Starting phenix.real_space_refine on Fri Jul 26 09:35:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rmm_19364/07_2024/8rmm_19364.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rmm_19364/07_2024/8rmm_19364.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rmm_19364/07_2024/8rmm_19364.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rmm_19364/07_2024/8rmm_19364.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rmm_19364/07_2024/8rmm_19364.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rmm_19364/07_2024/8rmm_19364.cif" } resolution = 3.26 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= 0.003 sd= 0.036 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 158 5.16 5 C 21092 2.51 5 N 5695 2.21 5 O 5937 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 130": "OE1" <-> "OE2" Residue "A GLU 154": "OE1" <-> "OE2" Residue "A GLU 230": "OE1" <-> "OE2" Residue "A GLU 233": "OE1" <-> "OE2" Residue "A GLU 259": "OE1" <-> "OE2" Residue "B GLU 154": "OE1" <-> "OE2" Residue "B GLU 228": "OE1" <-> "OE2" Residue "B GLU 230": "OE1" <-> "OE2" Residue "M GLU 46": "OE1" <-> "OE2" Residue "C GLU 85": "OE1" <-> "OE2" Residue "C GLU 126": "OE1" <-> "OE2" Residue "C GLU 134": "OE1" <-> "OE2" Residue "O GLU 44": "OE1" <-> "OE2" Residue "O GLU 46": "OE1" <-> "OE2" Residue "E GLU 262": "OE1" <-> "OE2" Residue "F GLU 261": "OE1" <-> "OE2" Residue "F GLU 262": "OE1" <-> "OE2" Residue "Q GLU 6": "OE1" <-> "OE2" Residue "Q GLU 44": "OE1" <-> "OE2" Residue "Q GLU 114": "OE1" <-> "OE2" Residue "G GLU 175": "OE1" <-> "OE2" Residue "G PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 44": "OE1" <-> "OE2" Residue "R GLU 89": "OE1" <-> "OE2" Residue "S GLU 89": "OE1" <-> "OE2" Residue "J GLU 134": "OE1" <-> "OE2" Residue "K GLU 130": "OE1" <-> "OE2" Residue "K GLU 176": "OE1" <-> "OE2" Residue "K GLU 228": "OE1" <-> "OE2" Residue "K GLU 230": "OE1" <-> "OE2" Residue "K GLU 237": "OE1" <-> "OE2" Residue "N GLU 6": "OE1" <-> "OE2" Residue "N GLU 44": "OE1" <-> "OE2" Residue "N GLU 114": "OE1" <-> "OE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 32888 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 2053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2053 Classifications: {'peptide': 263} Link IDs: {'PTRANS': 11, 'TRANS': 251} Chain breaks: 1 Chain: "L" Number of atoms: 733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 733 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 1, 'TRANS': 92} Chain breaks: 4 Chain: "B" Number of atoms: 2053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2053 Classifications: {'peptide': 263} Link IDs: {'PTRANS': 11, 'TRANS': 251} Chain breaks: 1 Chain: "M" Number of atoms: 733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 733 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 1, 'TRANS': 92} Chain breaks: 4 Chain: "C" Number of atoms: 2177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2177 Classifications: {'peptide': 282} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 14, 'TRANS': 267} Chain breaks: 1 Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 1, 'ASN:plan1': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 51 Chain: "D" Number of atoms: 2298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2298 Classifications: {'peptide': 288} Link IDs: {'PTRANS': 15, 'TRANS': 272} Chain breaks: 1 Chain: "O" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 960 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "E" Number of atoms: 2313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2313 Classifications: {'peptide': 290} Link IDs: {'PTRANS': 15, 'TRANS': 274} Chain breaks: 1 Chain: "P" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 960 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "F" Number of atoms: 2298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2298 Classifications: {'peptide': 288} Link IDs: {'PTRANS': 15, 'TRANS': 272} Chain breaks: 1 Chain: "Q" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 960 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "G" Number of atoms: 2298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2298 Classifications: {'peptide': 288} Link IDs: {'PTRANS': 15, 'TRANS': 272} Chain breaks: 1 Chain: "R" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 960 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "H" Number of atoms: 2289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2289 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 15, 'TRANS': 271} Chain breaks: 1 Chain: "S" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 960 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "I" Number of atoms: 2289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2289 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 15, 'TRANS': 271} Chain breaks: 1 Chain: "T" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 960 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "J" Number of atoms: 1778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1778 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 11, 'TRANS': 218} Chain breaks: 3 Unresolved non-hydrogen bonds: 88 Unresolved non-hydrogen angles: 111 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 9, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 63 Chain: "K" Number of atoms: 1871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1871 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 8, 'TRANS': 231} Chain breaks: 1 Chain: "U" Number of atoms: 733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 733 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 1, 'TRANS': 92} Chain breaks: 4 Chain: "N" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 960 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'PLC': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'PLC': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'PLC': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'PLC': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'PLC': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'PLC': 1} Classifications: {'undetermined': 1} Time building chain proxies: 17.88, per 1000 atoms: 0.54 Number of scatterers: 32888 At special positions: 0 Unit cell: (157.542, 197.904, 187.488, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 158 16.00 P 6 15.00 O 5937 8.00 N 5695 7.00 C 21092 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=28, symmetry=0 Simple disulfide: pdb=" SG CYS A 41 " - pdb=" SG CYS A 131 " distance=2.03 Simple disulfide: pdb=" SG CYS A 43 " - pdb=" SG CYS A 162 " distance=2.03 Simple disulfide: pdb=" SG CYS B 41 " - pdb=" SG CYS B 131 " distance=2.03 Simple disulfide: pdb=" SG CYS B 43 " - pdb=" SG CYS B 162 " distance=2.03 Simple disulfide: pdb=" SG CYS C 46 " - pdb=" SG CYS C 130 " distance=2.03 Simple disulfide: pdb=" SG CYS C 48 " - pdb=" SG CYS C 162 " distance=2.03 Simple disulfide: pdb=" SG CYS D 46 " - pdb=" SG CYS D 130 " distance=2.03 Simple disulfide: pdb=" SG CYS D 48 " - pdb=" SG CYS D 162 " distance=2.03 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 46 " - pdb=" SG CYS E 130 " distance=2.03 Simple disulfide: pdb=" SG CYS E 48 " - pdb=" SG CYS E 162 " distance=2.03 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS P 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 46 " - pdb=" SG CYS F 130 " distance=2.03 Simple disulfide: pdb=" SG CYS F 48 " - pdb=" SG CYS F 162 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 22 " - pdb=" SG CYS Q 96 " distance=2.04 Simple disulfide: pdb=" SG CYS G 46 " - pdb=" SG CYS G 130 " distance=2.03 Simple disulfide: pdb=" SG CYS G 48 " - pdb=" SG CYS G 162 " distance=2.03 Simple disulfide: pdb=" SG CYS R 22 " - pdb=" SG CYS R 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 46 " - pdb=" SG CYS H 130 " distance=2.03 Simple disulfide: pdb=" SG CYS H 48 " - pdb=" SG CYS H 162 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.04 Simple disulfide: pdb=" SG CYS I 46 " - pdb=" SG CYS I 130 " distance=2.03 Simple disulfide: pdb=" SG CYS I 48 " - pdb=" SG CYS I 162 " distance=2.03 Simple disulfide: pdb=" SG CYS T 22 " - pdb=" SG CYS T 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 48 " - pdb=" SG CYS J 162 " distance=2.03 Simple disulfide: pdb=" SG CYS K 41 " - pdb=" SG CYS K 131 " distance=2.03 Simple disulfide: pdb=" SG CYS K 43 " - pdb=" SG CYS K 162 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 12.29 Conformation dependent library (CDL) restraints added in 5.4 seconds 8142 Ramachandran restraints generated. 4071 Oldfield, 0 Emsley, 4071 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7778 Finding SS restraints... Secondary structure from input PDB file: 163 helices and 33 sheets defined 56.7% alpha, 15.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.53 Creating SS restraints... Processing helix chain 'A' and resid 5 through 15 Processing helix chain 'A' and resid 15 through 38 removed outlier: 4.190A pdb=" N ILE A 19 " --> pdb=" O ASN A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 70 Proline residue: A 59 - end of helix Processing helix chain 'A' and resid 71 through 82 removed outlier: 3.801A pdb=" N TRP A 75 " --> pdb=" O ARG A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 107 removed outlier: 4.023A pdb=" N ILE A 107 " --> pdb=" O ARG A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 126 removed outlier: 4.503A pdb=" N ALA A 114 " --> pdb=" O ARG A 110 " (cutoff:3.500A) Proline residue: A 115 - end of helix Processing helix chain 'A' and resid 126 through 133 Processing helix chain 'A' and resid 142 through 146 Processing helix chain 'A' and resid 151 through 160 removed outlier: 3.598A pdb=" N GLU A 155 " --> pdb=" O SER A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 208 Processing helix chain 'A' and resid 216 through 253 removed outlier: 3.554A pdb=" N TYR A 220 " --> pdb=" O LEU A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 273 removed outlier: 4.106A pdb=" N TRP A 272 " --> pdb=" O SER A 268 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N LYS A 273 " --> pdb=" O CYS A 269 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 268 through 273' Processing helix chain 'A' and resid 274 through 277 removed outlier: 3.772A pdb=" N VAL A 277 " --> pdb=" O ASP A 274 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 274 through 277' Processing helix chain 'L' and resid 87 through 91 Processing helix chain 'B' and resid 6 through 15 Processing helix chain 'B' and resid 15 through 38 removed outlier: 3.888A pdb=" N ILE B 19 " --> pdb=" O ASN B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 70 removed outlier: 3.633A pdb=" N GLY B 52 " --> pdb=" O ASN B 48 " (cutoff:3.500A) Proline residue: B 59 - end of helix Processing helix chain 'B' and resid 72 through 82 removed outlier: 3.798A pdb=" N THR B 76 " --> pdb=" O SER B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 126 removed outlier: 3.553A pdb=" N GLY B 109 " --> pdb=" O PHE B 105 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ARG B 110 " --> pdb=" O SER B 106 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ALA B 114 " --> pdb=" O ARG B 110 " (cutoff:3.500A) Proline residue: B 115 - end of helix Processing helix chain 'B' and resid 126 through 133 Processing helix chain 'B' and resid 151 through 160 Processing helix chain 'B' and resid 170 through 208 Processing helix chain 'B' and resid 214 through 252 removed outlier: 4.054A pdb=" N CYS B 219 " --> pdb=" O SER B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 275 removed outlier: 4.026A pdb=" N TRP B 272 " --> pdb=" O SER B 268 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N LYS B 273 " --> pdb=" O CYS B 269 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASP B 274 " --> pdb=" O GLN B 270 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ILE B 275 " --> pdb=" O ASP B 271 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 268 through 275' Processing helix chain 'M' and resid 62 through 65 Processing helix chain 'M' and resid 87 through 91 Processing helix chain 'C' and resid 20 through 43 Processing helix chain 'C' and resid 52 through 60 Processing helix chain 'C' and resid 61 through 76 removed outlier: 3.536A pdb=" N ASN C 76 " --> pdb=" O GLY C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 89 removed outlier: 4.517A pdb=" N TRP C 80 " --> pdb=" O ASN C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 111 removed outlier: 3.569A pdb=" N LEU C 102 " --> pdb=" O PRO C 98 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU C 107 " --> pdb=" O LEU C 103 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLY C 108 " --> pdb=" O SER C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 125 Processing helix chain 'C' and resid 125 through 133 Processing helix chain 'C' and resid 137 through 141 removed outlier: 3.784A pdb=" N LEU C 141 " --> pdb=" O PRO C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 159 Processing helix chain 'C' and resid 166 through 168 No H-bonds generated for 'chain 'C' and resid 166 through 168' Processing helix chain 'C' and resid 169 through 209 removed outlier: 3.989A pdb=" N GLU C 175 " --> pdb=" O ASP C 171 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ARG C 181 " --> pdb=" O SER C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 252 Processing helix chain 'C' and resid 257 through 267 Processing helix chain 'C' and resid 274 through 281 Processing helix chain 'C' and resid 297 through 306 Processing helix chain 'D' and resid 38 through 42 Processing helix chain 'D' and resid 52 through 76 removed outlier: 3.512A pdb=" N VAL D 63 " --> pdb=" O ALA D 59 " (cutoff:3.500A) Proline residue: D 64 - end of helix Processing helix chain 'D' and resid 79 through 90 removed outlier: 3.570A pdb=" N VAL D 83 " --> pdb=" O THR D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 111 removed outlier: 3.742A pdb=" N THR D 99 " --> pdb=" O SER D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 125 removed outlier: 3.841A pdb=" N ILE D 120 " --> pdb=" O THR D 116 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLY D 125 " --> pdb=" O SER D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 130 Processing helix chain 'D' and resid 137 through 141 Processing helix chain 'D' and resid 152 through 158 removed outlier: 3.503A pdb=" N ILE D 156 " --> pdb=" O HIS D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 163 Processing helix chain 'D' and resid 166 through 168 No H-bonds generated for 'chain 'D' and resid 166 through 168' Processing helix chain 'D' and resid 169 through 210 removed outlier: 3.541A pdb=" N GLU D 174 " --> pdb=" O SER D 170 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N PHE D 200 " --> pdb=" O ALA D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 213 through 252 removed outlier: 3.543A pdb=" N ASN D 226 " --> pdb=" O GLN D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 267 removed outlier: 3.665A pdb=" N GLU D 262 " --> pdb=" O LYS D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 280 Processing helix chain 'D' and resid 297 through 304 Processing helix chain 'D' and resid 323 through 329 Processing helix chain 'O' and resid 87 through 91 Processing helix chain 'E' and resid 36 through 42 removed outlier: 3.603A pdb=" N SER E 40 " --> pdb=" O GLN E 36 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL E 41 " --> pdb=" O GLU E 37 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N VAL E 42 " --> pdb=" O LEU E 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 36 through 42' Processing helix chain 'E' and resid 52 through 76 Proline residue: E 64 - end of helix removed outlier: 3.528A pdb=" N ASN E 76 " --> pdb=" O GLY E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 89 Processing helix chain 'E' and resid 95 through 111 removed outlier: 3.583A pdb=" N THR E 99 " --> pdb=" O SER E 95 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU E 101 " --> pdb=" O ALA E 97 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N SER E 105 " --> pdb=" O LEU E 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 125 removed outlier: 3.755A pdb=" N ILE E 120 " --> pdb=" O THR E 116 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU E 122 " --> pdb=" O SER E 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 125 through 133 Processing helix chain 'E' and resid 134 through 136 No H-bonds generated for 'chain 'E' and resid 134 through 136' Processing helix chain 'E' and resid 137 through 141 Processing helix chain 'E' and resid 152 through 159 removed outlier: 3.760A pdb=" N ILE E 156 " --> pdb=" O HIS E 152 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARG E 159 " --> pdb=" O GLU E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 163 Processing helix chain 'E' and resid 166 through 168 No H-bonds generated for 'chain 'E' and resid 166 through 168' Processing helix chain 'E' and resid 169 through 210 removed outlier: 3.652A pdb=" N ARG E 181 " --> pdb=" O SER E 177 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE E 200 " --> pdb=" O ALA E 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 213 through 252 removed outlier: 3.953A pdb=" N GLN E 232 " --> pdb=" O ASP E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 257 through 267 removed outlier: 3.840A pdb=" N GLU E 262 " --> pdb=" O LYS E 258 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA E 265 " --> pdb=" O GLU E 261 " (cutoff:3.500A) Processing helix chain 'E' and resid 274 through 280 Processing helix chain 'E' and resid 297 through 304 Processing helix chain 'E' and resid 323 through 329 removed outlier: 3.947A pdb=" N PHE E 329 " --> pdb=" O LEU E 325 " (cutoff:3.500A) Processing helix chain 'P' and resid 87 through 91 Processing helix chain 'F' and resid 38 through 42 Processing helix chain 'F' and resid 52 through 76 Proline residue: F 64 - end of helix Processing helix chain 'F' and resid 79 through 90 removed outlier: 3.515A pdb=" N ARG F 89 " --> pdb=" O GLU F 85 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ARG F 90 " --> pdb=" O CYS F 86 " (cutoff:3.500A) Processing helix chain 'F' and resid 95 through 111 removed outlier: 3.643A pdb=" N THR F 99 " --> pdb=" O SER F 95 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LEU F 101 " --> pdb=" O ALA F 97 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 125 removed outlier: 3.775A pdb=" N ILE F 120 " --> pdb=" O THR F 116 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU F 122 " --> pdb=" O SER F 118 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLY F 125 " --> pdb=" O SER F 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 125 through 132 removed outlier: 3.660A pdb=" N ALA F 131 " --> pdb=" O ALA F 127 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 141 Processing helix chain 'F' and resid 152 through 159 removed outlier: 3.645A pdb=" N ARG F 159 " --> pdb=" O GLU F 155 " (cutoff:3.500A) Processing helix chain 'F' and resid 160 through 163 Processing helix chain 'F' and resid 166 through 168 No H-bonds generated for 'chain 'F' and resid 166 through 168' Processing helix chain 'F' and resid 169 through 210 removed outlier: 3.635A pdb=" N PHE F 200 " --> pdb=" O ALA F 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 213 through 252 removed outlier: 3.624A pdb=" N ASN F 226 " --> pdb=" O GLN F 222 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLN F 229 " --> pdb=" O ALA F 225 " (cutoff:3.500A) Processing helix chain 'F' and resid 259 through 267 removed outlier: 3.523A pdb=" N LEU F 263 " --> pdb=" O ASP F 259 " (cutoff:3.500A) Processing helix chain 'F' and resid 274 through 280 Processing helix chain 'F' and resid 297 through 304 Processing helix chain 'F' and resid 323 through 329 removed outlier: 3.513A pdb=" N LEU F 328 " --> pdb=" O ALA F 324 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N PHE F 329 " --> pdb=" O LEU F 325 " (cutoff:3.500A) Processing helix chain 'Q' and resid 87 through 91 Processing helix chain 'G' and resid 38 through 42 Processing helix chain 'G' and resid 52 through 76 removed outlier: 3.504A pdb=" N VAL G 63 " --> pdb=" O ALA G 59 " (cutoff:3.500A) Proline residue: G 64 - end of helix Processing helix chain 'G' and resid 79 through 89 removed outlier: 3.594A pdb=" N ARG G 89 " --> pdb=" O GLU G 85 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 111 removed outlier: 3.822A pdb=" N THR G 99 " --> pdb=" O SER G 95 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU G 101 " --> pdb=" O ALA G 97 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 125 removed outlier: 3.656A pdb=" N ILE G 120 " --> pdb=" O THR G 116 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLY G 125 " --> pdb=" O SER G 121 " (cutoff:3.500A) Processing helix chain 'G' and resid 125 through 132 removed outlier: 3.527A pdb=" N ALA G 131 " --> pdb=" O ALA G 127 " (cutoff:3.500A) Processing helix chain 'G' and resid 133 through 136 Processing helix chain 'G' and resid 152 through 159 removed outlier: 3.604A pdb=" N ARG G 159 " --> pdb=" O GLU G 155 " (cutoff:3.500A) Processing helix chain 'G' and resid 160 through 163 Processing helix chain 'G' and resid 166 through 168 No H-bonds generated for 'chain 'G' and resid 166 through 168' Processing helix chain 'G' and resid 169 through 210 Processing helix chain 'G' and resid 215 through 252 removed outlier: 3.567A pdb=" N ASN G 226 " --> pdb=" O GLN G 222 " (cutoff:3.500A) Processing helix chain 'G' and resid 257 through 267 removed outlier: 3.926A pdb=" N GLU G 262 " --> pdb=" O LYS G 258 " (cutoff:3.500A) Processing helix chain 'G' and resid 274 through 280 Processing helix chain 'G' and resid 297 through 304 Processing helix chain 'G' and resid 323 through 329 removed outlier: 3.588A pdb=" N LEU G 328 " --> pdb=" O ALA G 324 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N PHE G 329 " --> pdb=" O LEU G 325 " (cutoff:3.500A) Processing helix chain 'R' and resid 87 through 91 Processing helix chain 'H' and resid 52 through 76 Proline residue: H 64 - end of helix Processing helix chain 'H' and resid 79 through 89 removed outlier: 3.578A pdb=" N ARG H 89 " --> pdb=" O GLU H 85 " (cutoff:3.500A) Processing helix chain 'H' and resid 95 through 111 removed outlier: 3.884A pdb=" N THR H 99 " --> pdb=" O SER H 95 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU H 102 " --> pdb=" O PRO H 98 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER H 105 " --> pdb=" O LEU H 101 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 125 removed outlier: 3.769A pdb=" N ILE H 120 " --> pdb=" O THR H 116 " (cutoff:3.500A) Processing helix chain 'H' and resid 125 through 132 Processing helix chain 'H' and resid 133 through 136 removed outlier: 3.693A pdb=" N VAL H 136 " --> pdb=" O SER H 133 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 133 through 136' Processing helix chain 'H' and resid 152 through 159 removed outlier: 3.635A pdb=" N ARG H 159 " --> pdb=" O GLU H 155 " (cutoff:3.500A) Processing helix chain 'H' and resid 166 through 168 No H-bonds generated for 'chain 'H' and resid 166 through 168' Processing helix chain 'H' and resid 169 through 210 removed outlier: 3.922A pdb=" N ARG H 181 " --> pdb=" O SER H 177 " (cutoff:3.500A) Processing helix chain 'H' and resid 213 through 252 removed outlier: 3.608A pdb=" N ALA H 218 " --> pdb=" O TYR H 214 " (cutoff:3.500A) Processing helix chain 'H' and resid 257 through 267 removed outlier: 3.574A pdb=" N GLU H 262 " --> pdb=" O LYS H 258 " (cutoff:3.500A) Processing helix chain 'H' and resid 274 through 280 Processing helix chain 'H' and resid 297 through 304 Processing helix chain 'H' and resid 323 through 328 Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.547A pdb=" N THR S 91 " --> pdb=" O PRO S 88 " (cutoff:3.500A) Processing helix chain 'I' and resid 52 through 76 removed outlier: 3.537A pdb=" N TYR I 56 " --> pdb=" O ARG I 52 " (cutoff:3.500A) Proline residue: I 64 - end of helix removed outlier: 3.550A pdb=" N GLY I 72 " --> pdb=" O LEU I 68 " (cutoff:3.500A) Processing helix chain 'I' and resid 77 through 90 removed outlier: 3.508A pdb=" N ASN I 81 " --> pdb=" O ASN I 77 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG I 90 " --> pdb=" O CYS I 86 " (cutoff:3.500A) Processing helix chain 'I' and resid 95 through 111 removed outlier: 3.902A pdb=" N THR I 99 " --> pdb=" O SER I 95 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU I 101 " --> pdb=" O ALA I 97 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU I 102 " --> pdb=" O PRO I 98 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER I 104 " --> pdb=" O PHE I 100 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU I 107 " --> pdb=" O LEU I 103 " (cutoff:3.500A) Processing helix chain 'I' and resid 111 through 125 removed outlier: 4.205A pdb=" N ILE I 120 " --> pdb=" O THR I 116 " (cutoff:3.500A) Processing helix chain 'I' and resid 125 through 132 Processing helix chain 'I' and resid 137 through 141 Processing helix chain 'I' and resid 152 through 159 Processing helix chain 'I' and resid 166 through 168 No H-bonds generated for 'chain 'I' and resid 166 through 168' Processing helix chain 'I' and resid 169 through 210 removed outlier: 3.517A pdb=" N TYR I 182 " --> pdb=" O ARG I 178 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N HIS I 207 " --> pdb=" O LYS I 203 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TYR I 208 " --> pdb=" O CYS I 204 " (cutoff:3.500A) Processing helix chain 'I' and resid 213 through 252 removed outlier: 3.558A pdb=" N ASP I 228 " --> pdb=" O ARG I 224 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N GLN I 229 " --> pdb=" O ALA I 225 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU I 230 " --> pdb=" O ASN I 226 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ARG I 249 " --> pdb=" O ASN I 245 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE I 250 " --> pdb=" O ASN I 246 " (cutoff:3.500A) Processing helix chain 'I' and resid 257 through 267 removed outlier: 4.183A pdb=" N GLU I 262 " --> pdb=" O LYS I 258 " (cutoff:3.500A) Processing helix chain 'I' and resid 274 through 280 Processing helix chain 'I' and resid 297 through 304 Processing helix chain 'I' and resid 323 through 328 Processing helix chain 'T' and resid 87 through 91 Processing helix chain 'J' and resid 52 through 76 removed outlier: 3.558A pdb=" N VAL J 63 " --> pdb=" O ALA J 59 " (cutoff:3.500A) Proline residue: J 64 - end of helix Processing helix chain 'J' and resid 77 through 89 removed outlier: 3.653A pdb=" N LEU J 82 " --> pdb=" O HIS J 78 " (cutoff:3.500A) Processing helix chain 'J' and resid 99 through 110 removed outlier: 3.612A pdb=" N ALA J 110 " --> pdb=" O ILE J 106 " (cutoff:3.500A) Processing helix chain 'J' and resid 111 through 125 removed outlier: 3.619A pdb=" N VAL J 115 " --> pdb=" O ALA J 111 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ARG J 124 " --> pdb=" O ILE J 120 " (cutoff:3.500A) Processing helix chain 'J' and resid 125 through 135 removed outlier: 3.573A pdb=" N VAL J 129 " --> pdb=" O GLY J 125 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N CYS J 130 " --> pdb=" O GLU J 126 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ALA J 131 " --> pdb=" O ALA J 127 " (cutoff:3.500A) Processing helix chain 'J' and resid 153 through 159 Processing helix chain 'J' and resid 170 through 210 removed outlier: 3.726A pdb=" N ARG J 179 " --> pdb=" O GLU J 175 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLY J 188 " --> pdb=" O SER J 184 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N TRP J 189 " --> pdb=" O GLN J 185 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N LEU J 190 " --> pdb=" O LEU J 186 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU J 191 " --> pdb=" O PHE J 187 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LYS J 203 " --> pdb=" O VAL J 199 " (cutoff:3.500A) Processing helix chain 'J' and resid 213 through 252 removed outlier: 3.876A pdb=" N GLN J 229 " --> pdb=" O ALA J 225 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL J 237 " --> pdb=" O ARG J 233 " (cutoff:3.500A) Processing helix chain 'J' and resid 257 through 267 removed outlier: 4.043A pdb=" N GLU J 262 " --> pdb=" O LYS J 258 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU J 263 " --> pdb=" O ASP J 259 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ILE J 264 " --> pdb=" O ASP J 260 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ALA J 265 " --> pdb=" O GLU J 261 " (cutoff:3.500A) Processing helix chain 'J' and resid 274 through 282 removed outlier: 3.736A pdb=" N ILE J 281 " --> pdb=" O GLN J 277 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N THR J 282 " --> pdb=" O TRP J 278 " (cutoff:3.500A) Processing helix chain 'J' and resid 297 through 303 Processing helix chain 'K' and resid 6 through 14 Processing helix chain 'K' and resid 15 through 36 removed outlier: 3.922A pdb=" N ILE K 19 " --> pdb=" O ASN K 15 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N SER K 36 " --> pdb=" O GLN K 32 " (cutoff:3.500A) Processing helix chain 'K' and resid 48 through 70 Proline residue: K 59 - end of helix removed outlier: 3.585A pdb=" N LEU K 63 " --> pdb=" O PRO K 59 " (cutoff:3.500A) Processing helix chain 'K' and resid 72 through 82 removed outlier: 3.510A pdb=" N THR K 76 " --> pdb=" O SER K 72 " (cutoff:3.500A) Processing helix chain 'K' and resid 95 through 112 removed outlier: 3.822A pdb=" N ARG K 110 " --> pdb=" O SER K 106 " (cutoff:3.500A) Processing helix chain 'K' and resid 112 through 126 removed outlier: 3.797A pdb=" N LEU K 116 " --> pdb=" O VAL K 112 " (cutoff:3.500A) Processing helix chain 'K' and resid 126 through 131 Processing helix chain 'K' and resid 151 through 158 Processing helix chain 'K' and resid 170 through 210 removed outlier: 3.704A pdb=" N ARG K 174 " --> pdb=" O VAL K 170 " (cutoff:3.500A) Processing helix chain 'K' and resid 216 through 252 removed outlier: 3.695A pdb=" N GLU K 230 " --> pdb=" O GLN K 226 " (cutoff:3.500A) Processing helix chain 'U' and resid 87 through 91 Processing helix chain 'N' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.803A pdb=" N VAL L 5 " --> pdb=" O ALA L 23 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR L 78 " --> pdb=" O ASP L 73 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 58 through 60 removed outlier: 6.439A pdb=" N TRP L 36 " --> pdb=" O VAL L 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'M' and resid 5 through 7 Processing sheet with id=AA4, first strand: chain 'M' and resid 58 through 60 removed outlier: 6.408A pdb=" N TRP M 36 " --> pdb=" O VAL M 48 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N VAL M 93 " --> pdb=" O GLN M 39 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 289 through 290 Processing sheet with id=AA6, first strand: chain 'O' and resid 3 through 7 Processing sheet with id=AA7, first strand: chain 'O' and resid 58 through 60 removed outlier: 5.256A pdb=" N GLY O 47 " --> pdb=" O ARG O 38 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ARG O 38 " --> pdb=" O GLY O 47 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA O 49 " --> pdb=" O TRP O 36 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ALA O 99 " --> pdb=" O TYR O 33 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLY O 35 " --> pdb=" O ALA O 97 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA O 98 " --> pdb=" O TYR O 115 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ASN O 105 " --> pdb=" O GLY O 109 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N HIS O 111 " --> pdb=" O GLN O 103 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN O 103 " --> pdb=" O HIS O 111 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'O' and resid 58 through 60 removed outlier: 5.256A pdb=" N GLY O 47 " --> pdb=" O ARG O 38 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ARG O 38 " --> pdb=" O GLY O 47 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA O 49 " --> pdb=" O TRP O 36 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ALA O 99 " --> pdb=" O TYR O 33 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLY O 35 " --> pdb=" O ALA O 97 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA O 98 " --> pdb=" O TYR O 115 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N TYR O 112 " --> pdb=" O GLU E 317 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N GLU E 317 " --> pdb=" O TYR O 112 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N GLU O 114 " --> pdb=" O ASN E 315 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N ASN E 315 " --> pdb=" O GLU O 114 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 289 through 290 Processing sheet with id=AB1, first strand: chain 'P' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'P' and resid 58 through 60 removed outlier: 5.671A pdb=" N GLY P 47 " --> pdb=" O ARG P 38 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ARG P 38 " --> pdb=" O GLY P 47 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ALA P 49 " --> pdb=" O TRP P 36 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N CYS P 96 " --> pdb=" O GLY P 117 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASN P 105 " --> pdb=" O GLY P 109 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N HIS P 111 " --> pdb=" O GLN P 103 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'P' and resid 58 through 60 removed outlier: 5.671A pdb=" N GLY P 47 " --> pdb=" O ARG P 38 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ARG P 38 " --> pdb=" O GLY P 47 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ALA P 49 " --> pdb=" O TRP P 36 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N CYS P 96 " --> pdb=" O GLY P 117 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N TYR P 112 " --> pdb=" O GLU F 317 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N GLU F 317 " --> pdb=" O TYR P 112 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N GLU P 114 " --> pdb=" O ASN F 315 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N ASN F 315 " --> pdb=" O GLU P 114 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 289 through 290 Processing sheet with id=AB5, first strand: chain 'Q' and resid 3 through 7 removed outlier: 3.543A pdb=" N THR Q 78 " --> pdb=" O ASP Q 73 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'Q' and resid 58 through 60 removed outlier: 6.936A pdb=" N TRP Q 36 " --> pdb=" O VAL Q 48 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N ALA Q 50 " --> pdb=" O LEU Q 34 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N LEU Q 34 " --> pdb=" O ALA Q 50 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA Q 99 " --> pdb=" O TYR Q 33 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLY Q 35 " --> pdb=" O ALA Q 97 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'Q' and resid 103 through 105 removed outlier: 3.537A pdb=" N GLN Q 103 " --> pdb=" O HIS Q 111 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASN Q 105 " --> pdb=" O GLY Q 109 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 289 through 290 Processing sheet with id=AB9, first strand: chain 'R' and resid 3 through 7 removed outlier: 3.672A pdb=" N GLN R 3 " --> pdb=" O SER R 25 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'R' and resid 58 through 60 removed outlier: 7.048A pdb=" N TRP R 36 " --> pdb=" O VAL R 48 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N ALA R 50 " --> pdb=" O LEU R 34 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N LEU R 34 " --> pdb=" O ALA R 50 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ASN R 105 " --> pdb=" O GLY R 109 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'R' and resid 58 through 60 removed outlier: 7.048A pdb=" N TRP R 36 " --> pdb=" O VAL R 48 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N ALA R 50 " --> pdb=" O LEU R 34 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N LEU R 34 " --> pdb=" O ALA R 50 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N TYR R 110 " --> pdb=" O MET H 318 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 289 through 290 Processing sheet with id=AC4, first strand: chain 'S' and resid 3 through 7 removed outlier: 3.680A pdb=" N SER S 21 " --> pdb=" O SER S 7 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU S 20 " --> pdb=" O LEU S 81 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'S' and resid 58 through 60 removed outlier: 6.933A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ALA S 50 " --> pdb=" O LEU S 34 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LEU S 34 " --> pdb=" O ALA S 50 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLY S 35 " --> pdb=" O ALA S 97 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA S 98 " --> pdb=" O TYR S 115 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ASN S 105 " --> pdb=" O GLY S 109 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLN S 103 " --> pdb=" O HIS S 111 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'S' and resid 58 through 60 removed outlier: 6.933A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ALA S 50 " --> pdb=" O LEU S 34 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LEU S 34 " --> pdb=" O ALA S 50 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLY S 35 " --> pdb=" O ALA S 97 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA S 98 " --> pdb=" O TYR S 115 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N TYR S 112 " --> pdb=" O GLU I 317 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N GLU I 317 " --> pdb=" O TYR S 112 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N GLU S 114 " --> pdb=" O ASN I 315 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N ASN I 315 " --> pdb=" O GLU S 114 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 289 through 290 Processing sheet with id=AC8, first strand: chain 'T' and resid 3 through 7 removed outlier: 3.533A pdb=" N SER T 7 " --> pdb=" O SER T 21 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU T 18 " --> pdb=" O MET T 83 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'T' and resid 58 through 60 removed outlier: 7.099A pdb=" N TRP T 36 " --> pdb=" O VAL T 48 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N ALA T 50 " --> pdb=" O LEU T 34 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N LEU T 34 " --> pdb=" O ALA T 50 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLY T 35 " --> pdb=" O ALA T 97 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'U' and resid 4 through 7 Processing sheet with id=AD2, first strand: chain 'U' and resid 10 through 13 removed outlier: 6.429A pdb=" N GLY U 10 " --> pdb=" O THR U 112 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N SER U 114 " --> pdb=" O GLY U 10 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N VAL U 12 " --> pdb=" O SER U 114 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N MET U 34 " --> pdb=" O ALA U 50 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N ALA U 50 " --> pdb=" O MET U 34 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N TRP U 36 " --> pdb=" O VAL U 48 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.543A pdb=" N THR N 78 " --> pdb=" O ASP N 73 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'N' and resid 58 through 60 removed outlier: 6.936A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N ALA N 50 " --> pdb=" O LEU N 34 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N LEU N 34 " --> pdb=" O ALA N 50 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ALA N 99 " --> pdb=" O TYR N 33 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLY N 35 " --> pdb=" O ALA N 97 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'N' and resid 58 through 60 removed outlier: 6.936A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N ALA N 50 " --> pdb=" O LEU N 34 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N LEU N 34 " --> pdb=" O ALA N 50 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ALA N 99 " --> pdb=" O TYR N 33 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLY N 35 " --> pdb=" O ALA N 97 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'N' and resid 103 through 105 removed outlier: 3.537A pdb=" N GLN N 103 " --> pdb=" O HIS N 111 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASN N 105 " --> pdb=" O GLY N 109 " (cutoff:3.500A) 1958 hydrogen bonds defined for protein. 5562 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: 11.20 Time building geometry restraints manager: 13.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 7063 1.33 - 1.46: 8960 1.46 - 1.58: 17440 1.58 - 1.71: 12 1.71 - 1.84: 193 Bond restraints: 33668 Sorted by residual: bond pdb=" N CYS A 43 " pdb=" CA CYS A 43 " ideal model delta sigma weight residual 1.455 1.491 -0.036 1.37e-02 5.33e+03 6.93e+00 bond pdb=" CB TYR T 33 " pdb=" CG TYR T 33 " ideal model delta sigma weight residual 1.512 1.569 -0.057 2.20e-02 2.07e+03 6.63e+00 bond pdb=" N ILE O 28 " pdb=" CA ILE O 28 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.35e-02 5.49e+03 6.24e+00 bond pdb=" N GLN E 36 " pdb=" CA GLN E 36 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.21e-02 6.83e+03 6.11e+00 bond pdb=" N ASP A 169 " pdb=" CA ASP A 169 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.35e-02 5.49e+03 5.99e+00 ... (remaining 33663 not shown) Histogram of bond angle deviations from ideal: 93.07 - 101.31: 33 101.31 - 109.55: 2978 109.55 - 117.79: 21733 117.79 - 126.03: 20369 126.03 - 134.27: 622 Bond angle restraints: 45735 Sorted by residual: angle pdb=" N ILE O 28 " pdb=" CA ILE O 28 " pdb=" C ILE O 28 " ideal model delta sigma weight residual 112.29 107.14 5.15 9.40e-01 1.13e+00 3.00e+01 angle pdb=" CA GLN K 238 " pdb=" CB GLN K 238 " pdb=" CG GLN K 238 " ideal model delta sigma weight residual 114.10 121.83 -7.73 2.00e+00 2.50e-01 1.49e+01 angle pdb=" CB GLN S 121 " pdb=" CG GLN S 121 " pdb=" CD GLN S 121 " ideal model delta sigma weight residual 112.60 119.09 -6.49 1.70e+00 3.46e-01 1.46e+01 angle pdb=" CA GLN S 121 " pdb=" CB GLN S 121 " pdb=" CG GLN S 121 " ideal model delta sigma weight residual 114.10 121.69 -7.59 2.00e+00 2.50e-01 1.44e+01 angle pdb=" N TYR F 287 " pdb=" CA TYR F 287 " pdb=" C TYR F 287 " ideal model delta sigma weight residual 111.17 116.51 -5.34 1.41e+00 5.03e-01 1.44e+01 ... (remaining 45730 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.83: 19489 34.83 - 69.67: 344 69.67 - 104.50: 34 104.50 - 139.33: 2 139.33 - 174.17: 22 Dihedral angle restraints: 19891 sinusoidal: 7793 harmonic: 12098 Sorted by residual: dihedral pdb=" C2' PLC H 401 " pdb=" C' PLC H 401 " pdb=" C1' PLC H 401 " pdb=" O2 PLC H 401 " ideal model delta sinusoidal sigma weight residual 169.53 -4.64 174.17 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C2' PLC H 401 " pdb=" C' PLC H 401 " pdb=" C1' PLC H 401 " pdb=" O' PLC H 401 " ideal model delta sinusoidal sigma weight residual 348.97 175.32 173.65 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C3 PLC G 401 " pdb=" C1 PLC G 401 " pdb=" C2 PLC G 401 " pdb=" O3P PLC G 401 " ideal model delta sinusoidal sigma weight residual 67.16 -120.26 -172.58 1 3.00e+01 1.11e-03 2.12e+01 ... (remaining 19888 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 4421 0.060 - 0.120: 576 0.120 - 0.180: 43 0.180 - 0.240: 6 0.240 - 0.300: 2 Chirality restraints: 5048 Sorted by residual: chirality pdb=" CB VAL K 112 " pdb=" CA VAL K 112 " pdb=" CG1 VAL K 112 " pdb=" CG2 VAL K 112 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.25e+00 chirality pdb=" CB VAL A 112 " pdb=" CA VAL A 112 " pdb=" CG1 VAL A 112 " pdb=" CG2 VAL A 112 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" CG LEU K 64 " pdb=" CB LEU K 64 " pdb=" CD1 LEU K 64 " pdb=" CD2 LEU K 64 " both_signs ideal model delta sigma weight residual False -2.59 -2.82 0.23 2.00e-01 2.50e+01 1.31e+00 ... (remaining 5045 not shown) Planarity restraints: 5822 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP T 52 " -0.061 2.00e-02 2.50e+03 4.01e-02 4.02e+01 pdb=" CG TRP T 52 " 0.106 2.00e-02 2.50e+03 pdb=" CD1 TRP T 52 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP T 52 " 0.013 2.00e-02 2.50e+03 pdb=" NE1 TRP T 52 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP T 52 " -0.010 2.00e-02 2.50e+03 pdb=" CE3 TRP T 52 " -0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP T 52 " -0.011 2.00e-02 2.50e+03 pdb=" CZ3 TRP T 52 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP T 52 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP S 52 " -0.037 2.00e-02 2.50e+03 2.97e-02 2.21e+01 pdb=" CG TRP S 52 " 0.080 2.00e-02 2.50e+03 pdb=" CD1 TRP S 52 " -0.032 2.00e-02 2.50e+03 pdb=" CD2 TRP S 52 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP S 52 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP S 52 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP S 52 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP S 52 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP S 52 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP S 52 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER E 49 " 0.058 5.00e-02 4.00e+02 8.59e-02 1.18e+01 pdb=" N PRO E 50 " -0.148 5.00e-02 4.00e+02 pdb=" CA PRO E 50 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO E 50 " 0.047 5.00e-02 4.00e+02 ... (remaining 5819 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 538 2.68 - 3.23: 32529 3.23 - 3.79: 50564 3.79 - 4.34: 67783 4.34 - 4.90: 110412 Nonbonded interactions: 261826 Sorted by model distance: nonbonded pdb=" OD1 ASP I 314 " pdb=" N ASN I 315 " model vdw 2.123 2.520 nonbonded pdb=" OH TYR B 142 " pdb=" OE1 GLU B 176 " model vdw 2.195 2.440 nonbonded pdb=" O LEU J 230 " pdb=" OG1 THR J 234 " model vdw 2.210 2.440 nonbonded pdb=" O MET K 144 " pdb=" NH2 ARG U 35 " model vdw 2.215 2.520 nonbonded pdb=" O LEU F 122 " pdb=" OG SER F 184 " model vdw 2.227 2.440 ... (remaining 261821 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 5 through 255) selection = (chain 'B' and resid 5 through 255) selection = chain 'K' } ncs_group { reference = (chain 'C' and resid 38 through 306) selection = (chain 'D' and (resid 38 through 89 or resid 96 through 138 or (resid 139 throug \ h 146 and (name N or name CA or name C or name O or name CB )) or resid 147 thro \ ugh 149 or (resid 150 through 151 and (name N or name CA or name C or name O or \ name CB )) or resid 152 through 162 or (resid 163 through 165 and (name N or nam \ e CA or name C or name O or name CB )) or resid 166 or (resid 167 through 168 an \ d (name N or name CA or name C or name O or name CB )) or resid 169 through 235 \ or (resid 236 and (name N or name CA or name C or name O or name CB )) or resid \ 237 through 256 or (resid 257 through 259 and (name N or name CA or name C or na \ me O or name CB )) or resid 260 or (resid 261 through 262 and (name N or name CA \ or name C or name O or name CB )) or resid 263 through 285 or (resid 286 and (n \ ame N or name CA or name C or name O or name CB )) or resid 287 through 289 or ( \ resid 290 through 291 and (name N or name CA or name C or name O or name CB )) o \ r resid 292 through 306)) selection = (chain 'E' and (resid 38 through 89 or resid 96 through 138 or (resid 139 throug \ h 146 and (name N or name CA or name C or name O or name CB )) or resid 147 thro \ ugh 149 or (resid 150 through 151 and (name N or name CA or name C or name O or \ name CB )) or resid 152 through 162 or (resid 163 through 165 and (name N or nam \ e CA or name C or name O or name CB )) or resid 166 or (resid 167 through 168 an \ d (name N or name CA or name C or name O or name CB )) or resid 169 through 235 \ or (resid 236 and (name N or name CA or name C or name O or name CB )) or resid \ 237 through 256 or (resid 257 through 259 and (name N or name CA or name C or na \ me O or name CB )) or resid 260 or (resid 261 through 262 and (name N or name CA \ or name C or name O or name CB )) or resid 263 through 285 or (resid 286 and (n \ ame N or name CA or name C or name O or name CB )) or resid 287 through 289 or ( \ resid 290 through 291 and (name N or name CA or name C or name O or name CB )) o \ r resid 292 through 306)) selection = (chain 'F' and (resid 38 through 89 or resid 96 through 138 or (resid 139 throug \ h 146 and (name N or name CA or name C or name O or name CB )) or resid 147 thro \ ugh 149 or (resid 150 through 151 and (name N or name CA or name C or name O or \ name CB )) or resid 152 through 162 or (resid 163 through 165 and (name N or nam \ e CA or name C or name O or name CB )) or resid 166 or (resid 167 through 168 an \ d (name N or name CA or name C or name O or name CB )) or resid 169 through 235 \ or (resid 236 and (name N or name CA or name C or name O or name CB )) or resid \ 237 through 256 or (resid 257 through 259 and (name N or name CA or name C or na \ me O or name CB )) or resid 260 or (resid 261 through 262 and (name N or name CA \ or name C or name O or name CB )) or resid 263 through 285 or (resid 286 and (n \ ame N or name CA or name C or name O or name CB )) or resid 287 through 289 or ( \ resid 290 through 291 and (name N or name CA or name C or name O or name CB )) o \ r resid 292 through 306)) selection = (chain 'G' and (resid 38 through 89 or resid 96 through 138 or (resid 139 throug \ h 146 and (name N or name CA or name C or name O or name CB )) or resid 147 thro \ ugh 149 or (resid 150 through 151 and (name N or name CA or name C or name O or \ name CB )) or resid 152 through 162 or (resid 163 through 165 and (name N or nam \ e CA or name C or name O or name CB )) or resid 166 or (resid 167 through 168 an \ d (name N or name CA or name C or name O or name CB )) or resid 169 through 235 \ or (resid 236 and (name N or name CA or name C or name O or name CB )) or resid \ 237 through 256 or (resid 257 through 259 and (name N or name CA or name C or na \ me O or name CB )) or resid 260 or (resid 261 through 262 and (name N or name CA \ or name C or name O or name CB )) or resid 263 through 285 or (resid 286 and (n \ ame N or name CA or name C or name O or name CB )) or resid 287 through 289 or ( \ resid 290 through 291 and (name N or name CA or name C or name O or name CB )) o \ r resid 292 through 306)) selection = (chain 'H' and (resid 38 through 89 or resid 96 through 138 or (resid 139 throug \ h 146 and (name N or name CA or name C or name O or name CB )) or resid 147 thro \ ugh 149 or (resid 150 through 151 and (name N or name CA or name C or name O or \ name CB )) or resid 152 through 162 or (resid 163 through 165 and (name N or nam \ e CA or name C or name O or name CB )) or resid 166 or (resid 167 through 168 an \ d (name N or name CA or name C or name O or name CB )) or resid 169 through 235 \ or (resid 236 and (name N or name CA or name C or name O or name CB )) or resid \ 237 through 256 or (resid 257 through 259 and (name N or name CA or name C or na \ me O or name CB )) or resid 260 or (resid 261 through 262 and (name N or name CA \ or name C or name O or name CB )) or resid 263 through 285 or (resid 286 and (n \ ame N or name CA or name C or name O or name CB )) or resid 287 through 289 or ( \ resid 290 through 291 and (name N or name CA or name C or name O or name CB )) o \ r resid 292 through 306)) selection = (chain 'I' and (resid 38 through 89 or resid 96 through 138 or (resid 139 throug \ h 146 and (name N or name CA or name C or name O or name CB )) or resid 147 thro \ ugh 149 or (resid 150 through 151 and (name N or name CA or name C or name O or \ name CB )) or resid 152 through 162 or (resid 163 through 165 and (name N or nam \ e CA or name C or name O or name CB )) or resid 166 or (resid 167 through 168 an \ d (name N or name CA or name C or name O or name CB )) or resid 169 through 235 \ or (resid 236 and (name N or name CA or name C or name O or name CB )) or resid \ 237 through 256 or (resid 257 through 259 and (name N or name CA or name C or na \ me O or name CB )) or resid 260 or (resid 261 through 262 and (name N or name CA \ or name C or name O or name CB )) or resid 263 through 285 or (resid 286 and (n \ ame N or name CA or name C or name O or name CB )) or resid 287 through 289 or ( \ resid 290 through 291 and (name N or name CA or name C or name O or name CB )) o \ r resid 292 through 306)) } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'U' } ncs_group { reference = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.060 Extract box with map and model: 1.390 Check model and map are aligned: 0.260 Set scattering table: 0.260 Process input model: 81.340 Find NCS groups from input model: 2.130 Set up NCS constraints: 0.170 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:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 89.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 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 : 0.003 0.070 33668 Z= 0.204 Angle : 0.671 11.024 45735 Z= 0.341 Chirality : 0.041 0.300 5048 Planarity : 0.005 0.100 5822 Dihedral : 14.988 174.169 12029 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.98 % Favored : 96.00 % Rotamer: Outliers : 0.79 % Allowed : 13.47 % Favored : 85.74 % 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: 0.62 (0.14), residues: 4071 helix: 0.67 (0.12), residues: 2058 sheet: 1.50 (0.20), residues: 622 loop : -0.34 (0.18), residues: 1391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.106 0.002 TRP T 52 HIS 0.008 0.001 HIS D 147 PHE 0.030 0.001 PHE U 97 TYR 0.040 0.001 TYR U 37 ARG 0.014 0.001 ARG P 29 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8142 Ramachandran restraints generated. 4071 Oldfield, 0 Emsley, 4071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8142 Ramachandran restraints generated. 4071 Oldfield, 0 Emsley, 4071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 3471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 403 time to evaluate : 3.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 39 GLN cc_start: 0.0751 (tp40) cc_final: 0.0515 (tp40) REVERT: M 82 GLN cc_start: 0.6426 (tp-100) cc_final: 0.6106 (tp-100) REVERT: C 100 PHE cc_start: 0.4494 (m-80) cc_final: 0.4237 (t80) REVERT: O 72 LEU cc_start: 0.5866 (tp) cc_final: 0.5589 (pt) REVERT: E 101 LEU cc_start: 0.8277 (mt) cc_final: 0.7893 (tt) REVERT: E 109 ARG cc_start: 0.7735 (tmm-80) cc_final: 0.7506 (ttt-90) REVERT: P 118 GLN cc_start: 0.7249 (mp10) cc_final: 0.7004 (mp10) REVERT: R 83 MET cc_start: 0.4724 (mmp) cc_final: 0.4286 (mmp) REVERT: S 60 TYR cc_start: 0.4745 (m-80) cc_final: 0.4519 (m-80) REVERT: S 67 ARG cc_start: 0.5325 (ttm110) cc_final: 0.4413 (mtp85) REVERT: J 134 GLU cc_start: 0.5708 (tt0) cc_final: 0.5094 (mt-10) REVERT: J 288 ARG cc_start: 0.2817 (mmt180) cc_final: 0.2471 (mmt90) REVERT: K 112 VAL cc_start: 0.7536 (p) cc_final: 0.7308 (m) REVERT: K 224 HIS cc_start: 0.2653 (t-90) cc_final: 0.2285 (t-90) REVERT: K 244 MET cc_start: 0.6194 (mmm) cc_final: 0.5849 (mmt) outliers start: 27 outliers final: 10 residues processed: 424 average time/residue: 0.4374 time to fit residues: 297.0750 Evaluate side-chains 352 residues out of total 3471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 342 time to evaluate : 3.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 174 ARG Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain Q residue 51 LEU Chi-restraints excluded: chain Q residue 89 GLU Chi-restraints excluded: chain R residue 84 ASN Chi-restraints excluded: chain H residue 257 ASN Chi-restraints excluded: chain S residue 72 LEU Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 185 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 407 random chunks: chunk 343 optimal weight: 7.9990 chunk 308 optimal weight: 9.9990 chunk 171 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 208 optimal weight: 2.9990 chunk 164 optimal weight: 0.0270 chunk 319 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 chunk 193 optimal weight: 0.8980 chunk 237 optimal weight: 1.9990 chunk 369 optimal weight: 6.9990 overall best weight: 1.5844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 ASN L 33 HIS C 279 ASN ** C 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 82 GLN P 111 HIS F 246 ASN Q 1 GLN G 246 ASN G 304 GLN ** R 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 246 ASN ** I 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 186 GLN ** K 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 1 GLN N 111 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.1381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 33668 Z= 0.240 Angle : 0.617 12.741 45735 Z= 0.315 Chirality : 0.040 0.225 5048 Planarity : 0.004 0.061 5822 Dihedral : 13.222 170.189 4813 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.57 % Allowed : 12.21 % Favored : 85.22 % 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: 1.46 (0.14), residues: 4071 helix: 1.66 (0.11), residues: 2115 sheet: 1.63 (0.21), residues: 575 loop : -0.36 (0.18), residues: 1381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP T 52 HIS 0.010 0.001 HIS E 88 PHE 0.027 0.001 PHE J 160 TYR 0.019 0.001 TYR E 287 ARG 0.006 0.000 ARG S 67 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8142 Ramachandran restraints generated. 4071 Oldfield, 0 Emsley, 4071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8142 Ramachandran restraints generated. 4071 Oldfield, 0 Emsley, 4071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 3471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 365 time to evaluate : 4.127 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: A 75 TRP cc_start: 0.6167 (t60) cc_final: 0.5882 (t60) REVERT: L 70 ILE cc_start: 0.6556 (tp) cc_final: 0.6008 (pt) REVERT: B 249 LYS cc_start: 0.5989 (ptpt) cc_final: 0.5559 (tptp) REVERT: O 110 TYR cc_start: 0.8354 (m-80) cc_final: 0.8021 (m-10) REVERT: E 109 ARG cc_start: 0.7746 (OUTLIER) cc_final: 0.7534 (ttt-90) REVERT: H 257 ASN cc_start: 0.6880 (OUTLIER) cc_final: 0.6404 (p0) REVERT: S 6 GLU cc_start: 0.4354 (pm20) cc_final: 0.3855 (pt0) REVERT: S 67 ARG cc_start: 0.5443 (ttm110) cc_final: 0.4695 (mtp85) REVERT: S 72 LEU cc_start: 0.7460 (OUTLIER) cc_final: 0.7165 (pp) REVERT: J 134 GLU cc_start: 0.5332 (tt0) cc_final: 0.4595 (mt-10) REVERT: J 189 TRP cc_start: 0.6964 (m100) cc_final: 0.6736 (m100) REVERT: J 288 ARG cc_start: 0.2909 (mmt180) cc_final: 0.2470 (mmt90) REVERT: K 244 MET cc_start: 0.6055 (mmm) cc_final: 0.5515 (tpt) outliers start: 88 outliers final: 46 residues processed: 427 average time/residue: 0.4487 time to fit residues: 314.6399 Evaluate side-chains 366 residues out of total 3471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 317 time to evaluate : 3.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASN Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 227 ASN Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 59 HIS Chi-restraints excluded: chain L residue 73 ASP Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain M residue 98 VAL Chi-restraints excluded: chain C residue 77 ASN Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain O residue 70 VAL Chi-restraints excluded: chain O residue 74 ASN Chi-restraints excluded: chain O residue 93 LEU Chi-restraints excluded: chain E residue 109 ARG Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 314 ASP Chi-restraints excluded: chain P residue 5 VAL Chi-restraints excluded: chain P residue 51 LEU Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain F residue 314 ASP Chi-restraints excluded: chain Q residue 22 CYS Chi-restraints excluded: chain Q residue 68 PHE Chi-restraints excluded: chain G residue 94 CYS Chi-restraints excluded: chain G residue 104 SER Chi-restraints excluded: chain G residue 182 TYR Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain R residue 84 ASN Chi-restraints excluded: chain R residue 100 THR Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain H residue 169 LEU Chi-restraints excluded: chain H residue 195 VAL Chi-restraints excluded: chain H residue 257 ASN Chi-restraints excluded: chain H residue 269 VAL Chi-restraints excluded: chain H residue 321 LEU Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 72 LEU Chi-restraints excluded: chain S residue 95 TYR Chi-restraints excluded: chain S residue 100 THR Chi-restraints excluded: chain I residue 86 CYS Chi-restraints excluded: chain J residue 71 ILE Chi-restraints excluded: chain J residue 76 ASN Chi-restraints excluded: chain J residue 212 LEU Chi-restraints excluded: chain K residue 195 LEU Chi-restraints excluded: chain U residue 73 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 407 random chunks: chunk 205 optimal weight: 0.9990 chunk 114 optimal weight: 1.9990 chunk 307 optimal weight: 3.9990 chunk 251 optimal weight: 1.9990 chunk 101 optimal weight: 0.9980 chunk 370 optimal weight: 6.9990 chunk 399 optimal weight: 20.0000 chunk 329 optimal weight: 7.9990 chunk 367 optimal weight: 8.9990 chunk 126 optimal weight: 7.9990 chunk 297 optimal weight: 0.1980 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 110 GLN ** C 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 111 HIS Q 121 GLN G 246 ASN R 121 GLN ** I 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 121 GLN K 31 GLN K 32 GLN ** K 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 239 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 33668 Z= 0.194 Angle : 0.570 13.343 45735 Z= 0.284 Chirality : 0.039 0.241 5048 Planarity : 0.003 0.037 5822 Dihedral : 12.672 170.211 4798 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.92 % Allowed : 13.03 % Favored : 84.05 % 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: 1.61 (0.14), residues: 4071 helix: 1.91 (0.11), residues: 2119 sheet: 1.53 (0.20), residues: 589 loop : -0.49 (0.18), residues: 1363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP J 220 HIS 0.008 0.001 HIS D 88 PHE 0.018 0.001 PHE G 329 TYR 0.018 0.001 TYR E 287 ARG 0.004 0.000 ARG C 124 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8142 Ramachandran restraints generated. 4071 Oldfield, 0 Emsley, 4071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8142 Ramachandran restraints generated. 4071 Oldfield, 0 Emsley, 4071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 3471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 358 time to evaluate : 3.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ASN cc_start: -0.0063 (m-40) cc_final: -0.0602 (t0) REVERT: L 70 ILE cc_start: 0.6634 (tp) cc_final: 0.6261 (pt) REVERT: C 229 GLN cc_start: 0.8122 (tp-100) cc_final: 0.7421 (tp-100) REVERT: O 74 ASN cc_start: 0.5738 (OUTLIER) cc_final: 0.5531 (t0) REVERT: O 110 TYR cc_start: 0.8390 (m-80) cc_final: 0.8041 (m-10) REVERT: E 91 THR cc_start: 0.0295 (OUTLIER) cc_final: -0.0046 (m) REVERT: E 109 ARG cc_start: 0.7740 (OUTLIER) cc_final: 0.7520 (ttt-90) REVERT: G 321 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8343 (pp) REVERT: R 33 TYR cc_start: 0.8391 (m-80) cc_final: 0.8187 (m-10) REVERT: H 257 ASN cc_start: 0.6756 (OUTLIER) cc_final: 0.6273 (p0) REVERT: S 6 GLU cc_start: 0.4610 (pm20) cc_final: 0.4332 (tm-30) REVERT: S 67 ARG cc_start: 0.5619 (ttm110) cc_final: 0.5210 (mtp85) REVERT: S 72 LEU cc_start: 0.7998 (OUTLIER) cc_final: 0.7606 (pp) REVERT: J 134 GLU cc_start: 0.5480 (tt0) cc_final: 0.4700 (mt-10) REVERT: J 288 ARG cc_start: 0.2923 (mmt180) cc_final: 0.2576 (mmt90) REVERT: K 192 LEU cc_start: 0.6570 (pp) cc_final: 0.5810 (mp) REVERT: K 244 MET cc_start: 0.6408 (mmm) cc_final: 0.6196 (tpp) outliers start: 100 outliers final: 49 residues processed: 433 average time/residue: 0.4748 time to fit residues: 340.7402 Evaluate side-chains 364 residues out of total 3471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 309 time to evaluate : 3.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 227 ASN Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 59 HIS Chi-restraints excluded: chain L residue 73 ASP Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain M residue 73 ASP Chi-restraints excluded: chain M residue 84 ASN Chi-restraints excluded: chain M residue 98 VAL Chi-restraints excluded: chain C residue 77 ASN Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain O residue 70 VAL Chi-restraints excluded: chain O residue 74 ASN Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 109 ARG Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 314 ASP Chi-restraints excluded: chain P residue 5 VAL Chi-restraints excluded: chain P residue 79 VAL Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain F residue 163 LYS Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain F residue 314 ASP Chi-restraints excluded: chain Q residue 22 CYS Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 104 SER Chi-restraints excluded: chain G residue 182 TYR Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain G residue 254 VAL Chi-restraints excluded: chain G residue 321 LEU Chi-restraints excluded: chain R residue 79 VAL Chi-restraints excluded: chain R residue 121 GLN Chi-restraints excluded: chain H residue 53 ASN Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain H residue 169 LEU Chi-restraints excluded: chain H residue 257 ASN Chi-restraints excluded: chain H residue 269 VAL Chi-restraints excluded: chain H residue 321 LEU Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 72 LEU Chi-restraints excluded: chain S residue 95 TYR Chi-restraints excluded: chain S residue 100 THR Chi-restraints excluded: chain I residue 86 CYS Chi-restraints excluded: chain J residue 76 ASN Chi-restraints excluded: chain J residue 212 LEU Chi-restraints excluded: chain J residue 256 LEU Chi-restraints excluded: chain K residue 195 LEU Chi-restraints excluded: chain K residue 239 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 407 random chunks: chunk 365 optimal weight: 40.0000 chunk 278 optimal weight: 0.8980 chunk 192 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 176 optimal weight: 6.9990 chunk 248 optimal weight: 20.0000 chunk 371 optimal weight: 9.9990 chunk 393 optimal weight: 0.0000 chunk 194 optimal weight: 2.9990 chunk 352 optimal weight: 20.0000 chunk 106 optimal weight: 3.9990 overall best weight: 1.9790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 141 HIS ** M 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 257 ASN ** P 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 77 ASN G 246 ASN ** R 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 121 GLN ** I 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 239 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 33668 Z= 0.255 Angle : 0.580 13.887 45735 Z= 0.288 Chirality : 0.040 0.246 5048 Planarity : 0.004 0.035 5822 Dihedral : 12.338 170.081 4796 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 3.42 % Allowed : 13.32 % Favored : 83.26 % 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: 1.58 (0.14), residues: 4071 helix: 1.92 (0.11), residues: 2117 sheet: 1.48 (0.20), residues: 589 loop : -0.55 (0.18), residues: 1365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP N 36 HIS 0.010 0.001 HIS E 88 PHE 0.015 0.001 PHE H 329 TYR 0.020 0.001 TYR E 287 ARG 0.007 0.000 ARG F 124 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8142 Ramachandran restraints generated. 4071 Oldfield, 0 Emsley, 4071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8142 Ramachandran restraints generated. 4071 Oldfield, 0 Emsley, 4071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 3471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 330 time to evaluate : 3.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ASN cc_start: 0.0250 (m-40) cc_final: -0.0558 (t0) REVERT: L 70 ILE cc_start: 0.6598 (tp) cc_final: 0.6284 (pt) REVERT: B 68 PHE cc_start: 0.7442 (OUTLIER) cc_final: 0.6177 (m-80) REVERT: B 170 VAL cc_start: 0.7048 (OUTLIER) cc_final: 0.6595 (p) REVERT: C 229 GLN cc_start: 0.8119 (tp-100) cc_final: 0.7430 (tp-100) REVERT: O 110 TYR cc_start: 0.8419 (m-80) cc_final: 0.8043 (m-10) REVERT: E 109 ARG cc_start: 0.7833 (OUTLIER) cc_final: 0.7191 (tmt170) REVERT: G 321 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8353 (pp) REVERT: R 33 TYR cc_start: 0.8547 (m-80) cc_final: 0.8279 (m-10) REVERT: R 83 MET cc_start: 0.4889 (mmp) cc_final: 0.4119 (mmt) REVERT: H 205 LEU cc_start: 0.8887 (tt) cc_final: 0.8677 (tp) REVERT: H 257 ASN cc_start: 0.6944 (OUTLIER) cc_final: 0.6553 (p0) REVERT: S 6 GLU cc_start: 0.4777 (pm20) cc_final: 0.4437 (tm-30) REVERT: S 67 ARG cc_start: 0.5769 (ttm110) cc_final: 0.5159 (mtp85) REVERT: I 262 GLU cc_start: 0.7650 (mm-30) cc_final: 0.7331 (mp0) REVERT: J 134 GLU cc_start: 0.5544 (tt0) cc_final: 0.4711 (mt-10) REVERT: J 288 ARG cc_start: 0.2823 (mmt180) cc_final: 0.2307 (mmt90) REVERT: K 192 LEU cc_start: 0.6734 (pp) cc_final: 0.6133 (mp) REVERT: K 244 MET cc_start: 0.6421 (mmm) cc_final: 0.6098 (tpp) REVERT: U 11 LEU cc_start: 0.2717 (OUTLIER) cc_final: 0.2446 (mp) outliers start: 117 outliers final: 70 residues processed: 425 average time/residue: 0.4024 time to fit residues: 281.0285 Evaluate side-chains 371 residues out of total 3471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 295 time to evaluate : 3.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 227 ASN Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 59 HIS Chi-restraints excluded: chain L residue 73 ASP Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 68 PHE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain M residue 73 ASP Chi-restraints excluded: chain M residue 84 ASN Chi-restraints excluded: chain M residue 98 VAL Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 77 ASN Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain O residue 79 VAL Chi-restraints excluded: chain O residue 93 LEU Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 109 ARG Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 314 ASP Chi-restraints excluded: chain E residue 321 LEU Chi-restraints excluded: chain P residue 4 LEU Chi-restraints excluded: chain P residue 5 VAL Chi-restraints excluded: chain P residue 79 VAL Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain F residue 163 LYS Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain F residue 314 ASP Chi-restraints excluded: chain F residue 321 LEU Chi-restraints excluded: chain Q residue 22 CYS Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 104 SER Chi-restraints excluded: chain G residue 182 TYR Chi-restraints excluded: chain G residue 192 ILE Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain G residue 254 VAL Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain G residue 321 LEU Chi-restraints excluded: chain R residue 79 VAL Chi-restraints excluded: chain R residue 100 THR Chi-restraints excluded: chain H residue 53 ASN Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain H residue 169 LEU Chi-restraints excluded: chain H residue 195 VAL Chi-restraints excluded: chain H residue 257 ASN Chi-restraints excluded: chain H residue 269 VAL Chi-restraints excluded: chain H residue 321 LEU Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain S residue 100 THR Chi-restraints excluded: chain I residue 86 CYS Chi-restraints excluded: chain I residue 269 VAL Chi-restraints excluded: chain J residue 76 ASN Chi-restraints excluded: chain J residue 198 LEU Chi-restraints excluded: chain J residue 212 LEU Chi-restraints excluded: chain J residue 256 LEU Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 195 LEU Chi-restraints excluded: chain U residue 11 LEU Chi-restraints excluded: chain U residue 73 ASP Chi-restraints excluded: chain U residue 93 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 407 random chunks: chunk 327 optimal weight: 10.0000 chunk 223 optimal weight: 0.9990 chunk 5 optimal weight: 6.9990 chunk 292 optimal weight: 20.0000 chunk 162 optimal weight: 0.8980 chunk 335 optimal weight: 7.9990 chunk 271 optimal weight: 0.0870 chunk 0 optimal weight: 30.0000 chunk 200 optimal weight: 0.9980 chunk 353 optimal weight: 20.0000 chunk 99 optimal weight: 1.9990 overall best weight: 0.9962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 246 ASN ** R 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 216 GLN S 121 GLN ** I 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 246 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 33668 Z= 0.172 Angle : 0.556 12.770 45735 Z= 0.272 Chirality : 0.038 0.271 5048 Planarity : 0.003 0.034 5822 Dihedral : 11.867 170.681 4794 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.78 % Allowed : 14.34 % Favored : 82.88 % 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: 1.71 (0.14), residues: 4071 helix: 2.07 (0.11), residues: 2122 sheet: 1.43 (0.20), residues: 589 loop : -0.52 (0.18), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP U 36 HIS 0.009 0.001 HIS K 239 PHE 0.022 0.001 PHE J 160 TYR 0.020 0.001 TYR O 33 ARG 0.007 0.000 ARG F 124 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8142 Ramachandran restraints generated. 4071 Oldfield, 0 Emsley, 4071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8142 Ramachandran restraints generated. 4071 Oldfield, 0 Emsley, 4071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 3471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 332 time to evaluate : 3.505 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: A 6 ASN cc_start: 0.0152 (m-40) cc_final: -0.0782 (t0) REVERT: L 70 ILE cc_start: 0.6829 (tp) cc_final: 0.6378 (pt) REVERT: C 229 GLN cc_start: 0.8091 (tp-100) cc_final: 0.7357 (tp-100) REVERT: D 285 TYR cc_start: 0.7834 (t80) cc_final: 0.7597 (t80) REVERT: E 91 THR cc_start: 0.0463 (OUTLIER) cc_final: 0.0091 (m) REVERT: E 109 ARG cc_start: 0.7790 (OUTLIER) cc_final: 0.7428 (ttt-90) REVERT: F 81 ASN cc_start: 0.8017 (p0) cc_final: 0.7797 (p0) REVERT: G 172 PHE cc_start: 0.7348 (m-80) cc_final: 0.6790 (t80) REVERT: G 321 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8328 (pp) REVERT: R 83 MET cc_start: 0.4830 (mmp) cc_final: 0.4129 (mmt) REVERT: H 205 LEU cc_start: 0.8872 (tt) cc_final: 0.8670 (tp) REVERT: H 257 ASN cc_start: 0.6725 (OUTLIER) cc_final: 0.6278 (p0) REVERT: S 6 GLU cc_start: 0.4781 (pm20) cc_final: 0.4426 (tp30) REVERT: S 60 TYR cc_start: 0.6782 (m-80) cc_final: 0.6078 (m-80) REVERT: S 67 ARG cc_start: 0.5584 (ttm110) cc_final: 0.4943 (mtp85) REVERT: I 262 GLU cc_start: 0.7454 (mm-30) cc_final: 0.7042 (mp0) REVERT: J 134 GLU cc_start: 0.5641 (tt0) cc_final: 0.4848 (mt-10) REVERT: K 192 LEU cc_start: 0.6717 (pp) cc_final: 0.6196 (mp) REVERT: U 11 LEU cc_start: 0.2721 (OUTLIER) cc_final: 0.2457 (mp) outliers start: 95 outliers final: 62 residues processed: 403 average time/residue: 0.4241 time to fit residues: 278.9387 Evaluate side-chains 378 residues out of total 3471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 311 time to evaluate : 3.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 59 HIS Chi-restraints excluded: chain L residue 73 ASP Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 237 GLU Chi-restraints excluded: chain M residue 73 ASP Chi-restraints excluded: chain M residue 98 VAL Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 77 ASN Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain O residue 79 VAL Chi-restraints excluded: chain O residue 93 LEU Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 109 ARG Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 314 ASP Chi-restraints excluded: chain E residue 321 LEU Chi-restraints excluded: chain P residue 4 LEU Chi-restraints excluded: chain P residue 5 VAL Chi-restraints excluded: chain P residue 79 VAL Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 239 SER Chi-restraints excluded: chain F residue 314 ASP Chi-restraints excluded: chain F residue 321 LEU Chi-restraints excluded: chain Q residue 22 CYS Chi-restraints excluded: chain Q residue 28 ILE Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 104 SER Chi-restraints excluded: chain G residue 192 ILE Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain G residue 254 VAL Chi-restraints excluded: chain G residue 321 LEU Chi-restraints excluded: chain R residue 34 LEU Chi-restraints excluded: chain R residue 79 VAL Chi-restraints excluded: chain R residue 84 ASN Chi-restraints excluded: chain R residue 100 THR Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain H residue 169 LEU Chi-restraints excluded: chain H residue 257 ASN Chi-restraints excluded: chain H residue 262 GLU Chi-restraints excluded: chain H residue 269 VAL Chi-restraints excluded: chain H residue 321 LEU Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain I residue 269 VAL Chi-restraints excluded: chain T residue 28 ILE Chi-restraints excluded: chain J residue 76 ASN Chi-restraints excluded: chain J residue 198 LEU Chi-restraints excluded: chain J residue 256 LEU Chi-restraints excluded: chain J residue 260 ASP Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 113 ILE Chi-restraints excluded: chain K residue 195 LEU Chi-restraints excluded: chain K residue 218 HIS Chi-restraints excluded: chain U residue 11 LEU Chi-restraints excluded: chain U residue 93 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 407 random chunks: chunk 132 optimal weight: 0.1980 chunk 354 optimal weight: 9.9990 chunk 77 optimal weight: 5.9990 chunk 230 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 393 optimal weight: 40.0000 chunk 326 optimal weight: 0.0770 chunk 182 optimal weight: 0.4980 chunk 32 optimal weight: 8.9990 chunk 130 optimal weight: 0.3980 chunk 206 optimal weight: 0.5980 overall best weight: 0.3538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 ASN ** A 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 300 HIS E 246 ASN ** P 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 246 ASN ** R 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 246 ASN ** S 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 238 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.2631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 33668 Z= 0.136 Angle : 0.540 13.318 45735 Z= 0.262 Chirality : 0.037 0.283 5048 Planarity : 0.003 0.040 5822 Dihedral : 11.148 169.887 4794 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.48 % Allowed : 14.67 % Favored : 82.85 % 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: 1.91 (0.14), residues: 4071 helix: 2.28 (0.11), residues: 2129 sheet: 1.49 (0.21), residues: 554 loop : -0.45 (0.18), residues: 1388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP U 36 HIS 0.009 0.001 HIS K 246 PHE 0.016 0.001 PHE Q 68 TYR 0.019 0.001 TYR K 220 ARG 0.009 0.000 ARG J 52 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8142 Ramachandran restraints generated. 4071 Oldfield, 0 Emsley, 4071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8142 Ramachandran restraints generated. 4071 Oldfield, 0 Emsley, 4071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 3471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 334 time to evaluate : 3.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ASN cc_start: 0.0227 (m-40) cc_final: -0.0771 (t0) REVERT: A 74 MET cc_start: 0.6467 (ppp) cc_final: 0.5419 (tmm) REVERT: L 21 SER cc_start: 0.6055 (t) cc_final: 0.5779 (m) REVERT: L 70 ILE cc_start: 0.6804 (tp) cc_final: 0.6361 (pt) REVERT: L 80 TYR cc_start: 0.4622 (m-10) cc_final: 0.4244 (m-10) REVERT: B 68 PHE cc_start: 0.7410 (OUTLIER) cc_final: 0.6174 (m-80) REVERT: C 229 GLN cc_start: 0.8077 (tp-100) cc_final: 0.7390 (tp-100) REVERT: D 285 TYR cc_start: 0.7710 (t80) cc_final: 0.7348 (t80) REVERT: O 60 TYR cc_start: 0.6828 (m-80) cc_final: 0.6584 (m-80) REVERT: E 91 THR cc_start: 0.1091 (OUTLIER) cc_final: 0.0665 (m) REVERT: E 109 ARG cc_start: 0.7609 (OUTLIER) cc_final: 0.7373 (ttt-90) REVERT: F 81 ASN cc_start: 0.8098 (p0) cc_final: 0.7839 (p0) REVERT: Q 57 GLN cc_start: 0.7240 (OUTLIER) cc_final: 0.6613 (tt0) REVERT: G 321 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8320 (pp) REVERT: R 83 MET cc_start: 0.4760 (mmp) cc_final: 0.4151 (mmt) REVERT: H 205 LEU cc_start: 0.8837 (tt) cc_final: 0.8621 (tp) REVERT: H 257 ASN cc_start: 0.6436 (OUTLIER) cc_final: 0.6124 (p0) REVERT: S 6 GLU cc_start: 0.4761 (pm20) cc_final: 0.4351 (tm-30) REVERT: S 60 TYR cc_start: 0.6569 (m-80) cc_final: 0.5946 (m-80) REVERT: I 262 GLU cc_start: 0.7433 (mm-30) cc_final: 0.6971 (mp0) REVERT: J 134 GLU cc_start: 0.5535 (tt0) cc_final: 0.4774 (mt-10) REVERT: J 198 LEU cc_start: 0.7470 (OUTLIER) cc_final: 0.7213 (mm) REVERT: J 288 ARG cc_start: 0.3016 (mmt180) cc_final: 0.2578 (mmt90) REVERT: K 192 LEU cc_start: 0.6770 (pp) cc_final: 0.6286 (mp) REVERT: U 11 LEU cc_start: 0.2712 (OUTLIER) cc_final: 0.2441 (mp) outliers start: 85 outliers final: 56 residues processed: 402 average time/residue: 0.4314 time to fit residues: 286.2702 Evaluate side-chains 363 residues out of total 3471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 299 time to evaluate : 3.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASN Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 59 HIS Chi-restraints excluded: chain L residue 73 ASP Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 68 PHE Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain M residue 73 ASP Chi-restraints excluded: chain M residue 98 VAL Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 77 ASN Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain O residue 39 GLN Chi-restraints excluded: chain O residue 79 VAL Chi-restraints excluded: chain O residue 93 LEU Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 109 ARG Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 314 ASP Chi-restraints excluded: chain P residue 4 LEU Chi-restraints excluded: chain P residue 79 VAL Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 239 SER Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain F residue 314 ASP Chi-restraints excluded: chain F residue 321 LEU Chi-restraints excluded: chain Q residue 22 CYS Chi-restraints excluded: chain Q residue 57 GLN Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 192 ILE Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain G residue 254 VAL Chi-restraints excluded: chain G residue 321 LEU Chi-restraints excluded: chain R residue 79 VAL Chi-restraints excluded: chain H residue 53 ASN Chi-restraints excluded: chain H residue 104 SER Chi-restraints excluded: chain H residue 169 LEU Chi-restraints excluded: chain H residue 257 ASN Chi-restraints excluded: chain H residue 262 GLU Chi-restraints excluded: chain H residue 321 LEU Chi-restraints excluded: chain S residue 51 LEU Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain T residue 28 ILE Chi-restraints excluded: chain J residue 76 ASN Chi-restraints excluded: chain J residue 198 LEU Chi-restraints excluded: chain J residue 256 LEU Chi-restraints excluded: chain J residue 260 ASP Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 195 LEU Chi-restraints excluded: chain U residue 11 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 407 random chunks: chunk 379 optimal weight: 7.9990 chunk 44 optimal weight: 0.7980 chunk 224 optimal weight: 0.2980 chunk 287 optimal weight: 9.9990 chunk 222 optimal weight: 0.8980 chunk 331 optimal weight: 1.9990 chunk 219 optimal weight: 2.9990 chunk 392 optimal weight: 9.9990 chunk 245 optimal weight: 1.9990 chunk 239 optimal weight: 0.9980 chunk 181 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 ASN ** A 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 234 GLN B 234 GLN ** M 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 304 GLN O 121 GLN E 246 ASN ** P 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 246 ASN G 246 ASN R 77 ASN ** R 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 246 ASN ** I 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 33668 Z= 0.158 Angle : 0.540 13.217 45735 Z= 0.265 Chirality : 0.038 0.220 5048 Planarity : 0.003 0.053 5822 Dihedral : 10.587 167.717 4794 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.51 % Allowed : 15.07 % Favored : 82.41 % 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: 1.96 (0.14), residues: 4071 helix: 2.33 (0.11), residues: 2128 sheet: 1.41 (0.21), residues: 557 loop : -0.41 (0.18), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP J 220 HIS 0.010 0.001 HIS J 300 PHE 0.020 0.001 PHE H 329 TYR 0.019 0.001 TYR O 33 ARG 0.008 0.000 ARG S 67 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8142 Ramachandran restraints generated. 4071 Oldfield, 0 Emsley, 4071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8142 Ramachandran restraints generated. 4071 Oldfield, 0 Emsley, 4071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 3471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 320 time to evaluate : 3.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ASN cc_start: -0.0064 (m-40) cc_final: -0.1113 (t0) REVERT: A 74 MET cc_start: 0.6619 (ppp) cc_final: 0.5649 (tmm) REVERT: A 181 HIS cc_start: 0.7101 (m-70) cc_final: 0.6863 (m90) REVERT: L 21 SER cc_start: 0.6039 (t) cc_final: 0.5714 (m) REVERT: L 70 ILE cc_start: 0.6755 (tp) cc_final: 0.6386 (pt) REVERT: L 80 TYR cc_start: 0.4758 (m-10) cc_final: 0.4374 (m-10) REVERT: C 75 LEU cc_start: 0.8765 (mp) cc_final: 0.8313 (tt) REVERT: C 229 GLN cc_start: 0.8078 (tp-100) cc_final: 0.7423 (tp-100) REVERT: D 285 TYR cc_start: 0.7753 (t80) cc_final: 0.7409 (t80) REVERT: O 19 ARG cc_start: 0.4969 (ttp80) cc_final: 0.4734 (ttp80) REVERT: E 91 THR cc_start: 0.0507 (OUTLIER) cc_final: 0.0143 (m) REVERT: E 109 ARG cc_start: 0.7751 (OUTLIER) cc_final: 0.7394 (ttt-90) REVERT: F 81 ASN cc_start: 0.8144 (p0) cc_final: 0.7867 (p0) REVERT: Q 57 GLN cc_start: 0.7250 (OUTLIER) cc_final: 0.6623 (tt0) REVERT: G 321 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8340 (pp) REVERT: R 77 ASN cc_start: 0.7252 (OUTLIER) cc_final: 0.6857 (t0) REVERT: R 83 MET cc_start: 0.4759 (mmp) cc_final: 0.4182 (mmt) REVERT: H 205 LEU cc_start: 0.8846 (tt) cc_final: 0.8641 (tp) REVERT: H 257 ASN cc_start: 0.6633 (OUTLIER) cc_final: 0.6315 (p0) REVERT: S 6 GLU cc_start: 0.4722 (pm20) cc_final: 0.4370 (tm-30) REVERT: S 60 TYR cc_start: 0.6672 (m-80) cc_final: 0.5595 (m-80) REVERT: S 67 ARG cc_start: 0.5840 (ttm110) cc_final: 0.4722 (mtp85) REVERT: S 95 TYR cc_start: 0.5758 (OUTLIER) cc_final: 0.5313 (m-80) REVERT: I 186 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.8070 (pp) REVERT: I 262 GLU cc_start: 0.7447 (mm-30) cc_final: 0.7102 (mp0) REVERT: J 134 GLU cc_start: 0.5676 (tt0) cc_final: 0.4921 (mt-10) REVERT: J 198 LEU cc_start: 0.7485 (OUTLIER) cc_final: 0.7212 (mm) REVERT: J 288 ARG cc_start: 0.3226 (mmt180) cc_final: 0.2826 (mmt90) REVERT: K 187 MET cc_start: 0.6348 (ptm) cc_final: 0.5828 (ptt) REVERT: K 192 LEU cc_start: 0.6906 (pp) cc_final: 0.6386 (mp) REVERT: U 11 LEU cc_start: 0.2734 (OUTLIER) cc_final: 0.2461 (mp) REVERT: U 83 MET cc_start: 0.3068 (mpp) cc_final: 0.2765 (mpp) outliers start: 86 outliers final: 60 residues processed: 386 average time/residue: 0.4133 time to fit residues: 263.9620 Evaluate side-chains 371 residues out of total 3471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 301 time to evaluate : 3.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASN Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 59 HIS Chi-restraints excluded: chain L residue 73 ASP Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain M residue 73 ASP Chi-restraints excluded: chain M residue 93 VAL Chi-restraints excluded: chain M residue 98 VAL Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 77 ASN Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain O residue 79 VAL Chi-restraints excluded: chain O residue 93 LEU Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 109 ARG Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 314 ASP Chi-restraints excluded: chain P residue 4 LEU Chi-restraints excluded: chain P residue 79 VAL Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 239 SER Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain F residue 314 ASP Chi-restraints excluded: chain F residue 321 LEU Chi-restraints excluded: chain Q residue 22 CYS Chi-restraints excluded: chain Q residue 57 GLN Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 192 ILE Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain G residue 254 VAL Chi-restraints excluded: chain G residue 321 LEU Chi-restraints excluded: chain R residue 77 ASN Chi-restraints excluded: chain R residue 96 CYS Chi-restraints excluded: chain R residue 100 THR Chi-restraints excluded: chain H residue 53 ASN Chi-restraints excluded: chain H residue 104 SER Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 169 LEU Chi-restraints excluded: chain H residue 257 ASN Chi-restraints excluded: chain H residue 262 GLU Chi-restraints excluded: chain H residue 321 LEU Chi-restraints excluded: chain S residue 95 TYR Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain I residue 88 HIS Chi-restraints excluded: chain I residue 186 LEU Chi-restraints excluded: chain T residue 28 ILE Chi-restraints excluded: chain J residue 76 ASN Chi-restraints excluded: chain J residue 198 LEU Chi-restraints excluded: chain J residue 256 LEU Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 195 LEU Chi-restraints excluded: chain U residue 11 LEU Chi-restraints excluded: chain U residue 93 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 407 random chunks: chunk 242 optimal weight: 5.9990 chunk 156 optimal weight: 0.6980 chunk 234 optimal weight: 2.9990 chunk 118 optimal weight: 0.9990 chunk 77 optimal weight: 0.0670 chunk 75 optimal weight: 5.9990 chunk 249 optimal weight: 20.0000 chunk 267 optimal weight: 4.9990 chunk 193 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 chunk 308 optimal weight: 8.9990 overall best weight: 0.7322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 ASN A 227 ASN ** M 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 246 ASN G 246 ASN R 77 ASN ** R 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 246 ASN ** I 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 moved from start: 0.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 33668 Z= 0.151 Angle : 0.537 13.114 45735 Z= 0.262 Chirality : 0.038 0.205 5048 Planarity : 0.003 0.051 5822 Dihedral : 10.058 166.257 4794 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.69 % Allowed : 14.72 % Favored : 82.59 % 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: 2.01 (0.14), residues: 4071 helix: 2.40 (0.11), residues: 2122 sheet: 1.38 (0.21), residues: 557 loop : -0.40 (0.18), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP J 220 HIS 0.011 0.001 HIS J 300 PHE 0.021 0.001 PHE F 329 TYR 0.017 0.001 TYR K 220 ARG 0.007 0.000 ARG F 124 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8142 Ramachandran restraints generated. 4071 Oldfield, 0 Emsley, 4071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8142 Ramachandran restraints generated. 4071 Oldfield, 0 Emsley, 4071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 3471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 321 time to evaluate : 3.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ASN cc_start: 0.0008 (m-40) cc_final: -0.1121 (t0) REVERT: A 74 MET cc_start: 0.6597 (ppp) cc_final: 0.5628 (tmm) REVERT: A 181 HIS cc_start: 0.7107 (m-70) cc_final: 0.6838 (m170) REVERT: L 70 ILE cc_start: 0.7098 (tp) cc_final: 0.6468 (pt) REVERT: B 68 PHE cc_start: 0.7379 (OUTLIER) cc_final: 0.6126 (m-80) REVERT: C 75 LEU cc_start: 0.8761 (mp) cc_final: 0.8312 (tt) REVERT: C 100 PHE cc_start: 0.3854 (t80) cc_final: 0.3196 (t80) REVERT: C 229 GLN cc_start: 0.8077 (tp-100) cc_final: 0.7386 (tp-100) REVERT: D 285 TYR cc_start: 0.7689 (t80) cc_final: 0.7362 (t80) REVERT: E 91 THR cc_start: 0.0498 (OUTLIER) cc_final: 0.0124 (m) REVERT: E 109 ARG cc_start: 0.7757 (OUTLIER) cc_final: 0.7402 (ttt-90) REVERT: F 81 ASN cc_start: 0.8135 (p0) cc_final: 0.7850 (p0) REVERT: F 298 ARG cc_start: 0.8630 (OUTLIER) cc_final: 0.7413 (ptp-170) REVERT: Q 57 GLN cc_start: 0.7233 (OUTLIER) cc_final: 0.6626 (tt0) REVERT: G 172 PHE cc_start: 0.7174 (m-80) cc_final: 0.6773 (t80) REVERT: G 321 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8337 (pp) REVERT: R 77 ASN cc_start: 0.7090 (OUTLIER) cc_final: 0.6800 (t0) REVERT: R 83 MET cc_start: 0.4688 (mmp) cc_final: 0.4154 (mmt) REVERT: H 205 LEU cc_start: 0.8825 (tt) cc_final: 0.8618 (tp) REVERT: H 257 ASN cc_start: 0.6644 (OUTLIER) cc_final: 0.6336 (p0) REVERT: S 67 ARG cc_start: 0.5868 (ttm110) cc_final: 0.4760 (mtp85) REVERT: I 186 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.8100 (pp) REVERT: I 262 GLU cc_start: 0.7462 (mm-30) cc_final: 0.7131 (mp0) REVERT: J 134 GLU cc_start: 0.5596 (tt0) cc_final: 0.4859 (mt-10) REVERT: J 198 LEU cc_start: 0.7456 (OUTLIER) cc_final: 0.7180 (mm) REVERT: J 288 ARG cc_start: 0.3216 (mmt180) cc_final: 0.2831 (mmt90) REVERT: K 187 MET cc_start: 0.6344 (ptm) cc_final: 0.5833 (ptt) REVERT: K 192 LEU cc_start: 0.6855 (pp) cc_final: 0.6343 (mp) REVERT: U 11 LEU cc_start: 0.2743 (OUTLIER) cc_final: 0.2465 (mp) REVERT: U 83 MET cc_start: 0.3373 (mpp) cc_final: 0.2966 (mpp) outliers start: 92 outliers final: 66 residues processed: 393 average time/residue: 0.4218 time to fit residues: 271.3643 Evaluate side-chains 378 residues out of total 3471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 301 time to evaluate : 3.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASN Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 59 HIS Chi-restraints excluded: chain L residue 73 ASP Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 68 PHE Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain M residue 73 ASP Chi-restraints excluded: chain M residue 98 VAL Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain O residue 39 GLN Chi-restraints excluded: chain O residue 79 VAL Chi-restraints excluded: chain O residue 93 LEU Chi-restraints excluded: chain O residue 96 CYS Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 109 ARG Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 314 ASP Chi-restraints excluded: chain P residue 4 LEU Chi-restraints excluded: chain P residue 79 VAL Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 239 SER Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain F residue 298 ARG Chi-restraints excluded: chain F residue 314 ASP Chi-restraints excluded: chain F residue 321 LEU Chi-restraints excluded: chain Q residue 22 CYS Chi-restraints excluded: chain Q residue 57 GLN Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 104 SER Chi-restraints excluded: chain G residue 192 ILE Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain G residue 254 VAL Chi-restraints excluded: chain G residue 321 LEU Chi-restraints excluded: chain R residue 77 ASN Chi-restraints excluded: chain R residue 79 VAL Chi-restraints excluded: chain R residue 96 CYS Chi-restraints excluded: chain R residue 100 THR Chi-restraints excluded: chain H residue 53 ASN Chi-restraints excluded: chain H residue 104 SER Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain H residue 169 LEU Chi-restraints excluded: chain H residue 257 ASN Chi-restraints excluded: chain H residue 269 VAL Chi-restraints excluded: chain H residue 321 LEU Chi-restraints excluded: chain I residue 88 HIS Chi-restraints excluded: chain I residue 186 LEU Chi-restraints excluded: chain T residue 28 ILE Chi-restraints excluded: chain J residue 76 ASN Chi-restraints excluded: chain J residue 198 LEU Chi-restraints excluded: chain J residue 212 LEU Chi-restraints excluded: chain J residue 256 LEU Chi-restraints excluded: chain J residue 260 ASP Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 195 LEU Chi-restraints excluded: chain U residue 11 LEU Chi-restraints excluded: chain U residue 93 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 407 random chunks: chunk 356 optimal weight: 5.9990 chunk 375 optimal weight: 4.9990 chunk 342 optimal weight: 10.0000 chunk 365 optimal weight: 20.0000 chunk 220 optimal weight: 4.9990 chunk 159 optimal weight: 0.6980 chunk 287 optimal weight: 5.9990 chunk 112 optimal weight: 2.9990 chunk 330 optimal weight: 10.0000 chunk 345 optimal weight: 0.9980 chunk 364 optimal weight: 5.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 ASN B 226 GLN ** M 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 304 GLN ** E 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 226 ASN ** P 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 246 ASN G 229 GLN G 246 ASN ** R 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 246 ASN ** S 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 246 ASN ** K 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.2956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 33668 Z= 0.348 Angle : 0.628 17.587 45735 Z= 0.313 Chirality : 0.042 0.186 5048 Planarity : 0.004 0.036 5822 Dihedral : 9.981 169.274 4794 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 2.72 % Allowed : 14.99 % Favored : 82.30 % 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: 1.68 (0.13), residues: 4071 helix: 2.07 (0.11), residues: 2114 sheet: 1.33 (0.21), residues: 557 loop : -0.48 (0.18), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP J 220 HIS 0.013 0.001 HIS E 88 PHE 0.016 0.002 PHE H 329 TYR 0.026 0.002 TYR O 33 ARG 0.009 0.001 ARG J 240 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8142 Ramachandran restraints generated. 4071 Oldfield, 0 Emsley, 4071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8142 Ramachandran restraints generated. 4071 Oldfield, 0 Emsley, 4071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 3471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 306 time to evaluate : 3.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ASN cc_start: 0.0074 (m-40) cc_final: -0.1268 (t0) REVERT: A 74 MET cc_start: 0.6707 (ppp) cc_final: 0.5613 (tmm) REVERT: L 83 MET cc_start: 0.6277 (mpp) cc_final: 0.6054 (mpp) REVERT: B 68 PHE cc_start: 0.7374 (OUTLIER) cc_final: 0.6406 (m-80) REVERT: C 75 LEU cc_start: 0.8788 (mp) cc_final: 0.8364 (tt) REVERT: C 229 GLN cc_start: 0.8120 (tp-100) cc_final: 0.7407 (tp-100) REVERT: E 91 THR cc_start: 0.0707 (OUTLIER) cc_final: 0.0476 (m) REVERT: E 109 ARG cc_start: 0.7917 (OUTLIER) cc_final: 0.7219 (tmt170) REVERT: F 298 ARG cc_start: 0.8810 (OUTLIER) cc_final: 0.7498 (ptp-170) REVERT: Q 57 GLN cc_start: 0.7333 (OUTLIER) cc_final: 0.6688 (tt0) REVERT: G 172 PHE cc_start: 0.7472 (m-80) cc_final: 0.7154 (t80) REVERT: G 321 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8418 (pp) REVERT: R 83 MET cc_start: 0.4762 (mmp) cc_final: 0.4271 (mmt) REVERT: H 257 ASN cc_start: 0.7270 (OUTLIER) cc_final: 0.6921 (p0) REVERT: I 262 GLU cc_start: 0.7548 (mm-30) cc_final: 0.7219 (mp0) REVERT: J 134 GLU cc_start: 0.5534 (tt0) cc_final: 0.4732 (mt-10) REVERT: J 198 LEU cc_start: 0.7450 (OUTLIER) cc_final: 0.7171 (mm) REVERT: J 288 ARG cc_start: 0.2866 (mmt180) cc_final: 0.2358 (mmt90) REVERT: K 192 LEU cc_start: 0.6975 (pp) cc_final: 0.6438 (mp) REVERT: K 244 MET cc_start: 0.6433 (mmm) cc_final: 0.5963 (mmt) REVERT: U 83 MET cc_start: 0.3364 (mpp) cc_final: 0.2937 (mpp) outliers start: 93 outliers final: 68 residues processed: 380 average time/residue: 0.4235 time to fit residues: 260.9466 Evaluate side-chains 358 residues out of total 3471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 282 time to evaluate : 3.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASN Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 59 HIS Chi-restraints excluded: chain L residue 73 ASP Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 68 PHE Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain M residue 73 ASP Chi-restraints excluded: chain M residue 93 VAL Chi-restraints excluded: chain M residue 98 VAL Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain O residue 79 VAL Chi-restraints excluded: chain O residue 93 LEU Chi-restraints excluded: chain O residue 96 CYS Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 109 ARG Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 314 ASP Chi-restraints excluded: chain P residue 4 LEU Chi-restraints excluded: chain P residue 5 VAL Chi-restraints excluded: chain P residue 79 VAL Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 239 SER Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain F residue 298 ARG Chi-restraints excluded: chain F residue 314 ASP Chi-restraints excluded: chain F residue 321 LEU Chi-restraints excluded: chain Q residue 28 ILE Chi-restraints excluded: chain Q residue 57 GLN Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 104 SER Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain G residue 192 ILE Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain G residue 321 LEU Chi-restraints excluded: chain R residue 84 ASN Chi-restraints excluded: chain R residue 96 CYS Chi-restraints excluded: chain R residue 100 THR Chi-restraints excluded: chain H residue 53 ASN Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain H residue 169 LEU Chi-restraints excluded: chain H residue 257 ASN Chi-restraints excluded: chain H residue 262 GLU Chi-restraints excluded: chain H residue 269 VAL Chi-restraints excluded: chain H residue 321 LEU Chi-restraints excluded: chain I residue 88 HIS Chi-restraints excluded: chain I residue 269 VAL Chi-restraints excluded: chain I residue 321 LEU Chi-restraints excluded: chain J residue 76 ASN Chi-restraints excluded: chain J residue 198 LEU Chi-restraints excluded: chain J residue 212 LEU Chi-restraints excluded: chain J residue 256 LEU Chi-restraints excluded: chain J residue 260 ASP Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 195 LEU Chi-restraints excluded: chain U residue 93 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 407 random chunks: chunk 240 optimal weight: 0.2980 chunk 386 optimal weight: 30.0000 chunk 235 optimal weight: 0.8980 chunk 183 optimal weight: 0.3980 chunk 268 optimal weight: 0.0870 chunk 405 optimal weight: 20.0000 chunk 373 optimal weight: 0.3980 chunk 322 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 249 optimal weight: 10.0000 chunk 197 optimal weight: 0.7980 overall best weight: 0.3958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 ASN ** M 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 110 GLN ** C 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 226 ASN P 13 GLN F 246 ASN G 246 ASN ** R 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 246 ASN H 300 HIS H 304 GLN ** S 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 246 ASN J 246 ASN K 234 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.3083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 33668 Z= 0.142 Angle : 0.567 13.118 45735 Z= 0.277 Chirality : 0.038 0.170 5048 Planarity : 0.003 0.034 5822 Dihedral : 9.520 171.078 4794 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.99 % Allowed : 16.18 % Favored : 81.83 % 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: 1.90 (0.14), residues: 4071 helix: 2.32 (0.11), residues: 2121 sheet: 1.28 (0.21), residues: 557 loop : -0.42 (0.18), residues: 1393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.001 TRP O 52 HIS 0.011 0.001 HIS K 246 PHE 0.018 0.001 PHE H 329 TYR 0.030 0.001 TYR K 220 ARG 0.011 0.000 ARG O 29 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8142 Ramachandran restraints generated. 4071 Oldfield, 0 Emsley, 4071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8142 Ramachandran restraints generated. 4071 Oldfield, 0 Emsley, 4071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 3471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 305 time to evaluate : 3.494 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 6 ASN cc_start: 0.0082 (m-40) cc_final: -0.1264 (t0) REVERT: A 23 ILE cc_start: 0.5993 (tt) cc_final: 0.5713 (tp) REVERT: A 74 MET cc_start: 0.6628 (ppp) cc_final: 0.5586 (tmm) REVERT: A 244 MET cc_start: 0.5719 (mmm) cc_final: 0.5512 (mmm) REVERT: L 70 ILE cc_start: 0.7288 (tp) cc_final: 0.7074 (tp) REVERT: B 68 PHE cc_start: 0.7501 (OUTLIER) cc_final: 0.6187 (m-80) REVERT: B 273 LYS cc_start: 0.5208 (mmtm) cc_final: 0.2691 (tptp) REVERT: C 75 LEU cc_start: 0.8752 (mp) cc_final: 0.8309 (tt) REVERT: C 229 GLN cc_start: 0.8077 (tp-100) cc_final: 0.7341 (tp-100) REVERT: D 285 TYR cc_start: 0.7867 (t80) cc_final: 0.7622 (t80) REVERT: E 91 THR cc_start: 0.0410 (OUTLIER) cc_final: 0.0187 (m) REVERT: E 109 ARG cc_start: 0.7816 (OUTLIER) cc_final: 0.7418 (ttt-90) REVERT: F 81 ASN cc_start: 0.7976 (p0) cc_final: 0.7775 (p0) REVERT: F 298 ARG cc_start: 0.8638 (OUTLIER) cc_final: 0.7254 (ptp-170) REVERT: Q 57 GLN cc_start: 0.7189 (OUTLIER) cc_final: 0.6634 (tt0) REVERT: Q 83 MET cc_start: 0.3981 (mmm) cc_final: 0.3687 (mmm) REVERT: G 321 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8315 (pp) REVERT: R 83 MET cc_start: 0.4799 (mmp) cc_final: 0.4461 (mmt) REVERT: H 257 ASN cc_start: 0.6895 (OUTLIER) cc_final: 0.6620 (p0) REVERT: S 57 GLN cc_start: 0.6047 (pm20) cc_final: 0.5544 (tm-30) REVERT: I 262 GLU cc_start: 0.7408 (mm-30) cc_final: 0.7080 (mp0) REVERT: J 134 GLU cc_start: 0.5656 (tt0) cc_final: 0.4886 (mt-10) REVERT: K 192 LEU cc_start: 0.6850 (pp) cc_final: 0.6389 (mp) REVERT: K 244 MET cc_start: 0.6239 (mmm) cc_final: 0.5755 (mmt) REVERT: U 83 MET cc_start: 0.3260 (mpp) cc_final: 0.2839 (mpp) outliers start: 68 outliers final: 53 residues processed: 359 average time/residue: 0.4218 time to fit residues: 247.1981 Evaluate side-chains 348 residues out of total 3471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 288 time to evaluate : 3.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASN Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 59 HIS Chi-restraints excluded: chain L residue 73 ASP Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 68 PHE Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain M residue 11 LEU Chi-restraints excluded: chain M residue 73 ASP Chi-restraints excluded: chain M residue 93 VAL Chi-restraints excluded: chain M residue 98 VAL Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain O residue 39 GLN Chi-restraints excluded: chain O residue 93 LEU Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 109 ARG Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 314 ASP Chi-restraints excluded: chain P residue 4 LEU Chi-restraints excluded: chain P residue 79 VAL Chi-restraints excluded: chain F residue 239 SER Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain F residue 298 ARG Chi-restraints excluded: chain F residue 314 ASP Chi-restraints excluded: chain F residue 321 LEU Chi-restraints excluded: chain Q residue 57 GLN Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain G residue 192 ILE Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain G residue 321 LEU Chi-restraints excluded: chain R residue 79 VAL Chi-restraints excluded: chain R residue 100 THR Chi-restraints excluded: chain H residue 53 ASN Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 169 LEU Chi-restraints excluded: chain H residue 257 ASN Chi-restraints excluded: chain H residue 321 LEU Chi-restraints excluded: chain I residue 88 HIS Chi-restraints excluded: chain I residue 321 LEU Chi-restraints excluded: chain T residue 28 ILE Chi-restraints excluded: chain J residue 76 ASN Chi-restraints excluded: chain J residue 256 LEU Chi-restraints excluded: chain J residue 260 ASP Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 113 ILE Chi-restraints excluded: chain K residue 195 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 407 random chunks: chunk 256 optimal weight: 5.9990 chunk 343 optimal weight: 8.9990 chunk 98 optimal weight: 0.2980 chunk 297 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 323 optimal weight: 0.5980 chunk 135 optimal weight: 9.9990 chunk 332 optimal weight: 20.0000 chunk 40 optimal weight: 0.9980 chunk 59 optimal weight: 6.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 ASN ** M 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 110 GLN ** C 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 246 ASN G 246 ASN ** R 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 246 ASN ** S 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 207 HIS ** J 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.183417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.139234 restraints weight = 64127.206| |-----------------------------------------------------------------------------| r_work (start): 0.3954 rms_B_bonded: 2.91 r_work: 0.3423 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.3131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 33668 Z= 0.220 Angle : 0.571 14.858 45735 Z= 0.282 Chirality : 0.039 0.178 5048 Planarity : 0.003 0.050 5822 Dihedral : 9.353 171.384 4794 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 1.96 % Allowed : 16.33 % Favored : 81.71 % 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: 1.84 (0.14), residues: 4071 helix: 2.26 (0.11), residues: 2126 sheet: 1.23 (0.21), residues: 557 loop : -0.43 (0.18), residues: 1388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP N 36 HIS 0.008 0.001 HIS A 246 PHE 0.016 0.001 PHE H 329 TYR 0.032 0.001 TYR K 220 ARG 0.014 0.000 ARG Q 67 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6953.30 seconds wall clock time: 125 minutes 5.34 seconds (7505.34 seconds total)