Starting phenix.real_space_refine on Sat Jun 28 02:46:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rmm_19364/06_2025/8rmm_19364.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rmm_19364/06_2025/8rmm_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/cci-nas-00/data/ceres_data/8rmm_19364/06_2025/8rmm_19364.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rmm_19364/06_2025/8rmm_19364.map" model { file = "/net/cci-nas-00/data/ceres_data/8rmm_19364/06_2025/8rmm_19364.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rmm_19364/06_2025/8rmm_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. Time to flip 34 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 19.67, per 1000 atoms: 0.60 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 - 3.00 Amino acid : True - 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: 8.93 Conformation dependent library (CDL) restraints added in 4.2 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: 4.36 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: 14.60 Time building geometry restraints manager: 9.47 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: 0.00 - 2.20: 44897 2.20 - 4.41: 666 4.41 - 6.61: 134 6.61 - 8.82: 29 8.82 - 11.02: 9 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 3.120 nonbonded pdb=" OH TYR B 142 " pdb=" OE1 GLU B 176 " model vdw 2.195 3.040 nonbonded pdb=" O LEU J 230 " pdb=" OG1 THR J 234 " model vdw 2.210 3.040 nonbonded pdb=" O MET K 144 " pdb=" NH2 ARG U 35 " model vdw 2.215 3.120 nonbonded pdb=" O LEU F 122 " pdb=" OG SER F 184 " model vdw 2.227 3.040 ... (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 Time spend for trying shortcut: 0.00 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: 1.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.140 Check model and map are aligned: 0.210 Set scattering table: 0.290 Process input model: 74.280 Find NCS groups from input model: 1.620 Set up NCS constraints: 0.400 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: 0.020 Load rotamer database and sin/cos tables:3.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.480 ------------------------------------------------------------------------------- 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 33696 Z= 0.149 Angle : 0.671 11.024 45791 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 Details of bonding type rmsd hydrogen bonds : bond 0.24791 ( 1887) hydrogen bonds : angle 7.95395 ( 5562) SS BOND : bond 0.00282 ( 28) SS BOND : angle 0.63167 ( 56) covalent geometry : bond 0.00314 (33668) covalent geometry : angle 0.67097 (45735) *********************** 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 to be fit. rotamer outliers: 27 poor density : 403 time to evaluate : 6.601 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: 0.6098 time to fit residues: 425.0535 Evaluate side-chains 352 residues out of total 3471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 342 time to evaluate : 5.767 ------------------------------------------------------------------------------- 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: 2.9990 chunk 308 optimal weight: 0.9990 chunk 171 optimal weight: 0.6980 chunk 105 optimal weight: 3.9990 chunk 208 optimal weight: 3.9990 chunk 164 optimal weight: 0.0040 chunk 319 optimal weight: 0.9990 chunk 123 optimal weight: 1.9990 chunk 193 optimal weight: 0.8980 chunk 237 optimal weight: 0.9980 chunk 369 optimal weight: 4.9990 overall best weight: 0.7194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 ASN C 279 ASN ** C 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 304 GLN 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 K 32 GLN 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: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4538 r_free = 0.4538 target = 0.184910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.140703 restraints weight = 63626.680| |-----------------------------------------------------------------------------| r_work (start): 0.3976 rms_B_bonded: 3.03 r_work: 0.3436 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 33696 Z= 0.134 Angle : 0.615 12.736 45791 Z= 0.312 Chirality : 0.040 0.224 5048 Planarity : 0.004 0.059 5822 Dihedral : 13.155 173.975 4813 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.37 % Allowed : 11.77 % Favored : 85.86 % 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: 1.51 (0.14), residues: 4071 helix: 1.70 (0.11), residues: 2108 sheet: 1.58 (0.20), residues: 605 loop : -0.34 (0.18), residues: 1358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP U 36 HIS 0.009 0.001 HIS D 88 PHE 0.027 0.001 PHE J 160 TYR 0.018 0.001 TYR O 60 ARG 0.006 0.001 ARG S 67 Details of bonding type rmsd hydrogen bonds : bond 0.04767 ( 1887) hydrogen bonds : angle 4.69180 ( 5562) SS BOND : bond 0.00408 ( 28) SS BOND : angle 0.96470 ( 56) covalent geometry : bond 0.00278 (33668) covalent geometry : angle 0.61461 (45735) *********************** 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 474 residues out of total 3471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 393 time to evaluate : 4.090 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: A 47 LYS cc_start: 0.6341 (mtmt) cc_final: 0.5831 (mptt) REVERT: A 75 TRP cc_start: 0.6711 (t60) cc_final: 0.6408 (t60) REVERT: A 181 HIS cc_start: 0.8276 (m-70) cc_final: 0.7991 (m-70) REVERT: L 70 ILE cc_start: 0.7435 (tp) cc_final: 0.7234 (tp) REVERT: L 80 TYR cc_start: 0.7230 (m-10) cc_final: 0.7004 (m-10) REVERT: B 240 SER cc_start: 0.5416 (OUTLIER) cc_final: 0.4537 (p) REVERT: B 246 HIS cc_start: 0.6078 (t70) cc_final: 0.5781 (m90) REVERT: B 249 LYS cc_start: 0.6469 (ptpt) cc_final: 0.5788 (tptp) REVERT: M 82 GLN cc_start: 0.7093 (tp-100) cc_final: 0.6838 (tp40) REVERT: O 78 THR cc_start: 0.5801 (t) cc_final: 0.5356 (t) REVERT: O 110 TYR cc_start: 0.8379 (m-80) cc_final: 0.8063 (m-10) REVERT: E 109 ARG cc_start: 0.8002 (OUTLIER) cc_final: 0.7759 (ttt-90) REVERT: G 137 ASP cc_start: 0.8062 (t0) cc_final: 0.7837 (t0) REVERT: R 33 TYR cc_start: 0.8345 (m-80) cc_final: 0.8068 (m-80) REVERT: R 77 ASN cc_start: 0.7128 (m-40) cc_final: 0.6899 (m-40) REVERT: S 67 ARG cc_start: 0.6680 (ttm110) cc_final: 0.5955 (mtp85) REVERT: S 72 LEU cc_start: 0.7902 (OUTLIER) cc_final: 0.7411 (pp) REVERT: I 259 ASP cc_start: 0.8525 (p0) cc_final: 0.8265 (p0) REVERT: I 329 PHE cc_start: 0.5482 (m-80) cc_final: 0.5240 (m-80) REVERT: J 76 ASN cc_start: 0.6051 (OUTLIER) cc_final: 0.5742 (m-40) REVERT: J 77 ASN cc_start: 0.8746 (p0) cc_final: 0.8453 (p0) REVERT: J 134 GLU cc_start: 0.6010 (OUTLIER) cc_final: 0.5556 (mt-10) REVERT: J 189 TRP cc_start: 0.7764 (m100) cc_final: 0.6875 (m100) REVERT: J 288 ARG cc_start: 0.2684 (mmt180) cc_final: 0.2147 (mmt90) REVERT: K 34 PHE cc_start: 0.5911 (m-10) cc_final: 0.5575 (t80) REVERT: K 142 TYR cc_start: 0.2682 (m-10) cc_final: 0.2296 (m-10) REVERT: K 244 MET cc_start: 0.7321 (mmm) cc_final: 0.6865 (tpt) outliers start: 81 outliers final: 29 residues processed: 453 average time/residue: 0.5602 time to fit residues: 426.5204 Evaluate side-chains 352 residues out of total 3471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 318 time to evaluate : 5.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASN Chi-restraints excluded: chain A residue 116 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 151 SER Chi-restraints excluded: chain B residue 240 SER 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 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 P residue 5 VAL Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain Q residue 68 PHE Chi-restraints excluded: chain G residue 182 TYR Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain H residue 169 LEU 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 I residue 86 CYS Chi-restraints excluded: chain J residue 76 ASN Chi-restraints excluded: chain J residue 134 GLU Chi-restraints excluded: chain J residue 212 LEU Chi-restraints excluded: chain K residue 195 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 407 random chunks: chunk 364 optimal weight: 10.0000 chunk 336 optimal weight: 30.0000 chunk 130 optimal weight: 6.9990 chunk 279 optimal weight: 0.5980 chunk 323 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 337 optimal weight: 20.0000 chunk 394 optimal weight: 20.0000 chunk 262 optimal weight: 0.8980 chunk 158 optimal weight: 0.7980 chunk 74 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 ASN B 141 HIS ** C 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 300 HIS E 304 GLN P 13 GLN Q 111 HIS Q 121 GLN R 121 GLN T 121 GLN ** J 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 246 ASN ** K 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4539 r_free = 0.4539 target = 0.184981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.141304 restraints weight = 63655.536| |-----------------------------------------------------------------------------| r_work (start): 0.3991 rms_B_bonded: 2.80 r_work: 0.3457 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 33696 Z= 0.123 Angle : 0.561 11.364 45791 Z= 0.280 Chirality : 0.039 0.238 5048 Planarity : 0.003 0.030 5822 Dihedral : 12.543 174.895 4794 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.48 % Allowed : 12.18 % Favored : 85.33 % 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: 1.65 (0.13), residues: 4071 helix: 1.93 (0.11), residues: 2117 sheet: 1.71 (0.21), residues: 549 loop : -0.46 (0.17), residues: 1405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP N 36 HIS 0.008 0.001 HIS D 88 PHE 0.019 0.001 PHE L 68 TYR 0.017 0.001 TYR L 60 ARG 0.004 0.000 ARG K 241 Details of bonding type rmsd hydrogen bonds : bond 0.04146 ( 1887) hydrogen bonds : angle 4.29671 ( 5562) SS BOND : bond 0.00618 ( 28) SS BOND : angle 0.88255 ( 56) covalent geometry : bond 0.00261 (33668) covalent geometry : angle 0.56022 (45735) *********************** 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 448 residues out of total 3471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 363 time to evaluate : 3.475 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 187 MET cc_start: 0.8480 (mmm) cc_final: 0.8199 (mmm) REVERT: A 244 MET cc_start: 0.7447 (ttt) cc_final: 0.6715 (mmm) REVERT: A 245 MET cc_start: 0.8148 (ptt) cc_final: 0.7495 (mmp) REVERT: L 34 MET cc_start: 0.2604 (mmp) cc_final: 0.2320 (mmp) REVERT: L 70 ILE cc_start: 0.7468 (tp) cc_final: 0.6926 (pt) REVERT: L 80 TYR cc_start: 0.6993 (m-10) cc_final: 0.6641 (m-10) REVERT: B 74 MET cc_start: 0.7619 (mmm) cc_final: 0.7096 (mmm) REVERT: M 82 GLN cc_start: 0.7128 (tp-100) cc_final: 0.6842 (tp40) REVERT: M 83 MET cc_start: 0.6058 (ptt) cc_final: 0.5613 (ptt) REVERT: O 34 LEU cc_start: 0.9004 (mt) cc_final: 0.8763 (mp) REVERT: O 76 LYS cc_start: 0.6708 (tptt) cc_final: 0.6508 (tttt) REVERT: O 78 THR cc_start: 0.5380 (t) cc_final: 0.2787 (t) REVERT: O 110 TYR cc_start: 0.8401 (m-80) cc_final: 0.8189 (m-80) REVERT: E 109 ARG cc_start: 0.7983 (OUTLIER) cc_final: 0.7742 (ttt-90) REVERT: E 329 PHE cc_start: 0.4355 (m-80) cc_final: 0.4148 (m-10) REVERT: F 81 ASN cc_start: 0.7728 (p0) cc_final: 0.7503 (p0) REVERT: Q 57 GLN cc_start: 0.7603 (OUTLIER) cc_final: 0.6550 (tt0) REVERT: G 128 TYR cc_start: 0.8616 (t80) cc_final: 0.8307 (t80) REVERT: G 137 ASP cc_start: 0.8087 (t0) cc_final: 0.7754 (t0) REVERT: G 171 ASP cc_start: 0.8132 (p0) cc_final: 0.7822 (m-30) REVERT: G 321 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8326 (pp) REVERT: R 33 TYR cc_start: 0.8545 (m-80) cc_final: 0.8257 (m-10) REVERT: R 77 ASN cc_start: 0.7164 (m-40) cc_final: 0.6952 (m-40) REVERT: R 80 TYR cc_start: 0.7022 (m-10) cc_final: 0.6754 (m-10) REVERT: H 205 LEU cc_start: 0.8829 (tt) cc_final: 0.8624 (tp) REVERT: S 6 GLU cc_start: 0.6339 (OUTLIER) cc_final: 0.4072 (pm20) REVERT: S 39 GLN cc_start: 0.7163 (pp30) cc_final: 0.6797 (tm-30) REVERT: S 45 ARG cc_start: 0.7382 (ttm170) cc_final: 0.6866 (ttp80) REVERT: S 67 ARG cc_start: 0.6680 (ttm110) cc_final: 0.6301 (mtp85) REVERT: S 72 LEU cc_start: 0.8102 (OUTLIER) cc_final: 0.7692 (pp) REVERT: I 186 LEU cc_start: 0.8286 (OUTLIER) cc_final: 0.7993 (pp) REVERT: I 259 ASP cc_start: 0.8511 (p0) cc_final: 0.8300 (p0) REVERT: J 134 GLU cc_start: 0.6183 (OUTLIER) cc_final: 0.5407 (mt-10) REVERT: J 189 TRP cc_start: 0.7676 (m100) cc_final: 0.7100 (m100) REVERT: J 288 ARG cc_start: 0.2866 (mmt180) cc_final: 0.2241 (mmt90) REVERT: K 192 LEU cc_start: 0.7537 (pp) cc_final: 0.6934 (mp) outliers start: 85 outliers final: 40 residues processed: 428 average time/residue: 0.4253 time to fit residues: 297.5461 Evaluate side-chains 361 residues out of total 3471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 314 time to evaluate : 3.356 ------------------------------------------------------------------------------- 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 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 95 TYR Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain M residue 98 VAL Chi-restraints excluded: chain M residue 112 THR Chi-restraints excluded: chain C residue 77 ASN 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 79 VAL 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 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 321 LEU Chi-restraints excluded: chain Q residue 57 GLN Chi-restraints excluded: chain G residue 91 THR 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 169 LEU Chi-restraints excluded: chain H residue 269 VAL Chi-restraints excluded: chain H residue 321 LEU Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 72 LEU Chi-restraints excluded: chain S residue 84 ASN Chi-restraints excluded: chain S residue 95 TYR Chi-restraints excluded: chain I residue 86 CYS Chi-restraints excluded: chain I residue 186 LEU Chi-restraints excluded: chain J residue 76 ASN Chi-restraints excluded: chain J residue 134 GLU Chi-restraints excluded: chain J residue 212 LEU Chi-restraints excluded: chain J residue 256 LEU Chi-restraints excluded: chain K residue 195 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 407 random chunks: chunk 224 optimal weight: 1.9990 chunk 76 optimal weight: 9.9990 chunk 12 optimal weight: 6.9990 chunk 360 optimal weight: 20.0000 chunk 367 optimal weight: 0.8980 chunk 136 optimal weight: 0.1980 chunk 325 optimal weight: 6.9990 chunk 216 optimal weight: 8.9990 chunk 109 optimal weight: 0.4980 chunk 291 optimal weight: 30.0000 chunk 196 optimal weight: 3.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 ASN A 246 HIS ** M 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 216 GLN ** C 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 216 GLN P 13 GLN ** P 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 74 ASN R 82 GLN R 121 GLN S 121 GLN ** I 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 246 ASN ** K 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4528 r_free = 0.4528 target = 0.183956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.139590 restraints weight = 63900.228| |-----------------------------------------------------------------------------| r_work (start): 0.3965 rms_B_bonded: 2.74 r_work: 0.3442 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 33696 Z= 0.143 Angle : 0.565 12.701 45791 Z= 0.281 Chirality : 0.039 0.247 5048 Planarity : 0.003 0.036 5822 Dihedral : 12.168 174.300 4794 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.04 % Allowed : 12.62 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.14), residues: 4071 helix: 2.00 (0.11), residues: 2123 sheet: 1.45 (0.20), residues: 619 loop : -0.52 (0.18), residues: 1329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP N 36 HIS 0.008 0.001 HIS E 88 PHE 0.016 0.001 PHE H 329 TYR 0.024 0.001 TYR M 60 ARG 0.004 0.000 ARG Q 29 Details of bonding type rmsd hydrogen bonds : bond 0.03880 ( 1887) hydrogen bonds : angle 4.09791 ( 5562) SS BOND : bond 0.00386 ( 28) SS BOND : angle 0.79762 ( 56) covalent geometry : bond 0.00327 (33668) covalent geometry : angle 0.56441 (45735) *********************** 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 444 residues out of total 3471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 340 time to evaluate : 3.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.7270 (ppp) cc_final: 0.6544 (tmm) REVERT: A 244 MET cc_start: 0.7463 (OUTLIER) cc_final: 0.7108 (mmm) REVERT: A 245 MET cc_start: 0.7818 (ptt) cc_final: 0.7435 (mmp) REVERT: L 70 ILE cc_start: 0.7617 (tp) cc_final: 0.7170 (pt) REVERT: L 80 TYR cc_start: 0.6905 (m-10) cc_final: 0.6664 (m-10) REVERT: B 74 MET cc_start: 0.7586 (mmm) cc_final: 0.7073 (mmm) REVERT: B 246 HIS cc_start: 0.6072 (t70) cc_final: 0.5749 (m90) REVERT: M 20 LEU cc_start: 0.7021 (mp) cc_final: 0.6562 (mt) REVERT: M 82 GLN cc_start: 0.7090 (tp-100) cc_final: 0.6872 (tp40) REVERT: O 34 LEU cc_start: 0.9005 (mt) cc_final: 0.8760 (mp) REVERT: O 78 THR cc_start: 0.5719 (t) cc_final: 0.5029 (t) REVERT: E 91 THR cc_start: 0.0780 (OUTLIER) cc_final: 0.0397 (m) REVERT: E 109 ARG cc_start: 0.7969 (OUTLIER) cc_final: 0.7745 (ttt-90) REVERT: Q 57 GLN cc_start: 0.7606 (OUTLIER) cc_final: 0.6596 (tt0) REVERT: Q 83 MET cc_start: 0.6765 (mmm) cc_final: 0.6372 (mmm) REVERT: G 137 ASP cc_start: 0.8166 (t0) cc_final: 0.7774 (t0) REVERT: G 171 ASP cc_start: 0.7937 (p0) cc_final: 0.7689 (m-30) REVERT: G 321 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8352 (pp) REVERT: R 77 ASN cc_start: 0.7227 (m-40) cc_final: 0.7025 (m-40) REVERT: R 83 MET cc_start: 0.6971 (mmp) cc_final: 0.5908 (mmt) REVERT: S 6 GLU cc_start: 0.6299 (OUTLIER) cc_final: 0.5900 (pt0) REVERT: S 39 GLN cc_start: 0.7370 (OUTLIER) cc_final: 0.7122 (tm-30) REVERT: S 45 ARG cc_start: 0.7482 (ttm170) cc_final: 0.7164 (ttp80) REVERT: S 67 ARG cc_start: 0.6823 (ttm110) cc_final: 0.6230 (mtp85) REVERT: S 72 LEU cc_start: 0.8253 (OUTLIER) cc_final: 0.8041 (pp) REVERT: I 186 LEU cc_start: 0.8266 (OUTLIER) cc_final: 0.7979 (pp) REVERT: I 262 GLU cc_start: 0.7955 (mm-30) cc_final: 0.7608 (mp0) REVERT: J 134 GLU cc_start: 0.6167 (OUTLIER) cc_final: 0.5397 (mt-10) REVERT: J 189 TRP cc_start: 0.7657 (m100) cc_final: 0.7090 (m100) REVERT: J 220 TRP cc_start: 0.6298 (t-100) cc_final: 0.5936 (t-100) REVERT: J 288 ARG cc_start: 0.3025 (mmt180) cc_final: 0.2337 (mmt90) REVERT: K 174 ARG cc_start: 0.7419 (ptm160) cc_final: 0.7143 (ttt180) REVERT: K 192 LEU cc_start: 0.7668 (pp) cc_final: 0.7127 (mp) REVERT: K 242 LEU cc_start: 0.8156 (OUTLIER) cc_final: 0.7949 (tp) REVERT: U 11 LEU cc_start: 0.2645 (OUTLIER) cc_final: 0.2249 (mp) REVERT: N 72 LEU cc_start: 0.2786 (OUTLIER) cc_final: 0.2450 (mp) outliers start: 104 outliers final: 61 residues processed: 417 average time/residue: 0.4231 time to fit residues: 290.9039 Evaluate side-chains 388 residues out of total 3471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 314 time to evaluate : 3.381 ------------------------------------------------------------------------------- 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 144 MET Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 244 MET 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 45 VAL Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain M residue 73 ASP Chi-restraints excluded: chain M residue 79 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 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 70 VAL 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 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 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 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 321 LEU Chi-restraints excluded: chain R residue 79 VAL Chi-restraints excluded: chain R residue 121 GLN Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 169 LEU Chi-restraints excluded: chain H residue 269 VAL Chi-restraints excluded: chain H residue 321 LEU Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 39 GLN Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 72 LEU Chi-restraints excluded: chain S residue 84 ASN Chi-restraints excluded: chain S residue 95 TYR Chi-restraints excluded: chain I residue 86 CYS Chi-restraints excluded: chain I residue 186 LEU Chi-restraints excluded: chain I residue 269 VAL Chi-restraints excluded: chain J residue 76 ASN Chi-restraints excluded: chain J residue 88 HIS Chi-restraints excluded: chain J residue 134 GLU 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 43 CYS Chi-restraints excluded: chain K residue 195 LEU Chi-restraints excluded: chain K residue 242 LEU Chi-restraints excluded: chain U residue 11 LEU Chi-restraints excluded: chain U residue 93 VAL Chi-restraints excluded: chain N residue 72 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 407 random chunks: chunk 101 optimal weight: 1.9990 chunk 322 optimal weight: 4.9990 chunk 255 optimal weight: 5.9990 chunk 217 optimal weight: 2.9990 chunk 62 optimal weight: 0.0770 chunk 248 optimal weight: 3.9990 chunk 235 optimal weight: 1.9990 chunk 247 optimal weight: 0.9980 chunk 323 optimal weight: 0.9980 chunk 193 optimal weight: 0.6980 chunk 209 optimal weight: 0.0370 overall best weight: 0.5616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 ASN A 246 HIS ** M 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 304 GLN P 13 GLN F 304 GLN ** R 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 121 GLN ** I 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 207 HIS ** 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 = 0.4539 r_free = 0.4539 target = 0.184966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.140902 restraints weight = 63742.762| |-----------------------------------------------------------------------------| r_work (start): 0.3983 rms_B_bonded: 2.82 r_work: 0.3462 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 33696 Z= 0.106 Angle : 0.549 13.370 45791 Z= 0.269 Chirality : 0.038 0.258 5048 Planarity : 0.003 0.032 5822 Dihedral : 11.651 174.831 4794 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.66 % Allowed : 13.41 % Favored : 83.93 % 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: 1.79 (0.14), residues: 4071 helix: 2.10 (0.11), residues: 2143 sheet: 1.51 (0.21), residues: 584 loop : -0.45 (0.18), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP U 36 HIS 0.010 0.001 HIS A 246 PHE 0.024 0.001 PHE J 160 TYR 0.022 0.001 TYR K 220 ARG 0.007 0.000 ARG F 124 Details of bonding type rmsd hydrogen bonds : bond 0.03523 ( 1887) hydrogen bonds : angle 3.95425 ( 5562) SS BOND : bond 0.00239 ( 28) SS BOND : angle 0.73719 ( 56) covalent geometry : bond 0.00226 (33668) covalent geometry : angle 0.54898 (45735) *********************** 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 437 residues out of total 3471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 346 time to evaluate : 3.850 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 74 MET cc_start: 0.7256 (ppp) cc_final: 0.6621 (tmm) REVERT: L 36 TRP cc_start: 0.6301 (m100) cc_final: 0.5786 (m100) REVERT: L 70 ILE cc_start: 0.7613 (tp) cc_final: 0.7213 (pt) REVERT: L 80 TYR cc_start: 0.7039 (m-10) cc_final: 0.6801 (m-10) REVERT: B 68 PHE cc_start: 0.7921 (OUTLIER) cc_final: 0.6631 (m-80) REVERT: B 144 MET cc_start: 0.7166 (ppp) cc_final: 0.6808 (ppp) REVERT: M 82 GLN cc_start: 0.7003 (tp-100) cc_final: 0.6647 (tp40) REVERT: O 19 ARG cc_start: 0.4818 (ttp80) cc_final: 0.4519 (ttp80) REVERT: O 34 LEU cc_start: 0.9041 (mt) cc_final: 0.8805 (mp) REVERT: O 78 THR cc_start: 0.5553 (t) cc_final: 0.5070 (t) REVERT: E 91 THR cc_start: 0.0695 (OUTLIER) cc_final: 0.0346 (m) REVERT: E 109 ARG cc_start: 0.7979 (OUTLIER) cc_final: 0.7697 (ttt-90) REVERT: F 81 ASN cc_start: 0.7803 (p0) cc_final: 0.7580 (p0) REVERT: Q 4 LEU cc_start: 0.7359 (mm) cc_final: 0.7055 (mt) REVERT: Q 57 GLN cc_start: 0.7510 (OUTLIER) cc_final: 0.6497 (tt0) REVERT: G 137 ASP cc_start: 0.8165 (t0) cc_final: 0.7751 (t0) REVERT: G 171 ASP cc_start: 0.7952 (p0) cc_final: 0.7706 (m-30) REVERT: G 321 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8355 (pp) REVERT: R 82 GLN cc_start: 0.5681 (mp10) cc_final: 0.4561 (mp10) REVERT: R 83 MET cc_start: 0.7004 (mmp) cc_final: 0.5887 (mmt) REVERT: S 6 GLU cc_start: 0.5887 (OUTLIER) cc_final: 0.5075 (tm-30) REVERT: S 39 GLN cc_start: 0.7563 (OUTLIER) cc_final: 0.7301 (tm-30) REVERT: S 45 ARG cc_start: 0.7722 (ttm170) cc_final: 0.7462 (ttp80) REVERT: S 60 TYR cc_start: 0.4743 (m-80) cc_final: 0.4505 (m-80) REVERT: S 67 ARG cc_start: 0.6782 (ttm110) cc_final: 0.6267 (mtp85) REVERT: S 72 LEU cc_start: 0.7986 (OUTLIER) cc_final: 0.7782 (pp) REVERT: I 186 LEU cc_start: 0.8183 (OUTLIER) cc_final: 0.7941 (pp) REVERT: I 262 GLU cc_start: 0.7910 (mm-30) cc_final: 0.7474 (mp0) REVERT: J 134 GLU cc_start: 0.6124 (OUTLIER) cc_final: 0.5364 (mt-10) REVERT: J 189 TRP cc_start: 0.7654 (m100) cc_final: 0.7099 (m100) REVERT: J 220 TRP cc_start: 0.6639 (t-100) cc_final: 0.6139 (t-100) REVERT: J 288 ARG cc_start: 0.3194 (mmt180) cc_final: 0.2474 (mmt90) REVERT: K 187 MET cc_start: 0.5820 (ptm) cc_final: 0.5581 (ptt) REVERT: K 192 LEU cc_start: 0.7621 (pp) cc_final: 0.7090 (mp) REVERT: K 242 LEU cc_start: 0.8125 (OUTLIER) cc_final: 0.7914 (tm) REVERT: U 11 LEU cc_start: 0.2614 (OUTLIER) cc_final: 0.2241 (mp) REVERT: N 36 TRP cc_start: 0.3864 (m100) cc_final: 0.3005 (m100) REVERT: N 95 TYR cc_start: 0.5952 (m-80) cc_final: 0.5714 (m-80) outliers start: 91 outliers final: 47 residues processed: 416 average time/residue: 0.4398 time to fit residues: 299.0931 Evaluate side-chains 375 residues out of total 3471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 316 time to evaluate : 3.603 ------------------------------------------------------------------------------- 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 68 PHE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 170 VAL 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 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 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 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 286 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 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 84 ASN Chi-restraints excluded: chain H residue 169 LEU Chi-restraints excluded: chain H residue 262 GLU Chi-restraints excluded: chain H residue 321 LEU Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 39 GLN Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 72 LEU Chi-restraints excluded: chain S residue 84 ASN Chi-restraints excluded: chain I residue 186 LEU Chi-restraints excluded: chain T residue 28 ILE Chi-restraints excluded: chain J residue 134 GLU Chi-restraints excluded: chain J residue 256 LEU Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 43 CYS Chi-restraints excluded: chain K residue 195 LEU Chi-restraints excluded: chain K residue 218 HIS Chi-restraints excluded: chain K residue 242 LEU Chi-restraints excluded: chain U residue 11 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 407 random chunks: chunk 287 optimal weight: 20.0000 chunk 126 optimal weight: 6.9990 chunk 258 optimal weight: 2.9990 chunk 0 optimal weight: 30.0000 chunk 155 optimal weight: 1.9990 chunk 141 optimal weight: 0.5980 chunk 79 optimal weight: 0.8980 chunk 167 optimal weight: 20.0000 chunk 229 optimal weight: 7.9990 chunk 177 optimal weight: 0.7980 chunk 201 optimal weight: 2.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 ASN A 234 GLN A 246 HIS ** M 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 229 GLN ** C 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 304 GLN R 121 GLN H 300 HIS H 304 GLN ** I 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 207 HIS ** K 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4525 r_free = 0.4525 target = 0.183736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.139525 restraints weight = 63779.169| |-----------------------------------------------------------------------------| r_work (start): 0.3966 rms_B_bonded: 3.13 r_work: 0.3405 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.2613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 33696 Z= 0.138 Angle : 0.558 12.254 45791 Z= 0.275 Chirality : 0.039 0.277 5048 Planarity : 0.003 0.033 5822 Dihedral : 11.245 174.540 4794 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.69 % Allowed : 13.67 % Favored : 83.64 % 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: 1.78 (0.14), residues: 4071 helix: 2.10 (0.11), residues: 2148 sheet: 1.62 (0.21), residues: 552 loop : -0.51 (0.18), residues: 1371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP U 36 HIS 0.010 0.001 HIS A 246 PHE 0.018 0.001 PHE H 329 TYR 0.034 0.001 TYR R 33 ARG 0.008 0.000 ARG F 124 Details of bonding type rmsd hydrogen bonds : bond 0.03562 ( 1887) hydrogen bonds : angle 3.88237 ( 5562) SS BOND : bond 0.00306 ( 28) SS BOND : angle 0.86856 ( 56) covalent geometry : bond 0.00316 (33668) covalent geometry : angle 0.55746 (45735) *********************** 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 427 residues out of total 3471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 335 time to evaluate : 3.804 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 74 MET cc_start: 0.7284 (ppp) cc_final: 0.6726 (tmm) REVERT: L 36 TRP cc_start: 0.6253 (m100) cc_final: 0.5753 (m100) REVERT: L 70 ILE cc_start: 0.7730 (tp) cc_final: 0.7302 (pt) REVERT: L 80 TYR cc_start: 0.6977 (m-10) cc_final: 0.6735 (m-10) REVERT: B 68 PHE cc_start: 0.7951 (OUTLIER) cc_final: 0.6808 (m-80) REVERT: B 74 MET cc_start: 0.7653 (mmm) cc_final: 0.7238 (mmm) REVERT: B 144 MET cc_start: 0.7205 (ppp) cc_final: 0.6844 (ppp) REVERT: O 78 THR cc_start: 0.5574 (t) cc_final: 0.5078 (t) REVERT: E 91 THR cc_start: 0.0764 (OUTLIER) cc_final: 0.0458 (m) REVERT: E 109 ARG cc_start: 0.8084 (OUTLIER) cc_final: 0.7720 (ttt-90) REVERT: P 29 ARG cc_start: 0.7320 (ptp90) cc_final: 0.6503 (ptp90) REVERT: F 298 ARG cc_start: 0.8731 (OUTLIER) cc_final: 0.7594 (ptp-170) REVERT: Q 57 GLN cc_start: 0.7648 (OUTLIER) cc_final: 0.6576 (tt0) REVERT: G 137 ASP cc_start: 0.8197 (t0) cc_final: 0.7758 (t0) REVERT: G 171 ASP cc_start: 0.7878 (p0) cc_final: 0.7673 (m-30) REVERT: G 321 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8417 (pp) REVERT: R 80 TYR cc_start: 0.7374 (m-10) cc_final: 0.7119 (m-10) REVERT: R 83 MET cc_start: 0.7067 (mmp) cc_final: 0.6041 (mmt) REVERT: S 6 GLU cc_start: 0.5901 (OUTLIER) cc_final: 0.5292 (tm-30) REVERT: S 39 GLN cc_start: 0.7579 (OUTLIER) cc_final: 0.7330 (tm-30) REVERT: S 45 ARG cc_start: 0.7740 (ttm170) cc_final: 0.7280 (ttp-110) REVERT: S 67 ARG cc_start: 0.6815 (ttm110) cc_final: 0.6312 (mtp85) REVERT: I 186 LEU cc_start: 0.8224 (OUTLIER) cc_final: 0.7967 (pp) REVERT: I 262 GLU cc_start: 0.7898 (mm-30) cc_final: 0.7384 (mp0) REVERT: J 134 GLU cc_start: 0.6142 (OUTLIER) cc_final: 0.5361 (mt-10) REVERT: J 198 LEU cc_start: 0.8265 (OUTLIER) cc_final: 0.8024 (mm) REVERT: J 220 TRP cc_start: 0.6525 (t-100) cc_final: 0.6066 (t-100) REVERT: J 288 ARG cc_start: 0.3015 (mmt180) cc_final: 0.2312 (mmt90) REVERT: K 187 MET cc_start: 0.5832 (ptm) cc_final: 0.5570 (ptt) REVERT: K 192 LEU cc_start: 0.7670 (pp) cc_final: 0.7207 (mp) REVERT: U 11 LEU cc_start: 0.2616 (OUTLIER) cc_final: 0.2248 (mp) outliers start: 92 outliers final: 58 residues processed: 406 average time/residue: 0.4283 time to fit residues: 286.4516 Evaluate side-chains 376 residues out of total 3471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 306 time to evaluate : 3.498 ------------------------------------------------------------------------------- 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 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 151 SER Chi-restraints excluded: chain B residue 170 VAL 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 112 VAL Chi-restraints excluded: chain C residue 169 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 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 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 286 LEU Chi-restraints excluded: chain F residue 298 ARG 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 34 LEU Chi-restraints excluded: chain R residue 79 VAL Chi-restraints excluded: chain R residue 84 ASN Chi-restraints excluded: chain R residue 121 GLN Chi-restraints excluded: chain R residue 125 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 269 VAL Chi-restraints excluded: chain H residue 321 LEU Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 39 GLN Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 51 LEU Chi-restraints excluded: chain S residue 84 ASN Chi-restraints excluded: chain I residue 186 LEU Chi-restraints excluded: chain T residue 28 ILE Chi-restraints excluded: chain J residue 134 GLU 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 43 CYS 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 407 random chunks: chunk 158 optimal weight: 2.9990 chunk 261 optimal weight: 0.0050 chunk 24 optimal weight: 6.9990 chunk 125 optimal weight: 9.9990 chunk 162 optimal weight: 0.9980 chunk 392 optimal weight: 7.9990 chunk 329 optimal weight: 0.0970 chunk 127 optimal weight: 8.9990 chunk 171 optimal weight: 10.0000 chunk 267 optimal weight: 0.9990 chunk 102 optimal weight: 2.9990 overall best weight: 1.0196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 ASN A 246 HIS ** M 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 13 GLN R 121 GLN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4530 r_free = 0.4530 target = 0.184215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.137533 restraints weight = 63766.670| |-----------------------------------------------------------------------------| r_work (start): 0.3922 rms_B_bonded: 2.98 r_work: 0.3422 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.2747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 33696 Z= 0.118 Angle : 0.550 11.851 45791 Z= 0.270 Chirality : 0.038 0.159 5048 Planarity : 0.003 0.109 5822 Dihedral : 10.812 174.932 4792 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.66 % Allowed : 14.26 % Favored : 83.09 % 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: 2.15 (0.11), residues: 2146 sheet: 1.46 (0.21), residues: 587 loop : -0.43 (0.18), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP U 36 HIS 0.012 0.001 HIS A 246 PHE 0.024 0.001 PHE J 160 TYR 0.018 0.001 TYR K 220 ARG 0.022 0.000 ARG Q 67 Details of bonding type rmsd hydrogen bonds : bond 0.03422 ( 1887) hydrogen bonds : angle 3.80877 ( 5562) SS BOND : bond 0.00249 ( 28) SS BOND : angle 0.91862 ( 56) covalent geometry : bond 0.00263 (33668) covalent geometry : angle 0.54932 (45735) *********************** 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 415 residues out of total 3471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 324 time to evaluate : 3.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 ILE cc_start: 0.6836 (mt) cc_final: 0.6569 (tt) REVERT: A 74 MET cc_start: 0.7311 (ppp) cc_final: 0.6684 (tmm) REVERT: L 21 SER cc_start: 0.7873 (m) cc_final: 0.7625 (p) REVERT: L 36 TRP cc_start: 0.6223 (m100) cc_final: 0.5759 (m100) REVERT: L 70 ILE cc_start: 0.7949 (tp) cc_final: 0.7395 (pt) REVERT: L 80 TYR cc_start: 0.6945 (m-10) cc_final: 0.6683 (m-10) REVERT: B 68 PHE cc_start: 0.7929 (OUTLIER) cc_final: 0.6740 (m-80) REVERT: B 144 MET cc_start: 0.7350 (ppp) cc_final: 0.6981 (ppp) REVERT: M 20 LEU cc_start: 0.5399 (mm) cc_final: 0.4911 (mm) REVERT: C 100 PHE cc_start: 0.3386 (t80) cc_final: 0.2845 (t80) REVERT: O 19 ARG cc_start: 0.4761 (ttp80) cc_final: 0.4372 (ttp80) REVERT: O 78 THR cc_start: 0.5469 (t) cc_final: 0.4988 (t) REVERT: E 91 THR cc_start: 0.0679 (OUTLIER) cc_final: 0.0377 (m) REVERT: E 109 ARG cc_start: 0.8058 (OUTLIER) cc_final: 0.7678 (ttt-90) REVERT: F 81 ASN cc_start: 0.7934 (p0) cc_final: 0.7671 (p0) REVERT: F 298 ARG cc_start: 0.8680 (OUTLIER) cc_final: 0.7368 (ptp-170) REVERT: Q 4 LEU cc_start: 0.7274 (mm) cc_final: 0.7061 (mt) REVERT: Q 57 GLN cc_start: 0.7600 (OUTLIER) cc_final: 0.6610 (tt0) REVERT: Q 83 MET cc_start: 0.6895 (mmm) cc_final: 0.6382 (mmm) REVERT: G 137 ASP cc_start: 0.8185 (t0) cc_final: 0.7742 (t0) REVERT: G 321 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8384 (pp) REVERT: R 83 MET cc_start: 0.7048 (mmp) cc_final: 0.6077 (mmt) REVERT: H 100 PHE cc_start: 0.8116 (m-80) cc_final: 0.7910 (m-80) REVERT: S 6 GLU cc_start: 0.5810 (OUTLIER) cc_final: 0.5276 (tm-30) REVERT: S 39 GLN cc_start: 0.7565 (OUTLIER) cc_final: 0.7286 (tm-30) REVERT: S 45 ARG cc_start: 0.7654 (ttm110) cc_final: 0.7190 (ttp-110) REVERT: S 67 ARG cc_start: 0.6766 (ttm110) cc_final: 0.6482 (ttm110) REVERT: S 68 PHE cc_start: 0.4783 (m-80) cc_final: 0.4378 (m-80) REVERT: I 186 LEU cc_start: 0.8178 (OUTLIER) cc_final: 0.7947 (pp) REVERT: I 262 GLU cc_start: 0.7880 (mm-30) cc_final: 0.7328 (mp0) REVERT: J 134 GLU cc_start: 0.6128 (OUTLIER) cc_final: 0.5316 (mt-10) REVERT: J 198 LEU cc_start: 0.8254 (OUTLIER) cc_final: 0.8005 (mm) REVERT: J 288 ARG cc_start: 0.3237 (mmt180) cc_final: 0.2503 (mmt90) REVERT: K 187 MET cc_start: 0.5952 (ptm) cc_final: 0.5650 (ptt) REVERT: K 192 LEU cc_start: 0.7855 (pp) cc_final: 0.7350 (mp) REVERT: U 11 LEU cc_start: 0.2604 (OUTLIER) cc_final: 0.2233 (mp) REVERT: N 36 TRP cc_start: 0.4012 (m100) cc_final: 0.3062 (m100) REVERT: N 95 TYR cc_start: 0.5792 (m-80) cc_final: 0.5567 (m-80) outliers start: 91 outliers final: 61 residues processed: 395 average time/residue: 0.4255 time to fit residues: 278.5958 Evaluate side-chains 375 residues out of total 3471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 302 time to evaluate : 3.550 ------------------------------------------------------------------------------- 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 176 GLU Chi-restraints excluded: chain A residue 246 HIS Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 59 HIS 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 151 SER Chi-restraints excluded: chain M residue 73 ASP Chi-restraints excluded: chain M residue 79 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 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 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 201 LEU Chi-restraints excluded: chain E residue 264 ILE Chi-restraints excluded: chain E residue 286 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 202 THR Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain F residue 298 ARG 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 34 LEU Chi-restraints excluded: chain R residue 84 ASN Chi-restraints excluded: chain R residue 125 SER Chi-restraints excluded: chain H residue 169 LEU 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 6 GLU Chi-restraints excluded: chain S residue 39 GLN Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 51 LEU Chi-restraints excluded: chain S residue 84 ASN Chi-restraints excluded: chain I residue 186 LEU Chi-restraints excluded: chain I residue 321 LEU Chi-restraints excluded: chain T residue 28 ILE Chi-restraints excluded: chain J residue 134 GLU 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 43 CYS 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 ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.8827 > 50: distance: 30 - 137: 27.746 distance: 68 - 90: 36.762 distance: 73 - 98: 35.337 distance: 77 - 103: 37.111 distance: 84 - 90: 34.364 distance: 90 - 91: 38.910 distance: 91 - 92: 11.499 distance: 91 - 94: 31.308 distance: 92 - 93: 48.877 distance: 92 - 98: 25.932 distance: 94 - 95: 10.788 distance: 95 - 96: 44.386 distance: 95 - 97: 14.704 distance: 98 - 99: 50.374 distance: 99 - 100: 46.517 distance: 99 - 102: 31.261 distance: 100 - 101: 18.755 distance: 100 - 103: 60.583 distance: 103 - 104: 14.884 distance: 104 - 105: 40.416 distance: 104 - 107: 46.416 distance: 105 - 106: 16.204 distance: 105 - 114: 52.920 distance: 107 - 108: 55.889 distance: 110 - 111: 21.840 distance: 111 - 112: 40.499 distance: 111 - 113: 46.474 distance: 114 - 115: 40.827 distance: 115 - 116: 32.000 distance: 115 - 118: 37.617 distance: 116 - 125: 56.407 distance: 118 - 119: 5.919 distance: 119 - 120: 9.762 distance: 119 - 121: 21.130 distance: 120 - 122: 39.564 distance: 121 - 123: 41.730 distance: 122 - 124: 36.518 distance: 123 - 124: 20.569 distance: 125 - 126: 18.231 distance: 126 - 127: 19.467 distance: 126 - 129: 36.892 distance: 127 - 128: 3.053 distance: 127 - 132: 39.994 distance: 129 - 130: 15.299 distance: 130 - 131: 56.716 distance: 132 - 133: 44.862 distance: 133 - 134: 32.179 distance: 133 - 136: 20.953 distance: 134 - 135: 21.954 distance: 134 - 138: 34.605 distance: 136 - 137: 8.588 distance: 138 - 139: 37.025 distance: 139 - 140: 51.964 distance: 139 - 142: 23.975 distance: 140 - 141: 4.045 distance: 140 - 147: 26.188 distance: 142 - 143: 42.938 distance: 143 - 144: 49.836 distance: 144 - 145: 32.025 distance: 145 - 146: 56.926 distance: 147 - 148: 34.842 distance: 148 - 149: 43.636 distance: 148 - 151: 42.091 distance: 149 - 156: 63.473 distance: 151 - 152: 52.939 distance: 152 - 153: 37.495 distance: 153 - 154: 3.741 distance: 156 - 157: 22.083 distance: 157 - 158: 44.538 distance: 157 - 160: 11.954 distance: 158 - 159: 26.983 distance: 158 - 164: 46.540 distance: 160 - 161: 39.892 distance: 161 - 163: 7.558 distance: 164 - 165: 24.502 distance: 164 - 170: 37.134 distance: 165 - 166: 27.507 distance: 165 - 168: 41.374 distance: 166 - 167: 9.811 distance: 166 - 171: 21.659 distance: 168 - 169: 38.715 distance: 169 - 170: 16.146