb=" O VAL A 445 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N PHE A 447 " --> pdb=" O VAL A 451 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N VAL A 451 " --> pdb=" O PHE A 447 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'A' and resid 269 through 270 Processing sheet with id=AG4, first strand: chain 'A' and resid 296 through 299 removed outlier: 3.702A pdb=" N SER A 299 " --> pdb=" O SER A 340 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N SER A 340 " --> pdb=" O SER A 299 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'A' and resid 320 through 323 removed outlier: 6.562A pdb=" N ASP A 327 " --> pdb=" O SER A 366 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N ILE A 368 " --> pdb=" O ASP A 327 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N TYR A 329 " --> pdb=" O ILE A 368 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N GLY A 370 " --> pdb=" O TYR A 329 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N LYS A 331 " --> pdb=" O GLY A 370 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N TYR A 372 " --> pdb=" O LYS A 331 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N ASP A 333 " --> pdb=" O TYR A 372 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N PHE A 365 " --> pdb=" O HIS A 386 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N HIS A 386 " --> pdb=" O PHE A 365 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N ALA A 367 " --> pdb=" O ILE A 384 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N ILE A 384 " --> pdb=" O ALA A 367 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N THR A 369 " --> pdb=" O ALA A 382 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ARG A 378 " --> pdb=" O SER A 373 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'A' and resid 349 through 350 Processing sheet with id=AG7, first strand: chain 'B' and resid 32 through 40 removed outlier: 4.441A pdb=" N ILE B 215 " --> pdb=" O HIS B 68 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N HIS B 68 " --> pdb=" O ILE B 215 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N TYR B 217 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N LEU B 66 " --> pdb=" O TYR B 217 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N LEU B 69 " --> pdb=" O ILE B 158 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER B 152 " --> pdb=" O LEU B 75 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'B' and resid 32 through 40 removed outlier: 4.441A pdb=" N ILE B 215 " --> pdb=" O HIS B 68 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N HIS B 68 " --> pdb=" O ILE B 215 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N TYR B 217 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N LEU B 66 " --> pdb=" O TYR B 217 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'B' and resid 42 through 44 removed outlier: 3.663A pdb=" N ILE B 178 " --> pdb=" O ILE B 58 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ASN B 96 " --> pdb=" O GLU B 111 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N GLU B 111 " --> pdb=" O ASN B 96 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N VAL B 98 " --> pdb=" O GLU B 109 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N GLU B 109 " --> pdb=" O VAL B 98 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ILE B 100 " --> pdb=" O ILE B 107 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'B' and resid 78 through 79 removed outlier: 6.780A pdb=" N VAL B 78 " --> pdb=" O ILE B 148 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'B' and resid 139 through 141 Processing sheet with id=AH3, first strand: chain 'B' and resid 227 through 236 removed outlier: 3.602A pdb=" N SER B 227 " --> pdb=" O VAL B 535 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASN B 530 " --> pdb=" O SER B 254 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N SER B 254 " --> pdb=" O ASN B 530 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N LEU B 532 " --> pdb=" O ALA B 252 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N ALA B 252 " --> pdb=" O LEU B 532 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA B 252 " --> pdb=" O ILE B 492 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'B' and resid 475 through 478 removed outlier: 3.862A pdb=" N ARG B 475 " --> pdb=" O VAL B 257 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N ALA B 252 " --> pdb=" O LEU B 532 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N LEU B 532 " --> pdb=" O ALA B 252 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N SER B 254 " --> pdb=" O ASN B 530 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASN B 530 " --> pdb=" O SER B 254 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'B' and resid 243 through 246 removed outlier: 3.868A pdb=" N ARG B 442 " --> pdb=" O VAL B 508 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TYR B 453 " --> pdb=" O VAL B 445 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N PHE B 447 " --> pdb=" O VAL B 451 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N VAL B 451 " --> pdb=" O PHE B 447 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'B' and resid 269 through 270 Processing sheet with id=AH7, first strand: chain 'B' and resid 296 through 299 removed outlier: 3.641A pdb=" N SER B 299 " --> pdb=" O SER B 340 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'B' and resid 320 through 323 removed outlier: 6.301A pdb=" N ASP B 327 " --> pdb=" O SER B 366 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N ILE B 368 " --> pdb=" O ASP B 327 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N TYR B 329 " --> pdb=" O ILE B 368 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N GLY B 370 " --> pdb=" O TYR B 329 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N LYS B 331 " --> pdb=" O GLY B 370 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N TYR B 372 " --> pdb=" O LYS B 331 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ASP B 333 " --> pdb=" O TYR B 372 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N PHE B 365 " --> pdb=" O HIS B 386 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N HIS B 386 " --> pdb=" O PHE B 365 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N ALA B 367 " --> pdb=" O ILE B 384 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N ILE B 384 " --> pdb=" O ALA B 367 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N THR B 369 " --> pdb=" O ALA B 382 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'B' and resid 349 through 350 984 hydrogen bonds defined for protein. 2610 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: 9.55 Time building geometry restraints manager: 10.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7975 1.34 - 1.46: 4322 1.46 - 1.57: 13179 1.57 - 1.69: 0 1.69 - 1.81: 126 Bond restraints: 25602 Sorted by residual: bond pdb=" N ASP E 25 " pdb=" CA ASP E 25 " ideal model delta sigma weight residual 1.458 1.486 -0.028 1.24e-02 6.50e+03 5.22e+00 bond pdb=" N ASP C 25 " pdb=" CA ASP C 25 " ideal model delta sigma weight residual 1.458 1.486 -0.028 1.24e-02 6.50e+03 5.11e+00 bond pdb=" C PHE C 481 " pdb=" N THR C 482 " ideal model delta sigma weight residual 1.340 1.258 0.082 5.87e-02 2.90e+02 1.95e+00 bond pdb=" C PHE E 481 " pdb=" N THR E 482 " ideal model delta sigma weight residual 1.340 1.259 0.081 5.87e-02 2.90e+02 1.90e+00 bond pdb=" CG LYS A 93 " pdb=" CD LYS A 93 " ideal model delta sigma weight residual 1.520 1.480 0.040 3.00e-02 1.11e+03 1.80e+00 ... (remaining 25597 not shown) Histogram of bond angle deviations from ideal: 99.03 - 106.03: 546 106.03 - 113.04: 14070 113.04 - 120.04: 8921 120.04 - 127.05: 11113 127.05 - 134.05: 210 Bond angle restraints: 34860 Sorted by residual: angle pdb=" C ARG D 233 " pdb=" CA ARG D 233 " pdb=" CB ARG D 233 " ideal model delta sigma weight residual 109.65 115.26 -5.61 1.75e+00 3.27e-01 1.03e+01 angle pdb=" C ARG B 233 " pdb=" CA ARG B 233 " pdb=" CB ARG B 233 " ideal model delta sigma weight residual 109.65 115.25 -5.60 1.75e+00 3.27e-01 1.02e+01 angle pdb=" N GLY E 409 " pdb=" CA GLY E 409 " pdb=" C GLY E 409 " ideal model delta sigma weight residual 113.18 120.34 -7.16 2.37e+00 1.78e-01 9.12e+00 angle pdb=" N GLY C 409 " pdb=" CA GLY C 409 " pdb=" C GLY C 409 " ideal model delta sigma weight residual 113.18 120.27 -7.09 2.37e+00 1.78e-01 8.94e+00 angle pdb=" C THR D 201 " pdb=" N PHE D 202 " pdb=" CA PHE D 202 " ideal model delta sigma weight residual 120.28 116.47 3.81 1.34e+00 5.57e-01 8.08e+00 ... (remaining 34855 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.32: 13837 17.32 - 34.64: 1256 34.64 - 51.96: 192 51.96 - 69.28: 47 69.28 - 86.60: 22 Dihedral angle restraints: 15354 sinusoidal: 5964 harmonic: 9390 Sorted by residual: dihedral pdb=" CA ARG B 353 " pdb=" C ARG B 353 " pdb=" N LYS B 354 " pdb=" CA LYS B 354 " ideal model delta harmonic sigma weight residual -180.00 -157.37 -22.63 0 5.00e+00 4.00e-02 2.05e+01 dihedral pdb=" CA ARG D 353 " pdb=" C ARG D 353 " pdb=" N LYS D 354 " pdb=" CA LYS D 354 " ideal model delta harmonic sigma weight residual -180.00 -157.52 -22.48 0 5.00e+00 4.00e-02 2.02e+01 dihedral pdb=" CA ARG E 353 " pdb=" C ARG E 353 " pdb=" N LYS E 354 " pdb=" CA LYS E 354 " ideal model delta harmonic sigma weight residual -180.00 -159.14 -20.86 0 5.00e+00 4.00e-02 1.74e+01 ... (remaining 15351 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 2466 0.043 - 0.086: 1094 0.086 - 0.129: 424 0.129 - 0.172: 44 0.172 - 0.215: 10 Chirality restraints: 4038 Sorted by residual: chirality pdb=" CA TYR F 62 " pdb=" N TYR F 62 " pdb=" C TYR F 62 " pdb=" CB TYR F 62 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CA TYR A 62 " pdb=" N TYR A 62 " pdb=" C TYR A 62 " pdb=" CB TYR A 62 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CA PRO F 144 " pdb=" N PRO F 144 " pdb=" C PRO F 144 " pdb=" CB PRO F 144 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.20 2.00e-01 2.50e+01 1.02e+00 ... (remaining 4035 not shown) Planarity restraints: 4446 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU B 200 " -0.015 2.00e-02 2.50e+03 2.98e-02 8.87e+00 pdb=" C GLU B 200 " 0.052 2.00e-02 2.50e+03 pdb=" O GLU B 200 " -0.019 2.00e-02 2.50e+03 pdb=" N THR B 201 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU D 200 " 0.015 2.00e-02 2.50e+03 2.97e-02 8.84e+00 pdb=" C GLU D 200 " -0.051 2.00e-02 2.50e+03 pdb=" O GLU D 200 " 0.019 2.00e-02 2.50e+03 pdb=" N THR D 201 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU F 200 " -0.014 2.00e-02 2.50e+03 2.74e-02 7.52e+00 pdb=" C GLU F 200 " 0.047 2.00e-02 2.50e+03 pdb=" O GLU F 200 " -0.018 2.00e-02 2.50e+03 pdb=" N THR F 201 " -0.016 2.00e-02 2.50e+03 ... (remaining 4443 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 1579 2.73 - 3.27: 22898 3.27 - 3.81: 37687 3.81 - 4.36: 45259 4.36 - 4.90: 79821 Nonbonded interactions: 187244 Sorted by model distance: nonbonded pdb=" OG SER C 356 " pdb=" N PHE C 357 " model vdw 2.182 2.520 nonbonded pdb=" OG SER E 356 " pdb=" N PHE E 357 " model vdw 2.182 2.520 nonbonded pdb=" O ILE F 390 " pdb=" OG1 THR F 393 " model vdw 2.217 2.440 nonbonded pdb=" O ILE A 390 " pdb=" OG1 THR A 393 " model vdw 2.218 2.440 nonbonded pdb=" OE2 GLU D 444 " pdb=" NH1 ARG D 446 " model vdw 2.247 2.520 ... (remaining 187239 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 18 through 93 or resid 95 through 356 or resid 358 through \ 547)) selection = (chain 'B' and (resid 18 through 93 or resid 95 through 356 or resid 358 through \ 547)) selection = (chain 'C' and (resid 18 through 93 or resid 95 through 356 or resid 358 through \ 547)) selection = (chain 'D' and (resid 18 through 93 or resid 95 through 356 or resid 358 through \ 547)) selection = (chain 'E' and (resid 18 through 93 or resid 95 through 356 or resid 358 through \ 547)) selection = (chain 'F' and (resid 18 through 93 or resid 95 through 356 or resid 358 through \ 547)) } 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=0.50 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: 0.750 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: 4.790 Check model and map are aligned: 0.430 Set scattering table: 0.270 Process input model: 86.550 Find NCS groups from input model: 1.720 Set up NCS constraints: 0.150 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: 0.010 Load rotamer database and sin/cos tables:3.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 97.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 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 : 0.007 0.082 25602 Z= 0.433 Angle : 0.788 11.477 34860 Z= 0.445 Chirality : 0.054 0.215 4038 Planarity : 0.005 0.050 4446 Dihedral : 13.861 86.599 9318 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 0.45 % Allowed : 10.44 % Favored : 89.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.13), residues: 3156 helix: -2.37 (0.18), residues: 438 sheet: -0.17 (0.15), residues: 984 loop : -0.71 (0.13), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.004 TRP E 400 HIS 0.009 0.002 HIS C 97 PHE 0.025 0.003 PHE D 427 TYR 0.026 0.003 TYR D 36 ARG 0.010 0.001 ARG E 461 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 843 residues out of total 2904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 830 time to evaluate : 3.430 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: E 73 LEU cc_start: 0.8918 (mt) cc_final: 0.8717 (mt) REVERT: E 104 ASN cc_start: 0.7071 (m-40) cc_final: 0.5147 (t0) REVERT: E 137 ASP cc_start: 0.7748 (m-30) cc_final: 0.7263 (m-30) REVERT: E 199 PHE cc_start: 0.8123 (t80) cc_final: 0.7907 (t80) REVERT: E 206 PHE cc_start: 0.6835 (t80) cc_final: 0.6596 (t80) REVERT: E 345 THR cc_start: 0.8603 (p) cc_final: 0.8211 (t) REVERT: E 371 THR cc_start: 0.7409 (m) cc_final: 0.7131 (p) REVERT: E 485 ILE cc_start: 0.8618 (mm) cc_final: 0.8298 (mm) REVERT: E 486 PHE cc_start: 0.7508 (m-80) cc_final: 0.7258 (m-80) REVERT: E 500 LYS cc_start: 0.6858 (mtpt) cc_final: 0.6205 (mmtp) REVERT: F 25 ASP cc_start: 0.6552 (OUTLIER) cc_final: 0.6330 (p0) REVERT: F 134 GLU cc_start: 0.7291 (tp30) cc_final: 0.6520 (tp30) REVERT: F 165 GLU cc_start: 0.7966 (mm-30) cc_final: 0.7669 (mm-30) REVERT: F 193 ARG cc_start: 0.8497 (pmt170) cc_final: 0.8276 (pmt170) REVERT: F 223 GLN cc_start: 0.7377 (mm-40) cc_final: 0.7042 (mp10) REVERT: F 297 ILE cc_start: 0.8020 (mt) cc_final: 0.7637 (mm) REVERT: F 423 ILE cc_start: 0.8793 (mt) cc_final: 0.8558 (mp) REVERT: F 524 GLN cc_start: 0.7852 (mt0) cc_final: 0.7651 (mp10) REVERT: D 40 SER cc_start: 0.7586 (t) cc_final: 0.7072 (p) REVERT: D 242 PRO cc_start: 0.9006 (Cg_endo) cc_final: 0.8636 (Cg_exo) REVERT: D 243 THR cc_start: 0.8646 (p) cc_final: 0.8031 (m) REVERT: D 278 GLN cc_start: 0.7089 (mm-40) cc_final: 0.6558 (tt0) REVERT: D 328 VAL cc_start: 0.7776 (t) cc_final: 0.7541 (p) REVERT: D 331 LYS cc_start: 0.8061 (mmtt) cc_final: 0.7817 (tppp) REVERT: D 371 THR cc_start: 0.7742 (m) cc_final: 0.7534 (t) REVERT: D 379 THR cc_start: 0.7695 (m) cc_final: 0.7440 (p) REVERT: D 431 ILE cc_start: 0.8223 (pt) cc_final: 0.7588 (mt) REVERT: D 434 LYS cc_start: 0.8031 (mmmt) cc_final: 0.7789 (mmmt) REVERT: D 453 TYR cc_start: 0.7548 (t80) cc_final: 0.7337 (t80) REVERT: D 503 LEU cc_start: 0.9236 (mt) cc_final: 0.8742 (mm) REVERT: C 73 LEU cc_start: 0.8911 (mt) cc_final: 0.8710 (mt) REVERT: C 104 ASN cc_start: 0.7055 (m-40) cc_final: 0.5140 (t0) REVERT: C 137 ASP cc_start: 0.7797 (m-30) cc_final: 0.7325 (m-30) REVERT: C 199 PHE cc_start: 0.8117 (t80) cc_final: 0.7874 (t80) REVERT: C 206 PHE cc_start: 0.6845 (t80) cc_final: 0.6594 (t80) REVERT: C 345 THR cc_start: 0.8594 (p) cc_final: 0.8205 (t) REVERT: C 363 LYS cc_start: 0.7260 (mtpp) cc_final: 0.7041 (tptt) REVERT: C 485 ILE cc_start: 0.8629 (mm) cc_final: 0.8309 (mm) REVERT: C 486 PHE cc_start: 0.7543 (m-80) cc_final: 0.7289 (m-80) REVERT: C 500 LYS cc_start: 0.6848 (mtpt) cc_final: 0.6213 (mmtp) REVERT: A 25 ASP cc_start: 0.6478 (OUTLIER) cc_final: 0.5860 (t0) REVERT: A 134 GLU cc_start: 0.7318 (tp30) cc_final: 0.6529 (tp30) REVERT: A 159 LYS cc_start: 0.8306 (tttt) cc_final: 0.8065 (tptp) REVERT: A 165 GLU cc_start: 0.7988 (mm-30) cc_final: 0.7688 (mm-30) REVERT: A 223 GLN cc_start: 0.7384 (mm-40) cc_final: 0.7077 (mp10) REVERT: A 297 ILE cc_start: 0.8025 (mt) cc_final: 0.7644 (mm) REVERT: A 423 ILE cc_start: 0.8793 (mt) cc_final: 0.8548 (mp) REVERT: B 40 SER cc_start: 0.7596 (t) cc_final: 0.7087 (p) REVERT: B 242 PRO cc_start: 0.9008 (Cg_endo) cc_final: 0.8688 (Cg_exo) REVERT: B 278 GLN cc_start: 0.7084 (mm-40) cc_final: 0.6557 (tt0) REVERT: B 328 VAL cc_start: 0.7769 (t) cc_final: 0.7533 (p) REVERT: B 331 LYS cc_start: 0.8068 (mmtt) cc_final: 0.7815 (tppp) REVERT: B 371 THR cc_start: 0.7727 (m) cc_final: 0.7514 (t) REVERT: B 379 THR cc_start: 0.7713 (m) cc_final: 0.7444 (p) REVERT: B 431 ILE cc_start: 0.8228 (pt) cc_final: 0.7599 (mt) REVERT: B 434 LYS cc_start: 0.8042 (mmmt) cc_final: 0.7801 (mmmt) REVERT: B 503 LEU cc_start: 0.9240 (mt) cc_final: 0.8743 (mm) outliers start: 13 outliers final: 6 residues processed: 840 average time/residue: 0.3899 time to fit residues: 500.2510 Evaluate side-chains 353 residues out of total 2904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 345 time to evaluate : 3.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 25 ASP Chi-restraints excluded: chain F residue 541 VAL Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain B residue 90 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 263 optimal weight: 5.9990 chunk 236 optimal weight: 7.9990 chunk 131 optimal weight: 1.9990 chunk 80 optimal weight: 5.9990 chunk 159 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 chunk 244 optimal weight: 5.9990 chunk 94 optimal weight: 10.0000 chunk 148 optimal weight: 0.8980 chunk 182 optimal weight: 0.9980 chunk 283 optimal weight: 0.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 516 HIS F 456 ASN D 27 GLN D 240 ASN C 516 HIS A 456 ASN B 240 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 25602 Z= 0.229 Angle : 0.635 13.208 34860 Z= 0.328 Chirality : 0.051 0.345 4038 Planarity : 0.004 0.045 4446 Dihedral : 4.637 26.638 3472 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.12 % Allowed : 16.14 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.14), residues: 3156 helix: -1.54 (0.21), residues: 498 sheet: 0.43 (0.16), residues: 924 loop : -0.31 (0.14), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP C 108 HIS 0.004 0.001 HIS A 516 PHE 0.016 0.001 PHE E 381 TYR 0.025 0.002 TYR E 262 ARG 0.010 0.001 ARG A 498 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 2904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 368 time to evaluate : 3.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 104 ASN cc_start: 0.7138 (m-40) cc_final: 0.5296 (t0) REVERT: E 137 ASP cc_start: 0.7754 (m-30) cc_final: 0.7216 (m-30) REVERT: E 199 PHE cc_start: 0.8036 (t80) cc_final: 0.7644 (t80) REVERT: E 206 PHE cc_start: 0.6928 (t80) cc_final: 0.6707 (t80) REVERT: E 212 LEU cc_start: 0.7863 (tp) cc_final: 0.7406 (tp) REVERT: E 339 MET cc_start: 0.7859 (mmm) cc_final: 0.7645 (mmm) REVERT: E 345 THR cc_start: 0.8336 (p) cc_final: 0.8002 (t) REVERT: E 455 GLU cc_start: 0.7182 (pt0) cc_final: 0.6858 (pt0) REVERT: E 486 PHE cc_start: 0.7498 (m-80) cc_final: 0.7246 (m-80) REVERT: E 500 LYS cc_start: 0.6385 (mtpt) cc_final: 0.5846 (mmtp) REVERT: F 25 ASP cc_start: 0.6573 (p0) cc_final: 0.6360 (p0) REVERT: F 134 GLU cc_start: 0.7242 (tp30) cc_final: 0.6547 (tp30) REVERT: F 165 GLU cc_start: 0.7869 (mm-30) cc_final: 0.7643 (mm-30) REVERT: F 193 ARG cc_start: 0.8556 (pmt170) cc_final: 0.8324 (pmt170) REVERT: F 287 TYR cc_start: 0.7309 (t80) cc_final: 0.7042 (t80) REVERT: F 297 ILE cc_start: 0.7863 (mt) cc_final: 0.7547 (mm) REVERT: F 547 MET cc_start: 0.5681 (ppp) cc_final: 0.5422 (ppp) REVERT: D 55 SER cc_start: 0.8629 (t) cc_final: 0.8029 (p) REVERT: D 242 PRO cc_start: 0.8932 (Cg_endo) cc_final: 0.8567 (Cg_exo) REVERT: D 371 THR cc_start: 0.7477 (m) cc_final: 0.7260 (t) REVERT: C 104 ASN cc_start: 0.7103 (m-40) cc_final: 0.5320 (t0) REVERT: C 137 ASP cc_start: 0.7744 (m-30) cc_final: 0.7203 (m-30) REVERT: C 199 PHE cc_start: 0.8034 (t80) cc_final: 0.7646 (t80) REVERT: C 206 PHE cc_start: 0.6936 (t80) cc_final: 0.6709 (t80) REVERT: C 339 MET cc_start: 0.7852 (mmm) cc_final: 0.7626 (mmm) REVERT: C 345 THR cc_start: 0.8357 (p) cc_final: 0.8003 (t) REVERT: C 363 LYS cc_start: 0.7423 (mtpp) cc_final: 0.7071 (tptt) REVERT: C 455 GLU cc_start: 0.7182 (pt0) cc_final: 0.6849 (pt0) REVERT: C 486 PHE cc_start: 0.7536 (m-80) cc_final: 0.7283 (m-80) REVERT: C 500 LYS cc_start: 0.6435 (mtpt) cc_final: 0.5882 (mmtp) REVERT: A 25 ASP cc_start: 0.6521 (p0) cc_final: 0.6285 (p0) REVERT: A 134 GLU cc_start: 0.7273 (tp30) cc_final: 0.6544 (tp30) REVERT: A 159 LYS cc_start: 0.8220 (tttt) cc_final: 0.7986 (tptp) REVERT: A 165 GLU cc_start: 0.7917 (mm-30) cc_final: 0.7594 (mm-30) REVERT: A 233 ARG cc_start: 0.6364 (ttp80) cc_final: 0.6155 (ttt90) REVERT: A 287 TYR cc_start: 0.7307 (t80) cc_final: 0.7045 (t80) REVERT: A 297 ILE cc_start: 0.7825 (mt) cc_final: 0.7520 (mm) REVERT: A 547 MET cc_start: 0.5655 (ppp) cc_final: 0.5385 (ppp) REVERT: B 55 SER cc_start: 0.8593 (t) cc_final: 0.7982 (p) REVERT: B 242 PRO cc_start: 0.8929 (Cg_endo) cc_final: 0.8584 (Cg_exo) outliers start: 61 outliers final: 44 residues processed: 421 average time/residue: 0.3447 time to fit residues: 234.2476 Evaluate side-chains 331 residues out of total 2904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 287 time to evaluate : 3.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 139 SER Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 333 ASP Chi-restraints excluded: chain E residue 531 ASP Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 213 SER Chi-restraints excluded: chain F residue 227 SER Chi-restraints excluded: chain F residue 355 ASN Chi-restraints excluded: chain F residue 445 VAL Chi-restraints excluded: chain F residue 478 THR Chi-restraints excluded: chain F residue 513 ASP Chi-restraints excluded: chain F residue 541 VAL Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 245 THR Chi-restraints excluded: chain D residue 256 SER Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 333 ASP Chi-restraints excluded: chain D residue 349 MET Chi-restraints excluded: chain D residue 376 THR Chi-restraints excluded: chain D residue 401 THR Chi-restraints excluded: chain D residue 508 VAL Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 371 THR Chi-restraints excluded: chain C residue 531 ASP Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 513 ASP Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 256 SER Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain B residue 349 MET Chi-restraints excluded: chain B residue 401 THR Chi-restraints excluded: chain B residue 508 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 157 optimal weight: 0.0470 chunk 87 optimal weight: 9.9990 chunk 235 optimal weight: 1.9990 chunk 192 optimal weight: 0.0270 chunk 78 optimal weight: 0.6980 chunk 283 optimal weight: 8.9990 chunk 306 optimal weight: 4.9990 chunk 252 optimal weight: 0.4980 chunk 281 optimal weight: 3.9990 chunk 96 optimal weight: 0.8980 chunk 227 optimal weight: 3.9990 overall best weight: 0.4336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 408 ASN ** E 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 408 ASN ** C 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 456 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.3570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 25602 Z= 0.138 Angle : 0.530 14.454 34860 Z= 0.270 Chirality : 0.048 0.267 4038 Planarity : 0.004 0.043 4446 Dihedral : 4.130 25.917 3468 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.46 % Allowed : 18.20 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.14), residues: 3156 helix: -0.98 (0.22), residues: 498 sheet: 0.41 (0.16), residues: 948 loop : 0.06 (0.14), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 108 HIS 0.008 0.001 HIS E 250 PHE 0.024 0.001 PHE C 381 TYR 0.018 0.001 TYR E 262 ARG 0.005 0.001 ARG F 404 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 2904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 353 time to evaluate : 2.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 104 ASN cc_start: 0.7206 (m-40) cc_final: 0.5478 (t0) REVERT: E 137 ASP cc_start: 0.7523 (m-30) cc_final: 0.7035 (m-30) REVERT: E 199 PHE cc_start: 0.7976 (t80) cc_final: 0.7676 (t80) REVERT: E 339 MET cc_start: 0.7814 (mmm) cc_final: 0.7512 (mmm) REVERT: E 345 THR cc_start: 0.8431 (p) cc_final: 0.8011 (t) REVERT: E 384 ILE cc_start: 0.7934 (mm) cc_final: 0.7666 (pt) REVERT: E 500 LYS cc_start: 0.6409 (mtpt) cc_final: 0.5918 (mmtp) REVERT: F 25 ASP cc_start: 0.6598 (p0) cc_final: 0.6385 (p0) REVERT: F 134 GLU cc_start: 0.7250 (tp30) cc_final: 0.6505 (tp30) REVERT: F 193 ARG cc_start: 0.8430 (pmt170) cc_final: 0.8064 (pmt170) REVERT: F 255 LEU cc_start: 0.8833 (mt) cc_final: 0.8611 (mt) REVERT: F 297 ILE cc_start: 0.7718 (mt) cc_final: 0.7346 (mm) REVERT: F 495 ASN cc_start: 0.6055 (OUTLIER) cc_final: 0.4643 (m-40) REVERT: F 547 MET cc_start: 0.5767 (ppp) cc_final: 0.5399 (ppp) REVERT: D 55 SER cc_start: 0.8572 (t) cc_final: 0.8012 (p) REVERT: D 242 PRO cc_start: 0.8764 (Cg_endo) cc_final: 0.8526 (Cg_exo) REVERT: C 104 ASN cc_start: 0.7195 (m-40) cc_final: 0.5520 (t0) REVERT: C 137 ASP cc_start: 0.7522 (m-30) cc_final: 0.7015 (m-30) REVERT: C 199 PHE cc_start: 0.7952 (t80) cc_final: 0.7660 (t80) REVERT: C 339 MET cc_start: 0.7790 (mmm) cc_final: 0.7503 (mmm) REVERT: C 345 THR cc_start: 0.8418 (p) cc_final: 0.7981 (t) REVERT: C 363 LYS cc_start: 0.7461 (mtpp) cc_final: 0.7169 (tptt) REVERT: C 486 PHE cc_start: 0.7485 (m-80) cc_final: 0.7267 (m-80) REVERT: C 500 LYS cc_start: 0.6340 (mtpt) cc_final: 0.5939 (mmtp) REVERT: A 25 ASP cc_start: 0.6530 (p0) cc_final: 0.6322 (p0) REVERT: A 134 GLU cc_start: 0.7283 (tp30) cc_final: 0.6521 (tp30) REVERT: A 233 ARG cc_start: 0.6356 (ttp80) cc_final: 0.6132 (ttt90) REVERT: A 297 ILE cc_start: 0.7712 (mt) cc_final: 0.7357 (mm) REVERT: A 495 ASN cc_start: 0.6068 (OUTLIER) cc_final: 0.4638 (m-40) REVERT: A 547 MET cc_start: 0.5769 (ppp) cc_final: 0.5412 (ppp) REVERT: B 55 SER cc_start: 0.8565 (t) cc_final: 0.8012 (p) REVERT: B 242 PRO cc_start: 0.8776 (Cg_endo) cc_final: 0.8545 (Cg_exo) outliers start: 42 outliers final: 24 residues processed: 390 average time/residue: 0.3435 time to fit residues: 215.5796 Evaluate side-chains 312 residues out of total 2904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 286 time to evaluate : 3.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 531 ASP Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 213 SER Chi-restraints excluded: chain F residue 355 ASN Chi-restraints excluded: chain F residue 392 ASP Chi-restraints excluded: chain F residue 425 ASP Chi-restraints excluded: chain F residue 495 ASN Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 245 THR Chi-restraints excluded: chain D residue 333 ASP Chi-restraints excluded: chain D residue 376 THR Chi-restraints excluded: chain D residue 401 THR Chi-restraints excluded: chain D residue 508 VAL Chi-restraints excluded: chain C residue 531 ASP Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 495 ASN Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 401 THR Chi-restraints excluded: chain B residue 508 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 280 optimal weight: 10.0000 chunk 213 optimal weight: 9.9990 chunk 147 optimal weight: 7.9990 chunk 31 optimal weight: 9.9990 chunk 135 optimal weight: 8.9990 chunk 190 optimal weight: 8.9990 chunk 284 optimal weight: 0.6980 chunk 301 optimal weight: 1.9990 chunk 148 optimal weight: 2.9990 chunk 269 optimal weight: 3.9990 chunk 81 optimal weight: 8.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 136 ASN E 221 ASN E 334 ASN ** E 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 96 ASN F 185 ASN F 515 ASN D 96 ASN D 250 HIS ** D 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 136 ASN C 334 ASN ** C 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 96 ASN A 185 ASN A 515 ASN B 96 ASN B 250 HIS ** B 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.4104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 25602 Z= 0.391 Angle : 0.682 16.939 34860 Z= 0.353 Chirality : 0.052 0.199 4038 Planarity : 0.005 0.045 4446 Dihedral : 4.704 26.940 3464 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 3.06 % Allowed : 17.95 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.14), residues: 3156 helix: -1.37 (0.21), residues: 504 sheet: 0.35 (0.16), residues: 924 loop : -0.28 (0.14), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP A 108 HIS 0.008 0.002 HIS B 250 PHE 0.017 0.002 PHE C 199 TYR 0.033 0.002 TYR B 287 ARG 0.009 0.001 ARG F 498 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 2904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 304 time to evaluate : 3.040 Fit side-chains REVERT: E 104 ASN cc_start: 0.6894 (m-40) cc_final: 0.5328 (t0) REVERT: E 137 ASP cc_start: 0.7764 (m-30) cc_final: 0.7307 (m-30) REVERT: E 199 PHE cc_start: 0.8030 (t80) cc_final: 0.7670 (t80) REVERT: E 500 LYS cc_start: 0.6449 (mtpt) cc_final: 0.6030 (mmtm) REVERT: F 193 ARG cc_start: 0.8551 (pmt170) cc_final: 0.8058 (pmt170) REVERT: F 297 ILE cc_start: 0.7560 (mt) cc_final: 0.7209 (mm) REVERT: D 55 SER cc_start: 0.8590 (t) cc_final: 0.8105 (p) REVERT: D 147 THR cc_start: 0.8515 (m) cc_final: 0.7943 (p) REVERT: C 104 ASN cc_start: 0.6885 (m-40) cc_final: 0.5341 (t0) REVERT: C 137 ASP cc_start: 0.7757 (m-30) cc_final: 0.7291 (m-30) REVERT: C 199 PHE cc_start: 0.8022 (t80) cc_final: 0.7659 (t80) REVERT: C 363 LYS cc_start: 0.7946 (mtpp) cc_final: 0.7180 (tptt) REVERT: C 455 GLU cc_start: 0.7012 (pt0) cc_final: 0.6743 (pt0) REVERT: C 500 LYS cc_start: 0.6595 (mtpt) cc_final: 0.6044 (mmtm) REVERT: A 297 ILE cc_start: 0.7554 (mt) cc_final: 0.7203 (mm) REVERT: B 55 SER cc_start: 0.8589 (t) cc_final: 0.8105 (p) REVERT: B 147 THR cc_start: 0.8543 (m) cc_final: 0.8047 (p) outliers start: 88 outliers final: 64 residues processed: 381 average time/residue: 0.3455 time to fit residues: 219.0505 Evaluate side-chains 317 residues out of total 2904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 253 time to evaluate : 3.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 333 ASP Chi-restraints excluded: chain E residue 456 ASN Chi-restraints excluded: chain E residue 503 LEU Chi-restraints excluded: chain E residue 531 ASP Chi-restraints excluded: chain F residue 40 SER Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 121 ASN Chi-restraints excluded: chain F residue 213 SER Chi-restraints excluded: chain F residue 227 SER Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 355 ASN Chi-restraints excluded: chain F residue 392 ASP Chi-restraints excluded: chain F residue 425 ASP Chi-restraints excluded: chain F residue 477 LEU Chi-restraints excluded: chain F residue 505 VAL Chi-restraints excluded: chain F residue 507 VAL Chi-restraints excluded: chain F residue 524 GLN Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 245 THR Chi-restraints excluded: chain D residue 256 SER Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 333 ASP Chi-restraints excluded: chain D residue 376 THR Chi-restraints excluded: chain D residue 401 THR Chi-restraints excluded: chain D residue 431 ILE Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 507 VAL Chi-restraints excluded: chain D residue 508 VAL Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 371 THR Chi-restraints excluded: chain C residue 456 ASN Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 531 ASP Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 256 SER Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 401 THR Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 508 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 251 optimal weight: 0.9980 chunk 171 optimal weight: 8.9990 chunk 4 optimal weight: 5.9990 chunk 224 optimal weight: 0.8980 chunk 124 optimal weight: 2.9990 chunk 257 optimal weight: 0.0060 chunk 208 optimal weight: 0.0270 chunk 0 optimal weight: 8.9990 chunk 153 optimal weight: 0.0370 chunk 270 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 overall best weight: 0.3932 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 516 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.4317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 25602 Z= 0.142 Angle : 0.548 16.316 34860 Z= 0.275 Chirality : 0.048 0.188 4038 Planarity : 0.004 0.042 4446 Dihedral : 4.037 20.828 3464 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.01 % Allowed : 20.29 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.15), residues: 3156 helix: -0.83 (0.23), residues: 498 sheet: 0.42 (0.17), residues: 948 loop : -0.04 (0.14), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP F 108 HIS 0.004 0.001 HIS C 516 PHE 0.016 0.001 PHE A 206 TYR 0.023 0.001 TYR D 287 ARG 0.006 0.000 ARG A 498 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 298 time to evaluate : 3.104 Fit side-chains revert: symmetry clash REVERT: E 104 ASN cc_start: 0.6838 (m-40) cc_final: 0.5291 (t0) REVERT: E 137 ASP cc_start: 0.7623 (m-30) cc_final: 0.7145 (m-30) REVERT: E 177 LYS cc_start: 0.9020 (ttmt) cc_final: 0.8528 (tttt) REVERT: E 339 MET cc_start: 0.7962 (mmm) cc_final: 0.7599 (mmm) REVERT: E 345 THR cc_start: 0.8313 (p) cc_final: 0.8075 (t) REVERT: E 453 TYR cc_start: 0.7965 (t80) cc_final: 0.7564 (t80) REVERT: E 455 GLU cc_start: 0.7158 (pt0) cc_final: 0.6044 (pt0) REVERT: E 500 LYS cc_start: 0.6398 (mtpt) cc_final: 0.5838 (mmtm) REVERT: F 193 ARG cc_start: 0.8398 (pmt170) cc_final: 0.7980 (pmt170) REVERT: F 255 LEU cc_start: 0.8787 (mt) cc_final: 0.8558 (mt) REVERT: F 297 ILE cc_start: 0.7503 (mt) cc_final: 0.7114 (mm) REVERT: D 55 SER cc_start: 0.8530 (t) cc_final: 0.8038 (p) REVERT: D 147 THR cc_start: 0.8565 (m) cc_final: 0.8034 (p) REVERT: D 293 ASP cc_start: 0.5675 (OUTLIER) cc_final: 0.5435 (m-30) REVERT: D 441 SER cc_start: 0.8795 (p) cc_final: 0.8523 (t) REVERT: C 104 ASN cc_start: 0.6842 (m-40) cc_final: 0.5327 (t0) REVERT: C 137 ASP cc_start: 0.7630 (m-30) cc_final: 0.7135 (m-30) REVERT: C 177 LYS cc_start: 0.9012 (ttmt) cc_final: 0.8591 (tttt) REVERT: C 339 MET cc_start: 0.7955 (mmm) cc_final: 0.7563 (mmm) REVERT: C 345 THR cc_start: 0.8363 (p) cc_final: 0.8116 (t) REVERT: C 453 TYR cc_start: 0.7979 (t80) cc_final: 0.7537 (t80) REVERT: C 455 GLU cc_start: 0.6978 (pt0) cc_final: 0.5798 (pt0) REVERT: C 500 LYS cc_start: 0.6399 (mtpt) cc_final: 0.5887 (mmtm) REVERT: A 297 ILE cc_start: 0.7493 (mt) cc_final: 0.7107 (mm) REVERT: B 55 SER cc_start: 0.8505 (t) cc_final: 0.8004 (p) REVERT: B 147 THR cc_start: 0.8554 (m) cc_final: 0.8023 (p) REVERT: B 287 TYR cc_start: 0.6899 (t80) cc_final: 0.6642 (t80) outliers start: 29 outliers final: 23 residues processed: 324 average time/residue: 0.3438 time to fit residues: 180.7100 Evaluate side-chains 284 residues out of total 2904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 260 time to evaluate : 3.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 531 ASP Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 227 SER Chi-restraints excluded: chain F residue 355 ASN Chi-restraints excluded: chain F residue 392 ASP Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 293 ASP Chi-restraints excluded: chain D residue 333 ASP Chi-restraints excluded: chain D residue 376 THR Chi-restraints excluded: chain D residue 401 THR Chi-restraints excluded: chain D residue 508 VAL Chi-restraints excluded: chain C residue 531 ASP Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 401 THR Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain B residue 508 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 101 optimal weight: 0.0050 chunk 271 optimal weight: 7.9990 chunk 59 optimal weight: 2.9990 chunk 177 optimal weight: 9.9990 chunk 74 optimal weight: 0.7980 chunk 301 optimal weight: 1.9990 chunk 250 optimal weight: 10.0000 chunk 139 optimal weight: 9.9990 chunk 25 optimal weight: 7.9990 chunk 99 optimal weight: 9.9990 chunk 158 optimal weight: 9.9990 overall best weight: 2.7600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 136 ASN ** E 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 136 ASN C 221 ASN ** C 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.4580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 25602 Z= 0.314 Angle : 0.632 16.997 34860 Z= 0.323 Chirality : 0.050 0.168 4038 Planarity : 0.004 0.047 4446 Dihedral : 4.462 25.048 3464 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.26 % Allowed : 19.31 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.15), residues: 3156 helix: -0.96 (0.23), residues: 498 sheet: 0.15 (0.17), residues: 954 loop : -0.21 (0.15), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 108 HIS 0.005 0.001 HIS E 250 PHE 0.023 0.002 PHE C 199 TYR 0.032 0.002 TYR D 287 ARG 0.005 0.001 ARG B 233 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 263 time to evaluate : 3.075 Fit side-chains REVERT: E 25 ASP cc_start: 0.7544 (m-30) cc_final: 0.7016 (p0) REVERT: E 104 ASN cc_start: 0.6844 (m-40) cc_final: 0.5120 (t0) REVERT: E 137 ASP cc_start: 0.7753 (m-30) cc_final: 0.7280 (m-30) REVERT: E 198 ASP cc_start: 0.8036 (t0) cc_final: 0.7789 (t0) REVERT: E 339 MET cc_start: 0.8075 (mmm) cc_final: 0.7807 (mmm) REVERT: F 193 ARG cc_start: 0.8558 (pmt170) cc_final: 0.8056 (pmt170) REVERT: F 297 ILE cc_start: 0.7186 (mt) cc_final: 0.6766 (mm) REVERT: F 422 PHE cc_start: 0.7734 (m-80) cc_final: 0.7468 (m-80) REVERT: D 55 SER cc_start: 0.8592 (t) cc_final: 0.8117 (p) REVERT: D 147 THR cc_start: 0.8581 (m) cc_final: 0.8110 (p) REVERT: D 293 ASP cc_start: 0.5876 (OUTLIER) cc_final: 0.5670 (m-30) REVERT: D 441 SER cc_start: 0.8921 (p) cc_final: 0.8619 (t) REVERT: C 25 ASP cc_start: 0.7583 (m-30) cc_final: 0.6999 (p0) REVERT: C 81 MET cc_start: 0.6164 (tpp) cc_final: 0.5745 (tpp) REVERT: C 104 ASN cc_start: 0.6812 (m-40) cc_final: 0.5090 (t0) REVERT: C 137 ASP cc_start: 0.7731 (m-30) cc_final: 0.7230 (m-30) REVERT: C 198 ASP cc_start: 0.8074 (t0) cc_final: 0.7826 (t0) REVERT: C 339 MET cc_start: 0.8084 (mmm) cc_final: 0.7809 (mmm) REVERT: C 453 TYR cc_start: 0.8153 (t80) cc_final: 0.7716 (t80) REVERT: C 455 GLU cc_start: 0.6959 (pt0) cc_final: 0.5767 (pt0) REVERT: C 500 LYS cc_start: 0.6523 (mtpt) cc_final: 0.5962 (mmtm) REVERT: A 422 PHE cc_start: 0.7687 (m-80) cc_final: 0.7417 (m-80) REVERT: B 55 SER cc_start: 0.8593 (t) cc_final: 0.8115 (p) REVERT: B 147 THR cc_start: 0.8589 (m) cc_final: 0.8116 (p) outliers start: 65 outliers final: 56 residues processed: 316 average time/residue: 0.3374 time to fit residues: 178.5296 Evaluate side-chains 306 residues out of total 2904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 249 time to evaluate : 3.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 361 ILE Chi-restraints excluded: chain E residue 456 ASN Chi-restraints excluded: chain E residue 503 LEU Chi-restraints excluded: chain E residue 531 ASP Chi-restraints excluded: chain F residue 121 ASN Chi-restraints excluded: chain F residue 129 SER Chi-restraints excluded: chain F residue 213 SER Chi-restraints excluded: chain F residue 227 SER Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 343 LEU Chi-restraints excluded: chain F residue 355 ASN Chi-restraints excluded: chain F residue 392 ASP Chi-restraints excluded: chain F residue 449 ASN Chi-restraints excluded: chain F residue 524 GLN Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 245 THR Chi-restraints excluded: chain D residue 256 SER Chi-restraints excluded: chain D residue 279 ASP Chi-restraints excluded: chain D residue 293 ASP Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 333 ASP Chi-restraints excluded: chain D residue 376 THR Chi-restraints excluded: chain D residue 401 THR Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 508 VAL Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 333 ASP Chi-restraints excluded: chain C residue 361 ILE Chi-restraints excluded: chain C residue 456 ASN Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 531 ASP Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 256 SER Chi-restraints excluded: chain B residue 279 ASP Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 401 THR Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 508 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 291 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 chunk 171 optimal weight: 0.9980 chunk 220 optimal weight: 4.9990 chunk 170 optimal weight: 1.9990 chunk 254 optimal weight: 0.8980 chunk 168 optimal weight: 4.9990 chunk 300 optimal weight: 0.7980 chunk 188 optimal weight: 10.0000 chunk 183 optimal weight: 2.9990 chunk 138 optimal weight: 9.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 265 ASN ** C 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.4696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 25602 Z= 0.205 Angle : 0.569 17.123 34860 Z= 0.288 Chirality : 0.048 0.186 4038 Planarity : 0.004 0.046 4446 Dihedral : 4.235 24.040 3464 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.77 % Allowed : 20.25 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.15), residues: 3156 helix: -0.85 (0.23), residues: 498 sheet: 0.33 (0.17), residues: 918 loop : -0.26 (0.15), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 108 HIS 0.008 0.001 HIS A 516 PHE 0.015 0.001 PHE E 199 TYR 0.024 0.001 TYR D 287 ARG 0.005 0.000 ARG A 498 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 267 time to evaluate : 3.155 Fit side-chains REVERT: E 81 MET cc_start: 0.6055 (tpp) cc_final: 0.5650 (tpp) REVERT: E 104 ASN cc_start: 0.6842 (m-40) cc_final: 0.5144 (t0) REVERT: E 137 ASP cc_start: 0.7725 (m-30) cc_final: 0.7237 (m-30) REVERT: E 198 ASP cc_start: 0.8139 (t0) cc_final: 0.7932 (t0) REVERT: E 339 MET cc_start: 0.8045 (mmm) cc_final: 0.7833 (mmm) REVERT: E 345 THR cc_start: 0.8323 (p) cc_final: 0.8062 (t) REVERT: E 455 GLU cc_start: 0.6924 (pt0) cc_final: 0.6285 (pt0) REVERT: F 193 ARG cc_start: 0.8466 (pmt170) cc_final: 0.8001 (pmt170) REVERT: F 255 LEU cc_start: 0.8789 (mt) cc_final: 0.8574 (mt) REVERT: F 297 ILE cc_start: 0.7320 (mt) cc_final: 0.6891 (mm) REVERT: F 422 PHE cc_start: 0.7640 (m-80) cc_final: 0.7393 (m-80) REVERT: D 55 SER cc_start: 0.8544 (t) cc_final: 0.8067 (p) REVERT: D 147 THR cc_start: 0.8584 (m) cc_final: 0.8129 (p) REVERT: D 269 LYS cc_start: 0.8782 (ttmt) cc_final: 0.8211 (ttmm) REVERT: D 441 SER cc_start: 0.8854 (p) cc_final: 0.8651 (t) REVERT: C 81 MET cc_start: 0.6080 (tpp) cc_final: 0.5681 (tpp) REVERT: C 104 ASN cc_start: 0.6818 (m-40) cc_final: 0.5113 (t0) REVERT: C 137 ASP cc_start: 0.7694 (m-30) cc_final: 0.7180 (m-30) REVERT: C 177 LYS cc_start: 0.9035 (ttmt) cc_final: 0.8518 (tttt) REVERT: C 339 MET cc_start: 0.8050 (mmm) cc_final: 0.7834 (mmm) REVERT: C 453 TYR cc_start: 0.8058 (t80) cc_final: 0.7594 (t80) REVERT: C 455 GLU cc_start: 0.7005 (pt0) cc_final: 0.5668 (pt0) REVERT: A 297 ILE cc_start: 0.7340 (mt) cc_final: 0.6806 (tp) REVERT: A 422 PHE cc_start: 0.7614 (m-80) cc_final: 0.7365 (m-80) REVERT: B 55 SER cc_start: 0.8538 (t) cc_final: 0.8056 (p) REVERT: B 147 THR cc_start: 0.8595 (m) cc_final: 0.8137 (p) REVERT: B 287 TYR cc_start: 0.6987 (t80) cc_final: 0.6626 (t80) outliers start: 51 outliers final: 41 residues processed: 314 average time/residue: 0.3145 time to fit residues: 164.7763 Evaluate side-chains 295 residues out of total 2904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 254 time to evaluate : 3.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 361 ILE Chi-restraints excluded: chain E residue 503 LEU Chi-restraints excluded: chain E residue 531 ASP Chi-restraints excluded: chain F residue 40 SER Chi-restraints excluded: chain F residue 121 ASN Chi-restraints excluded: chain F residue 213 SER Chi-restraints excluded: chain F residue 227 SER Chi-restraints excluded: chain F residue 355 ASN Chi-restraints excluded: chain F residue 392 ASP Chi-restraints excluded: chain F residue 478 THR Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 245 THR Chi-restraints excluded: chain D residue 256 SER Chi-restraints excluded: chain D residue 265 ASN Chi-restraints excluded: chain D residue 333 ASP Chi-restraints excluded: chain D residue 376 THR Chi-restraints excluded: chain D residue 401 THR Chi-restraints excluded: chain D residue 508 VAL Chi-restraints excluded: chain C residue 361 ILE Chi-restraints excluded: chain C residue 371 THR Chi-restraints excluded: chain C residue 456 ASN Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 531 ASP Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 256 SER Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 401 THR Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain B residue 508 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 186 optimal weight: 6.9990 chunk 120 optimal weight: 1.9990 chunk 179 optimal weight: 6.9990 chunk 90 optimal weight: 9.9990 chunk 59 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 191 optimal weight: 8.9990 chunk 204 optimal weight: 6.9990 chunk 148 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 chunk 236 optimal weight: 0.7980 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 136 ASN ** E 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 265 ASN C 136 ASN C 334 ASN ** C 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 ASN B 408 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.4833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 25602 Z= 0.273 Angle : 0.603 17.477 34860 Z= 0.306 Chirality : 0.049 0.327 4038 Planarity : 0.004 0.047 4446 Dihedral : 4.340 24.314 3464 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.40 % Allowed : 19.83 % Favored : 77.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.15), residues: 3156 helix: -0.95 (0.23), residues: 498 sheet: 0.17 (0.17), residues: 924 loop : -0.32 (0.15), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 108 HIS 0.006 0.001 HIS A 516 PHE 0.019 0.002 PHE B 202 TYR 0.026 0.002 TYR D 287 ARG 0.004 0.001 ARG F 498 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 250 time to evaluate : 3.116 Fit side-chains REVERT: E 81 MET cc_start: 0.6078 (tpp) cc_final: 0.5662 (tpp) REVERT: E 104 ASN cc_start: 0.6926 (m-40) cc_final: 0.5302 (t0) REVERT: E 137 ASP cc_start: 0.7768 (m-30) cc_final: 0.7290 (m-30) REVERT: E 198 ASP cc_start: 0.8146 (t0) cc_final: 0.7889 (t0) REVERT: E 339 MET cc_start: 0.8095 (mmm) cc_final: 0.7869 (mmm) REVERT: E 455 GLU cc_start: 0.6979 (pt0) cc_final: 0.6364 (pt0) REVERT: F 193 ARG cc_start: 0.8534 (pmt170) cc_final: 0.8098 (pmt170) REVERT: F 255 LEU cc_start: 0.8821 (mt) cc_final: 0.8607 (mt) REVERT: F 422 PHE cc_start: 0.7680 (m-80) cc_final: 0.7423 (m-80) REVERT: D 55 SER cc_start: 0.8570 (t) cc_final: 0.8109 (p) REVERT: D 147 THR cc_start: 0.8511 (m) cc_final: 0.8016 (p) REVERT: C 81 MET cc_start: 0.6010 (tpp) cc_final: 0.5606 (tpp) REVERT: C 104 ASN cc_start: 0.6903 (m-40) cc_final: 0.5277 (t0) REVERT: C 137 ASP cc_start: 0.7713 (m-30) cc_final: 0.7211 (m-30) REVERT: C 177 LYS cc_start: 0.9110 (ttmt) cc_final: 0.8650 (tttt) REVERT: C 339 MET cc_start: 0.8133 (mmm) cc_final: 0.7861 (mmm) REVERT: C 453 TYR cc_start: 0.8068 (t80) cc_final: 0.7615 (t80) REVERT: C 455 GLU cc_start: 0.6982 (pt0) cc_final: 0.5718 (pt0) REVERT: C 506 ARG cc_start: 0.8071 (OUTLIER) cc_final: 0.7630 (mtp85) REVERT: A 134 GLU cc_start: 0.7523 (tp30) cc_final: 0.6967 (tp30) REVERT: A 422 PHE cc_start: 0.7643 (m-80) cc_final: 0.7384 (m-80) REVERT: B 55 SER cc_start: 0.8563 (t) cc_final: 0.8103 (p) REVERT: B 147 THR cc_start: 0.8564 (m) cc_final: 0.8096 (p) outliers start: 69 outliers final: 66 residues processed: 309 average time/residue: 0.3108 time to fit residues: 160.8554 Evaluate side-chains 314 residues out of total 2904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 247 time to evaluate : 2.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 361 ILE Chi-restraints excluded: chain E residue 456 ASN Chi-restraints excluded: chain E residue 503 LEU Chi-restraints excluded: chain E residue 531 ASP Chi-restraints excluded: chain F residue 40 SER Chi-restraints excluded: chain F residue 121 ASN Chi-restraints excluded: chain F residue 213 SER Chi-restraints excluded: chain F residue 227 SER Chi-restraints excluded: chain F residue 355 ASN Chi-restraints excluded: chain F residue 392 ASP Chi-restraints excluded: chain F residue 425 ASP Chi-restraints excluded: chain F residue 431 ILE Chi-restraints excluded: chain F residue 449 ASN Chi-restraints excluded: chain F residue 478 THR Chi-restraints excluded: chain F residue 518 ILE Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 245 THR Chi-restraints excluded: chain D residue 256 SER Chi-restraints excluded: chain D residue 265 ASN Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 333 ASP Chi-restraints excluded: chain D residue 376 THR Chi-restraints excluded: chain D residue 401 THR Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 507 VAL Chi-restraints excluded: chain D residue 508 VAL Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 361 ILE Chi-restraints excluded: chain C residue 371 THR Chi-restraints excluded: chain C residue 456 ASN Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 506 ARG Chi-restraints excluded: chain C residue 531 ASP Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 449 ASN Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 256 SER Chi-restraints excluded: chain B residue 265 ASN Chi-restraints excluded: chain B residue 279 ASP Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 401 THR Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 508 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 273 optimal weight: 3.9990 chunk 288 optimal weight: 1.9990 chunk 262 optimal weight: 6.9990 chunk 280 optimal weight: 3.9990 chunk 168 optimal weight: 1.9990 chunk 122 optimal weight: 5.9990 chunk 220 optimal weight: 8.9990 chunk 85 optimal weight: 8.9990 chunk 253 optimal weight: 6.9990 chunk 265 optimal weight: 0.8980 chunk 279 optimal weight: 0.9980 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 136 ASN ** E 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 355 ASN B 265 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.4899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 25602 Z= 0.240 Angle : 0.588 16.936 34860 Z= 0.297 Chirality : 0.049 0.280 4038 Planarity : 0.004 0.047 4446 Dihedral : 4.298 23.944 3464 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.26 % Allowed : 20.32 % Favored : 77.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.15), residues: 3156 helix: -0.93 (0.23), residues: 498 sheet: 0.15 (0.17), residues: 924 loop : -0.33 (0.15), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP F 108 HIS 0.004 0.001 HIS E 250 PHE 0.015 0.001 PHE E 199 TYR 0.024 0.002 TYR D 287 ARG 0.004 0.001 ARG F 498 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 253 time to evaluate : 3.054 Fit side-chains REVERT: E 81 MET cc_start: 0.6064 (tpp) cc_final: 0.5645 (tpp) REVERT: E 104 ASN cc_start: 0.6875 (m-40) cc_final: 0.5257 (t0) REVERT: E 137 ASP cc_start: 0.7752 (m-30) cc_final: 0.7274 (m-30) REVERT: E 198 ASP cc_start: 0.8102 (t0) cc_final: 0.7860 (t0) REVERT: E 339 MET cc_start: 0.8129 (mmm) cc_final: 0.7908 (mmm) REVERT: E 455 GLU cc_start: 0.6984 (pt0) cc_final: 0.6298 (pt0) REVERT: E 506 ARG cc_start: 0.8072 (OUTLIER) cc_final: 0.7620 (mtp85) REVERT: E 547 MET cc_start: 0.5783 (mmm) cc_final: 0.5446 (mmm) REVERT: F 134 GLU cc_start: 0.7531 (tp30) cc_final: 0.6959 (tp30) REVERT: F 193 ARG cc_start: 0.8462 (pmt170) cc_final: 0.8030 (pmt170) REVERT: F 255 LEU cc_start: 0.8827 (mt) cc_final: 0.8615 (mt) REVERT: F 422 PHE cc_start: 0.7669 (m-80) cc_final: 0.7416 (m-80) REVERT: D 55 SER cc_start: 0.8552 (t) cc_final: 0.8095 (p) REVERT: D 147 THR cc_start: 0.8525 (m) cc_final: 0.8034 (p) REVERT: C 81 MET cc_start: 0.6009 (tpp) cc_final: 0.5599 (tpp) REVERT: C 104 ASN cc_start: 0.6844 (m-40) cc_final: 0.5245 (t0) REVERT: C 137 ASP cc_start: 0.7696 (m-30) cc_final: 0.7190 (m-30) REVERT: C 177 LYS cc_start: 0.8994 (ttmt) cc_final: 0.8686 (tttt) REVERT: C 339 MET cc_start: 0.8111 (mmm) cc_final: 0.7870 (mmm) REVERT: C 453 TYR cc_start: 0.8065 (t80) cc_final: 0.7618 (t80) REVERT: C 455 GLU cc_start: 0.7027 (pt0) cc_final: 0.5706 (pt0) REVERT: C 547 MET cc_start: 0.5849 (mmm) cc_final: 0.5465 (mmm) REVERT: A 134 GLU cc_start: 0.7510 (tp30) cc_final: 0.6989 (tp30) REVERT: A 422 PHE cc_start: 0.7630 (m-80) cc_final: 0.7372 (m-80) REVERT: B 55 SER cc_start: 0.8558 (t) cc_final: 0.8083 (p) REVERT: B 147 THR cc_start: 0.8540 (m) cc_final: 0.8047 (p) REVERT: B 287 TYR cc_start: 0.6947 (t80) cc_final: 0.6569 (t80) outliers start: 65 outliers final: 62 residues processed: 311 average time/residue: 0.3184 time to fit residues: 165.6937 Evaluate side-chains 305 residues out of total 2904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 242 time to evaluate : 3.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 333 ASP Chi-restraints excluded: chain E residue 361 ILE Chi-restraints excluded: chain E residue 503 LEU Chi-restraints excluded: chain E residue 506 ARG Chi-restraints excluded: chain E residue 531 ASP Chi-restraints excluded: chain F residue 40 SER Chi-restraints excluded: chain F residue 121 ASN Chi-restraints excluded: chain F residue 213 SER Chi-restraints excluded: chain F residue 227 SER Chi-restraints excluded: chain F residue 355 ASN Chi-restraints excluded: chain F residue 392 ASP Chi-restraints excluded: chain F residue 425 ASP Chi-restraints excluded: chain F residue 431 ILE Chi-restraints excluded: chain F residue 449 ASN Chi-restraints excluded: chain F residue 478 THR Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 245 THR Chi-restraints excluded: chain D residue 256 SER Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 333 ASP Chi-restraints excluded: chain D residue 376 THR Chi-restraints excluded: chain D residue 401 THR Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 507 VAL Chi-restraints excluded: chain D residue 508 VAL Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 361 ILE Chi-restraints excluded: chain C residue 371 THR Chi-restraints excluded: chain C residue 456 ASN Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 531 ASP Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 449 ASN Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 256 SER Chi-restraints excluded: chain B residue 265 ASN Chi-restraints excluded: chain B residue 279 ASP Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 401 THR Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 508 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 184 optimal weight: 0.7980 chunk 296 optimal weight: 7.9990 chunk 180 optimal weight: 10.0000 chunk 140 optimal weight: 6.9990 chunk 205 optimal weight: 3.9990 chunk 310 optimal weight: 5.9990 chunk 286 optimal weight: 4.9990 chunk 247 optimal weight: 0.3980 chunk 25 optimal weight: 5.9990 chunk 191 optimal weight: 3.9990 chunk 151 optimal weight: 0.0670 overall best weight: 1.8522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 355 ASN C 334 ASN ** C 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.4909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.148 25602 Z= 0.251 Angle : 0.712 59.200 34860 Z= 0.390 Chirality : 0.049 0.323 4038 Planarity : 0.004 0.047 4446 Dihedral : 4.304 23.933 3464 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.30 % Allowed : 20.35 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.15), residues: 3156 helix: -0.93 (0.23), residues: 498 sheet: 0.14 (0.17), residues: 924 loop : -0.33 (0.15), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP F 108 HIS 0.006 0.001 HIS A 516 PHE 0.014 0.001 PHE E 199 TYR 0.022 0.001 TYR D 287 ARG 0.004 0.000 ARG F 498 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 243 time to evaluate : 3.424 Fit side-chains REVERT: E 81 MET cc_start: 0.6062 (tpp) cc_final: 0.5644 (tpp) REVERT: E 104 ASN cc_start: 0.6872 (m-40) cc_final: 0.5278 (t0) REVERT: E 137 ASP cc_start: 0.7753 (m-30) cc_final: 0.7274 (m-30) REVERT: E 198 ASP cc_start: 0.8099 (t0) cc_final: 0.7860 (t0) REVERT: E 339 MET cc_start: 0.8133 (mmm) cc_final: 0.7906 (mmm) REVERT: E 455 GLU cc_start: 0.6971 (pt0) cc_final: 0.6297 (pt0) REVERT: E 506 ARG cc_start: 0.8071 (OUTLIER) cc_final: 0.7619 (mtp85) REVERT: E 547 MET cc_start: 0.5786 (mmm) cc_final: 0.5455 (mmm) REVERT: F 134 GLU cc_start: 0.7531 (tp30) cc_final: 0.6959 (tp30) REVERT: F 193 ARG cc_start: 0.8460 (pmt170) cc_final: 0.8030 (pmt170) REVERT: F 255 LEU cc_start: 0.8814 (mt) cc_final: 0.8603 (mt) REVERT: F 422 PHE cc_start: 0.7668 (m-80) cc_final: 0.7416 (m-80) REVERT: D 55 SER cc_start: 0.8552 (t) cc_final: 0.8095 (p) REVERT: D 147 THR cc_start: 0.8527 (m) cc_final: 0.8034 (p) REVERT: D 287 TYR cc_start: 0.7255 (t80) cc_final: 0.6961 (t80) REVERT: C 81 MET cc_start: 0.6004 (tpp) cc_final: 0.5597 (tpp) REVERT: C 104 ASN cc_start: 0.6848 (m-40) cc_final: 0.5244 (t0) REVERT: C 137 ASP cc_start: 0.7699 (m-30) cc_final: 0.7188 (m-30) REVERT: C 177 LYS cc_start: 0.8992 (ttmt) cc_final: 0.8686 (tttt) REVERT: C 339 MET cc_start: 0.8115 (mmm) cc_final: 0.7869 (mmm) REVERT: C 453 TYR cc_start: 0.8065 (t80) cc_final: 0.7612 (t80) REVERT: C 455 GLU cc_start: 0.7024 (pt0) cc_final: 0.5706 (pt0) REVERT: C 506 ARG cc_start: 0.8070 (OUTLIER) cc_final: 0.7614 (mtp85) REVERT: C 547 MET cc_start: 0.5855 (mmm) cc_final: 0.5472 (mmm) REVERT: A 134 GLU cc_start: 0.7514 (tp30) cc_final: 0.6987 (tp30) REVERT: A 422 PHE cc_start: 0.7630 (m-80) cc_final: 0.7372 (m-80) REVERT: B 55 SER cc_start: 0.8559 (t) cc_final: 0.8082 (p) REVERT: B 147 THR cc_start: 0.8542 (m) cc_final: 0.8043 (p) REVERT: B 287 TYR cc_start: 0.6948 (t80) cc_final: 0.6570 (t80) outliers start: 66 outliers final: 64 residues processed: 302 average time/residue: 0.3335 time to fit residues: 169.1773 Evaluate side-chains 308 residues out of total 2904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 242 time to evaluate : 3.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 333 ASP Chi-restraints excluded: chain E residue 361 ILE Chi-restraints excluded: chain E residue 503 LEU Chi-restraints excluded: chain E residue 506 ARG Chi-restraints excluded: chain E residue 531 ASP Chi-restraints excluded: chain F residue 40 SER Chi-restraints excluded: chain F residue 121 ASN Chi-restraints excluded: chain F residue 213 SER Chi-restraints excluded: chain F residue 227 SER Chi-restraints excluded: chain F residue 355 ASN Chi-restraints excluded: chain F residue 392 ASP Chi-restraints excluded: chain F residue 425 ASP Chi-restraints excluded: chain F residue 431 ILE Chi-restraints excluded: chain F residue 449 ASN Chi-restraints excluded: chain F residue 478 THR Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 245 THR Chi-restraints excluded: chain D residue 256 SER Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 333 ASP Chi-restraints excluded: chain D residue 376 THR Chi-restraints excluded: chain D residue 401 THR Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 507 VAL Chi-restraints excluded: chain D residue 508 VAL Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 361 ILE Chi-restraints excluded: chain C residue 371 THR Chi-restraints excluded: chain C residue 456 ASN Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 506 ARG Chi-restraints excluded: chain C residue 531 ASP Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 449 ASN Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 256 SER Chi-restraints excluded: chain B residue 279 ASP Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 401 THR Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 508 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 196 optimal weight: 4.9990 chunk 263 optimal weight: 3.9990 chunk 75 optimal weight: 5.9990 chunk 228 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 68 optimal weight: 0.9990 chunk 247 optimal weight: 0.0050 chunk 103 optimal weight: 0.9990 chunk 254 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 overall best weight: 0.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 334 ASN ** C 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.113970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.091666 restraints weight = 88129.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.094750 restraints weight = 47423.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.096079 restraints weight = 28559.638| |-----------------------------------------------------------------------------| r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3204 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3204 r_free = 0.3204 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3202 r_free = 0.3202 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3202 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.4905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.148 25602 Z= 0.251 Angle : 0.712 59.200 34860 Z= 0.390 Chirality : 0.049 0.323 4038 Planarity : 0.004 0.047 4446 Dihedral : 4.304 23.933 3464 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.30 % Allowed : 20.35 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.15), residues: 3156 helix: -0.93 (0.23), residues: 498 sheet: 0.14 (0.17), residues: 924 loop : -0.33 (0.15), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP F 108 HIS 0.006 0.001 HIS A 516 PHE 0.014 0.001 PHE E 199 TYR 0.022 0.001 TYR D 287 ARG 0.004 0.000 ARG F 498 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4975.82 seconds wall clock time: 92 minutes 5.21 seconds (5525.21 seconds total)