Starting phenix.real_space_refine on Tue Mar 19 14:58:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eea_28049/03_2024/8eea_28049_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eea_28049/03_2024/8eea_28049.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eea_28049/03_2024/8eea_28049.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eea_28049/03_2024/8eea_28049.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eea_28049/03_2024/8eea_28049_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eea_28049/03_2024/8eea_28049_neut_updated.pdb" } resolution = 2.6 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 ------------------------------------------------------------------------------- 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= 0.001 sd= 0.072 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 12 5.49 5 S 112 5.16 5 C 15408 2.51 5 N 4363 2.21 5 O 4585 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 24480 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 3032 Classifications: {'peptide': 375} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 360} Chain breaks: 1 Chain: "B" Number of atoms: 3010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 3010 Classifications: {'peptide': 372} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 357} Chain breaks: 2 Chain: "C" Number of atoms: 3573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3573 Classifications: {'peptide': 445} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 425} Chain breaks: 2 Chain: "D" Number of atoms: 3664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3664 Classifications: {'peptide': 456} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 436} Chain breaks: 1 Chain: "E" Number of atoms: 3664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3664 Classifications: {'peptide': 456} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 436} Chain breaks: 1 Chain: "F" Number of atoms: 3573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3573 Classifications: {'peptide': 445} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 425} Chain breaks: 2 Chain: "G" Number of atoms: 1920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1920 Classifications: {'peptide': 234} Link IDs: {'PTRANS': 5, 'TRANS': 228} Chain breaks: 1 Chain: "H" Number of atoms: 1920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1920 Classifications: {'peptide': 234} Link IDs: {'PTRANS': 5, 'TRANS': 228} Chain breaks: 1 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 12.78, per 1000 atoms: 0.52 Number of scatterers: 24480 At special positions: 0 Unit cell: (202.72, 113.12, 132.16, 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 112 16.00 P 12 15.00 O 4585 8.00 N 4363 7.00 C 15408 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.83 Conformation dependent library (CDL) restraints added in 4.3 seconds 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5750 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 137 helices and 28 sheets defined 43.9% alpha, 13.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.61 Creating SS restraints... Processing helix chain 'A' and resid 36 through 53 removed outlier: 3.665A pdb=" N LEU A 40 " --> pdb=" O LYS A 36 " (cutoff:3.500A) Proline residue: A 49 - end of helix Processing helix chain 'A' and resid 55 through 59 removed outlier: 3.701A pdb=" N TYR A 59 " --> pdb=" O ALA A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 65 No H-bonds generated for 'chain 'A' and resid 63 through 65' Processing helix chain 'A' and resid 69 through 71 No H-bonds generated for 'chain 'A' and resid 69 through 71' Processing helix chain 'A' and resid 119 through 135 Processing helix chain 'A' and resid 154 through 156 No H-bonds generated for 'chain 'A' and resid 154 through 156' Processing helix chain 'A' and resid 174 through 177 removed outlier: 3.534A pdb=" N PHE A 177 " --> pdb=" O ASN A 174 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 174 through 177' Processing helix chain 'A' and resid 179 through 183 Processing helix chain 'A' and resid 193 through 216 Processing helix chain 'A' and resid 225 through 250 removed outlier: 4.279A pdb=" N LEU A 245 " --> pdb=" O ALA A 241 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR A 246 " --> pdb=" O ILE A 242 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN A 247 " --> pdb=" O ASN A 243 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N GLN A 248 " --> pdb=" O CYS A 244 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N VAL A 249 " --> pdb=" O LEU A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 279 No H-bonds generated for 'chain 'A' and resid 277 through 279' Processing helix chain 'A' and resid 282 through 301 removed outlier: 3.618A pdb=" N ILE A 294 " --> pdb=" O MET A 290 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ARG A 297 " --> pdb=" O ASP A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 312 No H-bonds generated for 'chain 'A' and resid 309 through 312' Processing helix chain 'A' and resid 328 through 331 No H-bonds generated for 'chain 'A' and resid 328 through 331' Processing helix chain 'A' and resid 334 through 341 Processing helix chain 'A' and resid 354 through 357 Processing helix chain 'A' and resid 362 through 364 No H-bonds generated for 'chain 'A' and resid 362 through 364' Processing helix chain 'B' and resid 36 through 53 removed outlier: 3.659A pdb=" N LEU B 40 " --> pdb=" O LYS B 36 " (cutoff:3.500A) Proline residue: B 49 - end of helix Processing helix chain 'B' and resid 55 through 59 removed outlier: 3.742A pdb=" N TYR B 59 " --> pdb=" O ALA B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 65 No H-bonds generated for 'chain 'B' and resid 63 through 65' Processing helix chain 'B' and resid 69 through 71 No H-bonds generated for 'chain 'B' and resid 69 through 71' Processing helix chain 'B' and resid 119 through 135 removed outlier: 3.788A pdb=" N GLN B 123 " --> pdb=" O LYS B 119 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU B 124 " --> pdb=" O MET B 120 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR B 125 " --> pdb=" O ALA B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 156 No H-bonds generated for 'chain 'B' and resid 154 through 156' Processing helix chain 'B' and resid 174 through 177 removed outlier: 3.512A pdb=" N PHE B 177 " --> pdb=" O ASN B 174 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 174 through 177' Processing helix chain 'B' and resid 179 through 183 removed outlier: 3.595A pdb=" N TYR B 183 " --> pdb=" O LEU B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 216 Processing helix chain 'B' and resid 225 through 250 removed outlier: 3.649A pdb=" N GLN B 229 " --> pdb=" O GLY B 225 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LEU B 245 " --> pdb=" O ALA B 241 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N GLN B 248 " --> pdb=" O CYS B 244 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N VAL B 249 " --> pdb=" O LEU B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 279 No H-bonds generated for 'chain 'B' and resid 277 through 279' Processing helix chain 'B' and resid 282 through 301 removed outlier: 3.612A pdb=" N ILE B 294 " --> pdb=" O MET B 290 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ARG B 297 " --> pdb=" O ASP B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 312 No H-bonds generated for 'chain 'B' and resid 309 through 312' Processing helix chain 'B' and resid 328 through 331 No H-bonds generated for 'chain 'B' and resid 328 through 331' Processing helix chain 'B' and resid 334 through 341 Processing helix chain 'B' and resid 354 through 357 Processing helix chain 'B' and resid 362 through 364 No H-bonds generated for 'chain 'B' and resid 362 through 364' Processing helix chain 'C' and resid 36 through 46 Processing helix chain 'C' and resid 48 through 53 removed outlier: 3.797A pdb=" N GLY C 53 " --> pdb=" O PRO C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 58 No H-bonds generated for 'chain 'C' and resid 55 through 58' Processing helix chain 'C' and resid 63 through 65 No H-bonds generated for 'chain 'C' and resid 63 through 65' Processing helix chain 'C' and resid 69 through 71 No H-bonds generated for 'chain 'C' and resid 69 through 71' Processing helix chain 'C' and resid 119 through 135 removed outlier: 3.839A pdb=" N GLN C 123 " --> pdb=" O LYS C 119 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU C 124 " --> pdb=" O MET C 120 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N THR C 125 " --> pdb=" O ALA C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 183 removed outlier: 3.944A pdb=" N GLY C 182 " --> pdb=" O SER C 178 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N TYR C 183 " --> pdb=" O ARG C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 216 removed outlier: 3.607A pdb=" N GLN C 214 " --> pdb=" O HIS C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 246 removed outlier: 3.633A pdb=" N LEU C 245 " --> pdb=" O ALA C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 279 No H-bonds generated for 'chain 'C' and resid 277 through 279' Processing helix chain 'C' and resid 282 through 301 Processing helix chain 'C' and resid 303 through 312 removed outlier: 6.810A pdb=" N ASN C 307 " --> pdb=" O HIS C 304 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA C 309 " --> pdb=" O GLN C 306 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N ALA C 310 " --> pdb=" O ASN C 307 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LYS C 312 " --> pdb=" O ALA C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 341 Processing helix chain 'C' and resid 354 through 359 removed outlier: 4.274A pdb=" N THR C 359 " --> pdb=" O GLN C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 364 No H-bonds generated for 'chain 'C' and resid 362 through 364' Processing helix chain 'C' and resid 390 through 396 Processing helix chain 'C' and resid 409 through 420 Processing helix chain 'C' and resid 427 through 440 Processing helix chain 'C' and resid 445 through 456 Processing helix chain 'D' and resid 35 through 46 Processing helix chain 'D' and resid 48 through 54 removed outlier: 3.747A pdb=" N GLY D 53 " --> pdb=" O PRO D 49 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N PHE D 54 " --> pdb=" O PHE D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 60 No H-bonds generated for 'chain 'D' and resid 58 through 60' Processing helix chain 'D' and resid 63 through 65 No H-bonds generated for 'chain 'D' and resid 63 through 65' Processing helix chain 'D' and resid 69 through 71 No H-bonds generated for 'chain 'D' and resid 69 through 71' Processing helix chain 'D' and resid 119 through 136 Processing helix chain 'D' and resid 176 through 183 removed outlier: 3.580A pdb=" N SER D 181 " --> pdb=" O PHE D 177 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N GLY D 182 " --> pdb=" O SER D 178 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N TYR D 183 " --> pdb=" O ARG D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 216 Processing helix chain 'D' and resid 218 through 250 removed outlier: 5.403A pdb=" N LEU D 222 " --> pdb=" O SER D 219 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N GLY D 225 " --> pdb=" O LEU D 222 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N VAL D 226 " --> pdb=" O LYS D 223 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N VAL D 228 " --> pdb=" O GLY D 225 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N CYS D 244 " --> pdb=" O ALA D 241 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N GLN D 247 " --> pdb=" O CYS D 244 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N GLN D 248 " --> pdb=" O LEU D 245 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL D 249 " --> pdb=" O THR D 246 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N THR D 250 " --> pdb=" O GLN D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 279 No H-bonds generated for 'chain 'D' and resid 277 through 279' Processing helix chain 'D' and resid 282 through 301 removed outlier: 3.796A pdb=" N ILE D 294 " --> pdb=" O MET D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 328 through 331 No H-bonds generated for 'chain 'D' and resid 328 through 331' Processing helix chain 'D' and resid 334 through 341 Processing helix chain 'D' and resid 354 through 359 removed outlier: 4.103A pdb=" N THR D 359 " --> pdb=" O GLN D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 364 No H-bonds generated for 'chain 'D' and resid 362 through 364' Processing helix chain 'D' and resid 390 through 396 Processing helix chain 'D' and resid 409 through 420 Processing helix chain 'D' and resid 427 through 440 Processing helix chain 'D' and resid 445 through 460 Processing helix chain 'E' and resid 35 through 46 Processing helix chain 'E' and resid 48 through 54 removed outlier: 3.721A pdb=" N GLY E 53 " --> pdb=" O PRO E 49 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N PHE E 54 " --> pdb=" O PHE E 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 58 through 60 No H-bonds generated for 'chain 'E' and resid 58 through 60' Processing helix chain 'E' and resid 63 through 65 No H-bonds generated for 'chain 'E' and resid 63 through 65' Processing helix chain 'E' and resid 69 through 71 No H-bonds generated for 'chain 'E' and resid 69 through 71' Processing helix chain 'E' and resid 119 through 136 Processing helix chain 'E' and resid 176 through 183 removed outlier: 3.615A pdb=" N SER E 181 " --> pdb=" O PHE E 177 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N GLY E 182 " --> pdb=" O SER E 178 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N TYR E 183 " --> pdb=" O ARG E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 193 through 216 Processing helix chain 'E' and resid 218 through 250 removed outlier: 5.415A pdb=" N LEU E 222 " --> pdb=" O SER E 219 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N GLY E 225 " --> pdb=" O LEU E 222 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N VAL E 226 " --> pdb=" O LYS E 223 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N VAL E 228 " --> pdb=" O GLY E 225 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N GLN E 247 " --> pdb=" O CYS E 244 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N GLN E 248 " --> pdb=" O LEU E 245 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL E 249 " --> pdb=" O THR E 246 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N THR E 250 " --> pdb=" O GLN E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 277 through 279 No H-bonds generated for 'chain 'E' and resid 277 through 279' Processing helix chain 'E' and resid 282 through 301 removed outlier: 3.805A pdb=" N ILE E 294 " --> pdb=" O MET E 290 " (cutoff:3.500A) Processing helix chain 'E' and resid 328 through 331 No H-bonds generated for 'chain 'E' and resid 328 through 331' Processing helix chain 'E' and resid 334 through 341 Processing helix chain 'E' and resid 354 through 359 removed outlier: 4.113A pdb=" N THR E 359 " --> pdb=" O GLN E 355 " (cutoff:3.500A) Processing helix chain 'E' and resid 362 through 364 No H-bonds generated for 'chain 'E' and resid 362 through 364' Processing helix chain 'E' and resid 390 through 396 Processing helix chain 'E' and resid 407 through 421 removed outlier: 4.275A pdb=" N ALA E 410 " --> pdb=" O LYS E 407 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASP E 411 " --> pdb=" O GLU E 408 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ASP E 420 " --> pdb=" O GLY E 417 " (cutoff:3.500A) Processing helix chain 'E' and resid 427 through 440 Processing helix chain 'E' and resid 445 through 460 Processing helix chain 'F' and resid 36 through 46 Processing helix chain 'F' and resid 48 through 53 removed outlier: 3.782A pdb=" N GLY F 53 " --> pdb=" O PRO F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 58 No H-bonds generated for 'chain 'F' and resid 55 through 58' Processing helix chain 'F' and resid 63 through 65 No H-bonds generated for 'chain 'F' and resid 63 through 65' Processing helix chain 'F' and resid 69 through 71 No H-bonds generated for 'chain 'F' and resid 69 through 71' Processing helix chain 'F' and resid 119 through 135 removed outlier: 3.842A pdb=" N GLN F 123 " --> pdb=" O LYS F 119 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU F 124 " --> pdb=" O MET F 120 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N THR F 125 " --> pdb=" O ALA F 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 176 through 183 removed outlier: 3.949A pdb=" N GLY F 182 " --> pdb=" O SER F 178 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N TYR F 183 " --> pdb=" O ARG F 179 " (cutoff:3.500A) Processing helix chain 'F' and resid 193 through 216 removed outlier: 3.595A pdb=" N GLN F 214 " --> pdb=" O HIS F 210 " (cutoff:3.500A) Processing helix chain 'F' and resid 226 through 246 removed outlier: 3.668A pdb=" N LEU F 245 " --> pdb=" O ALA F 241 " (cutoff:3.500A) Processing helix chain 'F' and resid 277 through 279 No H-bonds generated for 'chain 'F' and resid 277 through 279' Processing helix chain 'F' and resid 282 through 301 Processing helix chain 'F' and resid 303 through 312 removed outlier: 6.790A pdb=" N ASN F 307 " --> pdb=" O HIS F 304 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA F 309 " --> pdb=" O GLN F 306 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N ALA F 310 " --> pdb=" O ASN F 307 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS F 312 " --> pdb=" O ALA F 309 " (cutoff:3.500A) Processing helix chain 'F' and resid 331 through 333 No H-bonds generated for 'chain 'F' and resid 331 through 333' Processing helix chain 'F' and resid 335 through 341 Processing helix chain 'F' and resid 354 through 359 removed outlier: 4.296A pdb=" N THR F 359 " --> pdb=" O GLN F 355 " (cutoff:3.500A) Processing helix chain 'F' and resid 362 through 364 No H-bonds generated for 'chain 'F' and resid 362 through 364' Processing helix chain 'F' and resid 390 through 396 Processing helix chain 'F' and resid 409 through 420 Processing helix chain 'F' and resid 427 through 440 Processing helix chain 'F' and resid 445 through 456 Processing helix chain 'G' and resid 12 through 17 Processing helix chain 'G' and resid 25 through 49 removed outlier: 4.010A pdb=" N ARG G 36 " --> pdb=" O TRP G 32 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N ARG G 37 " --> pdb=" O ARG G 33 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ASP G 38 " --> pdb=" O ASN G 34 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LYS G 39 " --> pdb=" O PHE G 35 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N ALA G 40 " --> pdb=" O ARG G 36 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N ALA G 41 " --> pdb=" O ARG G 37 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N VAL G 42 " --> pdb=" O ASP G 38 " (cutoff:3.500A) Processing helix chain 'G' and resid 61 through 64 No H-bonds generated for 'chain 'G' and resid 61 through 64' Processing helix chain 'G' and resid 80 through 82 No H-bonds generated for 'chain 'G' and resid 80 through 82' Processing helix chain 'G' and resid 86 through 88 No H-bonds generated for 'chain 'G' and resid 86 through 88' Processing helix chain 'G' and resid 112 through 114 No H-bonds generated for 'chain 'G' and resid 112 through 114' Processing helix chain 'G' and resid 116 through 120 removed outlier: 3.657A pdb=" N ASP G 120 " --> pdb=" O GLN G 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 116 through 120' Processing helix chain 'G' and resid 136 through 138 No H-bonds generated for 'chain 'G' and resid 136 through 138' Processing helix chain 'G' and resid 157 through 168 Processing helix chain 'G' and resid 173 through 196 Processing helix chain 'G' and resid 204 through 208 Processing helix chain 'G' and resid 220 through 226 Processing helix chain 'G' and resid 228 through 237 removed outlier: 4.015A pdb=" N GLU G 232 " --> pdb=" O GLN G 228 " (cutoff:3.500A) Processing helix chain 'H' and resid 12 through 17 Processing helix chain 'H' and resid 25 through 49 removed outlier: 4.009A pdb=" N ARG H 36 " --> pdb=" O TRP H 32 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N ARG H 37 " --> pdb=" O ARG H 33 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ASP H 38 " --> pdb=" O ASN H 34 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LYS H 39 " --> pdb=" O PHE H 35 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N ALA H 40 " --> pdb=" O ARG H 36 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N ALA H 41 " --> pdb=" O ARG H 37 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N VAL H 42 " --> pdb=" O ASP H 38 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 64 No H-bonds generated for 'chain 'H' and resid 61 through 64' Processing helix chain 'H' and resid 80 through 82 No H-bonds generated for 'chain 'H' and resid 80 through 82' Processing helix chain 'H' and resid 86 through 88 No H-bonds generated for 'chain 'H' and resid 86 through 88' Processing helix chain 'H' and resid 112 through 114 No H-bonds generated for 'chain 'H' and resid 112 through 114' Processing helix chain 'H' and resid 116 through 120 removed outlier: 3.653A pdb=" N ASP H 120 " --> pdb=" O GLN H 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 116 through 120' Processing helix chain 'H' and resid 136 through 138 No H-bonds generated for 'chain 'H' and resid 136 through 138' Processing helix chain 'H' and resid 157 through 168 Processing helix chain 'H' and resid 173 through 196 Processing helix chain 'H' and resid 204 through 208 Processing helix chain 'H' and resid 220 through 226 Processing helix chain 'H' and resid 228 through 237 removed outlier: 4.008A pdb=" N GLU H 232 " --> pdb=" O GLN H 228 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 16 through 20 removed outlier: 6.750A pdb=" N THR A 94 " --> pdb=" O ASP A 4 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N LEU A 6 " --> pdb=" O THR A 92 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N THR A 92 " --> pdb=" O LEU A 6 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N LEU A 8 " --> pdb=" O LYS A 90 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LYS A 90 " --> pdb=" O LEU A 8 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 376 through 379 removed outlier: 7.969A pdb=" N ARG A 366 " --> pdb=" O ILE A 25 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ILE A 27 " --> pdb=" O ARG A 366 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N LEU A 368 " --> pdb=" O ILE A 27 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N VAL A 29 " --> pdb=" O LEU A 368 " (cutoff:3.500A) removed outlier: 9.451A pdb=" N GLN A 370 " --> pdb=" O VAL A 29 " (cutoff:3.500A) removed outlier: 8.154A pdb=" N THR A 26 " --> pdb=" O ILE A 345 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N PHE A 347 " --> pdb=" O THR A 26 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N LEU A 28 " --> pdb=" O PHE A 347 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N VAL A 349 " --> pdb=" O LEU A 28 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N GLY A 315 " --> pdb=" O GLN A 346 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N ILE A 348 " --> pdb=" O GLY A 315 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N VAL A 317 " --> pdb=" O ILE A 348 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N THR A 350 " --> pdb=" O VAL A 317 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N ILE A 319 " --> pdb=" O THR A 350 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N LEU A 148 " --> pdb=" O ILE A 316 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N LEU A 318 " --> pdb=" O LEU A 148 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N LEU A 150 " --> pdb=" O LEU A 318 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 74 through 77 Processing sheet with id= D, first strand: chain 'A' and resid 256 through 258 Processing sheet with id= E, first strand: chain 'B' and resid 16 through 20 removed outlier: 6.733A pdb=" N THR B 94 " --> pdb=" O ASP B 4 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N LEU B 6 " --> pdb=" O THR B 92 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N THR B 92 " --> pdb=" O LEU B 6 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N LEU B 8 " --> pdb=" O LYS B 90 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LYS B 90 " --> pdb=" O LEU B 8 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 377 through 379 removed outlier: 7.989A pdb=" N ARG B 366 " --> pdb=" O ILE B 25 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ILE B 27 " --> pdb=" O ARG B 366 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N LEU B 368 " --> pdb=" O ILE B 27 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N VAL B 29 " --> pdb=" O LEU B 368 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N THR B 26 " --> pdb=" O ILE B 345 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N PHE B 347 " --> pdb=" O THR B 26 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N LEU B 28 " --> pdb=" O PHE B 347 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N VAL B 349 " --> pdb=" O LEU B 28 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N GLY B 315 " --> pdb=" O GLN B 346 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N ILE B 348 " --> pdb=" O GLY B 315 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N VAL B 317 " --> pdb=" O ILE B 348 " (cutoff:3.500A) removed outlier: 8.257A pdb=" N THR B 350 " --> pdb=" O VAL B 317 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N ILE B 319 " --> pdb=" O THR B 350 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N LEU B 148 " --> pdb=" O ILE B 316 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N LEU B 318 " --> pdb=" O LEU B 148 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N LEU B 150 " --> pdb=" O LEU B 318 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 74 through 77 Processing sheet with id= H, first strand: chain 'B' and resid 256 through 258 Processing sheet with id= I, first strand: chain 'C' and resid 16 through 20 removed outlier: 6.725A pdb=" N THR C 94 " --> pdb=" O ASP C 4 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N LEU C 6 " --> pdb=" O THR C 92 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N THR C 92 " --> pdb=" O LEU C 6 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N LEU C 8 " --> pdb=" O LYS C 90 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N LYS C 90 " --> pdb=" O LEU C 8 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 377 through 379 removed outlier: 7.948A pdb=" N ARG C 366 " --> pdb=" O ILE C 25 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ILE C 27 " --> pdb=" O ARG C 366 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N LEU C 368 " --> pdb=" O ILE C 27 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N VAL C 29 " --> pdb=" O LEU C 368 " (cutoff:3.500A) removed outlier: 8.168A pdb=" N THR C 26 " --> pdb=" O ILE C 345 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N PHE C 347 " --> pdb=" O THR C 26 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N LEU C 28 " --> pdb=" O PHE C 347 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N VAL C 349 " --> pdb=" O LEU C 28 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N GLY C 315 " --> pdb=" O GLN C 346 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N ILE C 348 " --> pdb=" O GLY C 315 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N VAL C 317 " --> pdb=" O ILE C 348 " (cutoff:3.500A) removed outlier: 8.371A pdb=" N THR C 350 " --> pdb=" O VAL C 317 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N ILE C 319 " --> pdb=" O THR C 350 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N LEU C 148 " --> pdb=" O ILE C 316 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N LEU C 318 " --> pdb=" O LEU C 148 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N LEU C 150 " --> pdb=" O LEU C 318 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 74 through 77 Processing sheet with id= L, first strand: chain 'C' and resid 256 through 258 Processing sheet with id= M, first strand: chain 'D' and resid 16 through 20 removed outlier: 6.721A pdb=" N THR D 94 " --> pdb=" O ASP D 4 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N LEU D 6 " --> pdb=" O THR D 92 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N THR D 92 " --> pdb=" O LEU D 6 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N LEU D 8 " --> pdb=" O LYS D 90 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N LYS D 90 " --> pdb=" O LEU D 8 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 376 through 379 removed outlier: 8.014A pdb=" N ARG D 366 " --> pdb=" O ILE D 25 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ILE D 27 " --> pdb=" O ARG D 366 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N LEU D 368 " --> pdb=" O ILE D 27 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL D 29 " --> pdb=" O LEU D 368 " (cutoff:3.500A) removed outlier: 9.041A pdb=" N GLN D 370 " --> pdb=" O VAL D 29 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N THR D 26 " --> pdb=" O ILE D 345 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N PHE D 347 " --> pdb=" O THR D 26 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N LEU D 28 " --> pdb=" O PHE D 347 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N VAL D 349 " --> pdb=" O LEU D 28 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N GLY D 315 " --> pdb=" O GLN D 346 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N ILE D 348 " --> pdb=" O GLY D 315 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N VAL D 317 " --> pdb=" O ILE D 348 " (cutoff:3.500A) removed outlier: 8.384A pdb=" N THR D 350 " --> pdb=" O VAL D 317 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N ILE D 319 " --> pdb=" O THR D 350 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N LEU D 148 " --> pdb=" O ILE D 316 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N LEU D 318 " --> pdb=" O LEU D 148 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N LEU D 150 " --> pdb=" O LEU D 318 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 73 through 75 removed outlier: 4.309A pdb=" N ARG D 73 " --> pdb=" O SER D 86 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE D 75 " --> pdb=" O GLU D 84 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N GLU D 84 " --> pdb=" O ILE D 75 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 256 through 258 Processing sheet with id= Q, first strand: chain 'E' and resid 16 through 20 removed outlier: 6.736A pdb=" N THR E 94 " --> pdb=" O ASP E 4 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N LEU E 6 " --> pdb=" O THR E 92 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N THR E 92 " --> pdb=" O LEU E 6 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N LEU E 8 " --> pdb=" O LYS E 90 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LYS E 90 " --> pdb=" O LEU E 8 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 376 through 379 removed outlier: 8.056A pdb=" N ARG E 366 " --> pdb=" O ILE E 25 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ILE E 27 " --> pdb=" O ARG E 366 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N LEU E 368 " --> pdb=" O ILE E 27 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL E 29 " --> pdb=" O LEU E 368 " (cutoff:3.500A) removed outlier: 9.004A pdb=" N GLN E 370 " --> pdb=" O VAL E 29 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N THR E 26 " --> pdb=" O ILE E 345 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N PHE E 347 " --> pdb=" O THR E 26 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N LEU E 28 " --> pdb=" O PHE E 347 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N VAL E 349 " --> pdb=" O LEU E 28 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N GLY E 315 " --> pdb=" O GLN E 346 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N ILE E 348 " --> pdb=" O GLY E 315 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N VAL E 317 " --> pdb=" O ILE E 348 " (cutoff:3.500A) removed outlier: 8.386A pdb=" N THR E 350 " --> pdb=" O VAL E 317 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N ILE E 319 " --> pdb=" O THR E 350 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N LEU E 148 " --> pdb=" O ILE E 316 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N LEU E 318 " --> pdb=" O LEU E 148 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N LEU E 150 " --> pdb=" O LEU E 318 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'E' and resid 73 through 75 removed outlier: 4.340A pdb=" N ARG E 73 " --> pdb=" O SER E 86 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE E 75 " --> pdb=" O GLU E 84 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N GLU E 84 " --> pdb=" O ILE E 75 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 256 through 258 Processing sheet with id= U, first strand: chain 'F' and resid 16 through 20 removed outlier: 6.765A pdb=" N THR F 94 " --> pdb=" O ASP F 4 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N LEU F 6 " --> pdb=" O THR F 92 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N THR F 92 " --> pdb=" O LEU F 6 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N LEU F 8 " --> pdb=" O LYS F 90 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LYS F 90 " --> pdb=" O LEU F 8 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'F' and resid 377 through 379 removed outlier: 7.966A pdb=" N ARG F 366 " --> pdb=" O ILE F 25 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ILE F 27 " --> pdb=" O ARG F 366 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N LEU F 368 " --> pdb=" O ILE F 27 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N VAL F 29 " --> pdb=" O LEU F 368 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N THR F 26 " --> pdb=" O ILE F 345 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N PHE F 347 " --> pdb=" O THR F 26 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N LEU F 28 " --> pdb=" O PHE F 347 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N VAL F 349 " --> pdb=" O LEU F 28 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N GLY F 315 " --> pdb=" O GLN F 346 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N ILE F 348 " --> pdb=" O GLY F 315 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N VAL F 317 " --> pdb=" O ILE F 348 " (cutoff:3.500A) removed outlier: 8.353A pdb=" N THR F 350 " --> pdb=" O VAL F 317 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N ILE F 319 " --> pdb=" O THR F 350 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N LEU F 148 " --> pdb=" O ILE F 316 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N LEU F 318 " --> pdb=" O LEU F 148 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N LEU F 150 " --> pdb=" O LEU F 318 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'F' and resid 73 through 77 removed outlier: 4.104A pdb=" N ARG F 73 " --> pdb=" O SER F 86 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'F' and resid 256 through 258 Processing sheet with id= Y, first strand: chain 'G' and resid 68 through 72 Processing sheet with id= Z, first strand: chain 'G' and resid 139 through 141 Processing sheet with id= AA, first strand: chain 'H' and resid 68 through 72 Processing sheet with id= AB, first strand: chain 'H' and resid 139 through 141 908 hydrogen bonds defined for protein. 2424 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: 8.43 Time building geometry restraints manager: 9.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8219 1.34 - 1.46: 4224 1.46 - 1.58: 12328 1.58 - 1.69: 20 1.69 - 1.81: 192 Bond restraints: 24983 Sorted by residual: bond pdb=" N MET H 1 " pdb=" CA MET H 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.92e+00 bond pdb=" N MET G 1 " pdb=" CA MET G 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.83e+00 bond pdb=" N MET F 1 " pdb=" CA MET F 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.80e+00 bond pdb=" N MET B 1 " pdb=" CA MET B 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.79e+00 bond pdb=" N MET E 1 " pdb=" CA MET E 1 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.74e+00 ... (remaining 24978 not shown) Histogram of bond angle deviations from ideal: 99.54 - 107.62: 1026 107.62 - 115.71: 15296 115.71 - 123.80: 16780 123.80 - 131.89: 645 131.89 - 139.98: 76 Bond angle restraints: 33823 Sorted by residual: angle pdb=" N VAL D 60 " pdb=" CA VAL D 60 " pdb=" C VAL D 60 " ideal model delta sigma weight residual 112.29 107.70 4.59 9.40e-01 1.13e+00 2.38e+01 angle pdb=" N PHE F 11 " pdb=" CA PHE F 11 " pdb=" C PHE F 11 " ideal model delta sigma weight residual 109.86 104.85 5.01 1.55e+00 4.16e-01 1.04e+01 angle pdb=" N ASN B 307 " pdb=" CA ASN B 307 " pdb=" C ASN B 307 " ideal model delta sigma weight residual 114.75 110.72 4.03 1.26e+00 6.30e-01 1.03e+01 angle pdb=" C3' ATP B 501 " pdb=" C4' ATP B 501 " pdb=" O4' ATP B 501 " ideal model delta sigma weight residual 105.22 101.49 3.73 1.30e+00 5.94e-01 8.28e+00 angle pdb=" C3' ATP A 501 " pdb=" C4' ATP A 501 " pdb=" O4' ATP A 501 " ideal model delta sigma weight residual 105.22 101.54 3.68 1.30e+00 5.94e-01 8.04e+00 ... (remaining 33818 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.63: 13541 17.63 - 35.27: 1298 35.27 - 52.90: 288 52.90 - 70.53: 80 70.53 - 88.17: 28 Dihedral angle restraints: 15235 sinusoidal: 6401 harmonic: 8834 Sorted by residual: dihedral pdb=" CA PHE B 11 " pdb=" C PHE B 11 " pdb=" N ARG B 12 " pdb=" CA ARG B 12 " ideal model delta harmonic sigma weight residual -180.00 -150.64 -29.36 0 5.00e+00 4.00e-02 3.45e+01 dihedral pdb=" CA THR D 246 " pdb=" C THR D 246 " pdb=" N GLN D 247 " pdb=" CA GLN D 247 " ideal model delta harmonic sigma weight residual -180.00 -158.90 -21.10 0 5.00e+00 4.00e-02 1.78e+01 dihedral pdb=" CA THR E 246 " pdb=" C THR E 246 " pdb=" N GLN E 247 " pdb=" CA GLN E 247 " ideal model delta harmonic sigma weight residual -180.00 -159.54 -20.46 0 5.00e+00 4.00e-02 1.67e+01 ... (remaining 15232 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 3307 0.059 - 0.118: 352 0.118 - 0.178: 35 0.178 - 0.237: 1 0.237 - 0.296: 11 Chirality restraints: 3706 Sorted by residual: chirality pdb=" C2' ATP C 501 " pdb=" C1' ATP C 501 " pdb=" C3' ATP C 501 " pdb=" O2' ATP C 501 " both_signs ideal model delta sigma weight residual False -2.68 -2.98 0.30 2.00e-01 2.50e+01 2.19e+00 chirality pdb=" C2' ATP F 501 " pdb=" C1' ATP F 501 " pdb=" C3' ATP F 501 " pdb=" O2' ATP F 501 " both_signs ideal model delta sigma weight residual False -2.68 -2.98 0.30 2.00e-01 2.50e+01 2.18e+00 chirality pdb=" C3' ATP A 501 " pdb=" C2' ATP A 501 " pdb=" C4' ATP A 501 " pdb=" O3' ATP A 501 " both_signs ideal model delta sigma weight residual False -2.63 -2.93 0.29 2.00e-01 2.50e+01 2.18e+00 ... (remaining 3703 not shown) Planarity restraints: 4369 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS B 269 " 0.035 5.00e-02 4.00e+02 5.35e-02 4.58e+00 pdb=" N PRO B 270 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO B 270 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 270 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 296 " -0.015 2.00e-02 2.50e+03 1.59e-02 4.41e+00 pdb=" CG PHE A 296 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 PHE A 296 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE A 296 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE A 296 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE A 296 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE A 296 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 296 " 0.014 2.00e-02 2.50e+03 1.52e-02 4.02e+00 pdb=" CG PHE B 296 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 PHE B 296 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE B 296 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE B 296 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE B 296 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE B 296 " 0.004 2.00e-02 2.50e+03 ... (remaining 4366 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 125 2.57 - 3.15: 18636 3.15 - 3.73: 35166 3.73 - 4.32: 53033 4.32 - 4.90: 89574 Nonbonded interactions: 196534 Sorted by model distance: nonbonded pdb=" OG1 THR G 211 " pdb=" OD1 ASP G 213 " model vdw 1.983 2.440 nonbonded pdb=" OG1 THR H 211 " pdb=" OD1 ASP H 213 " model vdw 1.994 2.440 nonbonded pdb=" O ALA E 309 " pdb=" OG1 THR E 313 " model vdw 2.046 2.440 nonbonded pdb=" OE1 GLU A 224 " pdb=" NE2 GLN E 78 " model vdw 2.071 2.520 nonbonded pdb=" O ALA D 309 " pdb=" OG1 THR D 313 " model vdw 2.106 2.440 ... (remaining 196529 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 219 or resid 224 through 382 or resid 501)) selection = (chain 'B' and (resid 1 through 163 or resid 171 through 382 or resid 501)) } ncs_group { reference = (chain 'C' and resid 1 through 460) selection = (chain 'D' and (resid 1 through 160 or resid 171 through 218 or resid 224 throug \ h 460)) selection = (chain 'E' and (resid 1 through 160 or resid 171 through 218 or resid 224 throug \ h 460)) selection = (chain 'F' and resid 1 through 460) } ncs_group { reference = chain 'G' selection = chain 'H' } 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: 1.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 8.100 Check model and map are aligned: 0.390 Set scattering table: 0.230 Process input model: 65.000 Find NCS groups from input model: 1.630 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.010 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 89.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 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 0.032 24983 Z= 0.191 Angle : 0.518 6.872 33823 Z= 0.283 Chirality : 0.042 0.296 3706 Planarity : 0.004 0.054 4369 Dihedral : 15.178 88.165 9485 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.61 (0.16), residues: 2979 helix: 1.77 (0.15), residues: 1164 sheet: -0.52 (0.21), residues: 544 loop : -0.38 (0.18), residues: 1271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 199 HIS 0.007 0.001 HIS A 352 PHE 0.036 0.001 PHE A 296 TYR 0.026 0.001 TYR A 272 ARG 0.005 0.000 ARG F 12 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 2640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 433 time to evaluate : 2.909 Fit side-chains REVERT: A 5 LYS cc_start: 0.8874 (tptm) cc_final: 0.8596 (tptp) REVERT: A 15 LYS cc_start: 0.9009 (tttt) cc_final: 0.8772 (tttp) REVERT: A 90 LYS cc_start: 0.9053 (ttmm) cc_final: 0.8674 (mtpt) REVERT: A 118 ASP cc_start: 0.8737 (p0) cc_final: 0.8455 (p0) REVERT: A 363 GLU cc_start: 0.8231 (mp0) cc_final: 0.7982 (mp0) REVERT: A 372 GLU cc_start: 0.7457 (pm20) cc_final: 0.7231 (pm20) REVERT: A 373 ASN cc_start: 0.8126 (m-40) cc_final: 0.7599 (m-40) REVERT: B 1 MET cc_start: 0.7635 (ttt) cc_final: 0.7106 (ttt) REVERT: B 85 MET cc_start: 0.8856 (ttm) cc_final: 0.8316 (ttm) REVERT: B 134 ARG cc_start: 0.8025 (mtp180) cc_final: 0.7768 (mtp180) REVERT: B 248 GLN cc_start: 0.8316 (tm-30) cc_final: 0.8062 (tm-30) REVERT: C 18 ASP cc_start: 0.7572 (p0) cc_final: 0.7324 (p0) REVERT: C 84 GLU cc_start: 0.7411 (tt0) cc_final: 0.7211 (tt0) REVERT: C 110 ARG cc_start: 0.6922 (ttm-80) cc_final: 0.6649 (ttt-90) REVERT: C 126 ARG cc_start: 0.6879 (mmp80) cc_final: 0.6160 (mtm180) REVERT: C 210 HIS cc_start: 0.7153 (m-70) cc_final: 0.6332 (t70) REVERT: C 396 SER cc_start: 0.7742 (t) cc_final: 0.7468 (m) REVERT: D 41 ASP cc_start: 0.7669 (m-30) cc_final: 0.7391 (m-30) REVERT: D 101 LYS cc_start: 0.7532 (tptp) cc_final: 0.7324 (tptp) REVERT: D 126 ARG cc_start: 0.7390 (mmp80) cc_final: 0.6663 (mtm-85) REVERT: D 143 GLN cc_start: 0.7634 (mm-40) cc_final: 0.7344 (mm-40) REVERT: D 171 ARG cc_start: 0.7839 (ptm160) cc_final: 0.7598 (ptm-80) REVERT: D 267 MET cc_start: 0.8900 (mtp) cc_final: 0.8449 (mtt) REVERT: D 372 GLU cc_start: 0.7401 (pm20) cc_final: 0.6900 (pm20) REVERT: D 380 MET cc_start: 0.8487 (mtt) cc_final: 0.8157 (mtm) REVERT: D 407 LYS cc_start: 0.8023 (mtmm) cc_final: 0.7772 (mtmm) REVERT: D 443 LYS cc_start: 0.7779 (mttt) cc_final: 0.7442 (mtpm) REVERT: D 451 GLN cc_start: 0.6890 (mm110) cc_final: 0.6512 (mm-40) REVERT: E 41 ASP cc_start: 0.7567 (m-30) cc_final: 0.7281 (m-30) REVERT: E 77 ARG cc_start: 0.7322 (mtp180) cc_final: 0.7101 (mtm-85) REVERT: E 126 ARG cc_start: 0.7389 (mmp80) cc_final: 0.6536 (mtm-85) REVERT: E 372 GLU cc_start: 0.7391 (pm20) cc_final: 0.6833 (pm20) REVERT: E 380 MET cc_start: 0.8544 (mtt) cc_final: 0.8239 (mtm) REVERT: E 443 LYS cc_start: 0.7864 (mttt) cc_final: 0.7532 (mtpm) REVERT: E 451 GLN cc_start: 0.6914 (mm110) cc_final: 0.6477 (mm-40) REVERT: F 18 ASP cc_start: 0.7427 (p0) cc_final: 0.7195 (p0) REVERT: F 84 GLU cc_start: 0.7402 (tt0) cc_final: 0.7155 (tt0) REVERT: F 110 ARG cc_start: 0.7000 (ttm-80) cc_final: 0.6784 (ttt-90) REVERT: F 126 ARG cc_start: 0.6671 (mmp80) cc_final: 0.5865 (mtt180) REVERT: F 210 HIS cc_start: 0.7469 (m-70) cc_final: 0.6816 (t70) REVERT: F 267 MET cc_start: 0.8778 (mtt) cc_final: 0.8420 (mtp) REVERT: F 373 ASN cc_start: 0.7567 (m110) cc_final: 0.7292 (m-40) REVERT: F 396 SER cc_start: 0.7664 (t) cc_final: 0.7363 (m) REVERT: F 443 LYS cc_start: 0.7939 (pttt) cc_final: 0.7734 (ptpp) REVERT: F 451 GLN cc_start: 0.7768 (mm-40) cc_final: 0.7549 (mm-40) REVERT: G 205 GLN cc_start: 0.7569 (mt0) cc_final: 0.7325 (mt0) REVERT: H 190 PHE cc_start: 0.7449 (t80) cc_final: 0.7194 (t80) REVERT: H 191 ASP cc_start: 0.7003 (m-30) cc_final: 0.6713 (m-30) REVERT: H 236 GLN cc_start: 0.6781 (tt0) cc_final: 0.6552 (mt0) outliers start: 0 outliers final: 1 residues processed: 433 average time/residue: 1.6857 time to fit residues: 813.8898 Evaluate side-chains 337 residues out of total 2640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 336 time to evaluate : 2.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 116 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 251 optimal weight: 0.1980 chunk 225 optimal weight: 0.3980 chunk 125 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 152 optimal weight: 0.9990 chunk 120 optimal weight: 1.9990 chunk 233 optimal weight: 4.9990 chunk 90 optimal weight: 6.9990 chunk 142 optimal weight: 4.9990 chunk 173 optimal weight: 0.8980 chunk 270 optimal weight: 2.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 HIS D 214 GLN E 130 GLN G 202 GLN G 236 GLN H 202 GLN ** H 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.0946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 24983 Z= 0.159 Angle : 0.484 7.012 33823 Z= 0.265 Chirality : 0.040 0.149 3706 Planarity : 0.004 0.052 4369 Dihedral : 7.496 89.268 3404 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.44 % Allowed : 7.46 % Favored : 91.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.67 (0.15), residues: 2979 helix: 1.77 (0.15), residues: 1156 sheet: -0.35 (0.21), residues: 544 loop : -0.36 (0.18), residues: 1279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP F 199 HIS 0.006 0.001 HIS A 352 PHE 0.026 0.001 PHE A 296 TYR 0.016 0.001 TYR A 272 ARG 0.005 0.000 ARG A 179 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 2640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 366 time to evaluate : 2.920 Fit side-chains REVERT: A 1 MET cc_start: 0.8035 (ttt) cc_final: 0.7810 (ttm) REVERT: A 2 ARG cc_start: 0.8635 (ttp-110) cc_final: 0.8323 (ttp-110) REVERT: A 118 ASP cc_start: 0.8572 (p0) cc_final: 0.8323 (p0) REVERT: A 372 GLU cc_start: 0.7513 (pm20) cc_final: 0.7148 (mp0) REVERT: B 85 MET cc_start: 0.8824 (ttm) cc_final: 0.8298 (ttm) REVERT: B 106 MET cc_start: 0.9004 (OUTLIER) cc_final: 0.8777 (tmt) REVERT: B 134 ARG cc_start: 0.8031 (mtp180) cc_final: 0.7732 (mtp180) REVERT: B 248 GLN cc_start: 0.8400 (tm-30) cc_final: 0.8118 (tm-30) REVERT: C 18 ASP cc_start: 0.7545 (p0) cc_final: 0.7260 (p0) REVERT: C 110 ARG cc_start: 0.6929 (ttm-80) cc_final: 0.6630 (ttt-90) REVERT: C 126 ARG cc_start: 0.6899 (mmp80) cc_final: 0.6014 (mtm180) REVERT: C 210 HIS cc_start: 0.7160 (m-70) cc_final: 0.6363 (t70) REVERT: C 262 ASN cc_start: 0.7168 (m110) cc_final: 0.6831 (m110) REVERT: C 293 ASP cc_start: 0.8108 (OUTLIER) cc_final: 0.7691 (m-30) REVERT: C 396 SER cc_start: 0.7757 (t) cc_final: 0.7474 (m) REVERT: C 407 LYS cc_start: 0.7951 (mttt) cc_final: 0.7562 (ttmt) REVERT: C 443 LYS cc_start: 0.7948 (pttt) cc_final: 0.6133 (tptt) REVERT: D 41 ASP cc_start: 0.7737 (m-30) cc_final: 0.7464 (m-30) REVERT: D 126 ARG cc_start: 0.7361 (mmp80) cc_final: 0.6617 (mtm-85) REVERT: D 143 GLN cc_start: 0.7497 (mm-40) cc_final: 0.7216 (mm-40) REVERT: D 171 ARG cc_start: 0.7822 (ptm160) cc_final: 0.7580 (ptm-80) REVERT: D 296 PHE cc_start: 0.8082 (OUTLIER) cc_final: 0.7492 (p90) REVERT: D 324 MET cc_start: 0.7491 (OUTLIER) cc_final: 0.7209 (ttp) REVERT: D 372 GLU cc_start: 0.7289 (pm20) cc_final: 0.7032 (pm20) REVERT: D 380 MET cc_start: 0.8472 (mtt) cc_final: 0.8113 (mtm) REVERT: D 443 LYS cc_start: 0.7848 (mttt) cc_final: 0.7551 (mtpm) REVERT: D 451 GLN cc_start: 0.6834 (mm110) cc_final: 0.6401 (mm-40) REVERT: E 126 ARG cc_start: 0.7295 (mmp80) cc_final: 0.6541 (mtm-85) REVERT: E 314 GLN cc_start: 0.8623 (mt0) cc_final: 0.8421 (mt0) REVERT: E 333 GLN cc_start: 0.7870 (OUTLIER) cc_final: 0.7297 (mt0) REVERT: E 372 GLU cc_start: 0.7299 (pm20) cc_final: 0.7001 (pm20) REVERT: E 443 LYS cc_start: 0.7818 (mttt) cc_final: 0.7503 (mtpm) REVERT: E 451 GLN cc_start: 0.6871 (mm110) cc_final: 0.6388 (mm-40) REVERT: F 18 ASP cc_start: 0.7509 (p0) cc_final: 0.7289 (p0) REVERT: F 84 GLU cc_start: 0.7209 (tt0) cc_final: 0.6992 (tt0) REVERT: F 110 ARG cc_start: 0.7013 (ttm-80) cc_final: 0.6737 (ttt-90) REVERT: F 126 ARG cc_start: 0.6704 (mmp80) cc_final: 0.5888 (mtt180) REVERT: F 210 HIS cc_start: 0.7433 (m-70) cc_final: 0.6727 (t70) REVERT: F 262 ASN cc_start: 0.7638 (m110) cc_final: 0.7331 (m110) REVERT: F 369 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.8008 (pm20) REVERT: F 396 SER cc_start: 0.7718 (t) cc_final: 0.7402 (m) REVERT: F 442 GLU cc_start: 0.7301 (OUTLIER) cc_final: 0.6998 (mm-30) REVERT: F 443 LYS cc_start: 0.7963 (pttt) cc_final: 0.7669 (ptpp) REVERT: F 451 GLN cc_start: 0.7869 (mm-40) cc_final: 0.7634 (mm-40) REVERT: G 205 GLN cc_start: 0.7595 (mt0) cc_final: 0.7352 (mt0) REVERT: H 71 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7664 (tp30) REVERT: H 190 PHE cc_start: 0.7511 (t80) cc_final: 0.7236 (t80) REVERT: H 191 ASP cc_start: 0.6765 (m-30) cc_final: 0.6433 (m-30) REVERT: H 236 GLN cc_start: 0.6828 (tt0) cc_final: 0.6562 (mt0) outliers start: 38 outliers final: 12 residues processed: 380 average time/residue: 1.6786 time to fit residues: 714.1864 Evaluate side-chains 345 residues out of total 2640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 325 time to evaluate : 2.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain B residue 106 MET Chi-restraints excluded: chain B residue 116 HIS Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain B residue 229 GLN Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 293 ASP Chi-restraints excluded: chain C residue 391 ASN Chi-restraints excluded: chain D residue 231 MET Chi-restraints excluded: chain D residue 296 PHE Chi-restraints excluded: chain D residue 324 MET Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain E residue 333 GLN Chi-restraints excluded: chain F residue 369 GLU Chi-restraints excluded: chain F residue 442 GLU Chi-restraints excluded: chain G residue 193 HIS Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 193 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 150 optimal weight: 0.0470 chunk 83 optimal weight: 3.9990 chunk 225 optimal weight: 2.9990 chunk 184 optimal weight: 5.9990 chunk 74 optimal weight: 2.9990 chunk 271 optimal weight: 8.9990 chunk 292 optimal weight: 6.9990 chunk 241 optimal weight: 0.6980 chunk 268 optimal weight: 6.9990 chunk 92 optimal weight: 1.9990 chunk 217 optimal weight: 0.6980 overall best weight: 1.2882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 GLN C 214 GLN E 214 GLN F 373 ASN G 201 GLN G 236 GLN H 202 GLN H 205 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.1203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 24983 Z= 0.232 Angle : 0.520 7.462 33823 Z= 0.282 Chirality : 0.042 0.181 3706 Planarity : 0.005 0.056 4369 Dihedral : 7.132 81.263 3404 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.05 % Allowed : 9.89 % Favored : 88.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.57 (0.15), residues: 2979 helix: 1.67 (0.15), residues: 1150 sheet: -0.28 (0.21), residues: 569 loop : -0.44 (0.17), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP F 199 HIS 0.007 0.001 HIS A 352 PHE 0.026 0.002 PHE A 296 TYR 0.020 0.001 TYR A 272 ARG 0.006 0.000 ARG C 208 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 2640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 333 time to evaluate : 3.170 Fit side-chains REVERT: A 106 MET cc_start: 0.8983 (tmm) cc_final: 0.8595 (tmt) REVERT: A 372 GLU cc_start: 0.7531 (pm20) cc_final: 0.7282 (pm20) REVERT: B 85 MET cc_start: 0.8843 (ttm) cc_final: 0.8355 (ttm) REVERT: B 106 MET cc_start: 0.9029 (OUTLIER) cc_final: 0.8668 (tmt) REVERT: B 134 ARG cc_start: 0.8068 (mtp180) cc_final: 0.7829 (mtp180) REVERT: B 248 GLN cc_start: 0.8371 (tm-30) cc_final: 0.8075 (tm-30) REVERT: C 18 ASP cc_start: 0.7538 (p0) cc_final: 0.7283 (p0) REVERT: C 110 ARG cc_start: 0.7018 (ttm-80) cc_final: 0.6735 (ttt-90) REVERT: C 126 ARG cc_start: 0.6911 (mmp80) cc_final: 0.6030 (mtm180) REVERT: C 195 GLN cc_start: 0.7373 (OUTLIER) cc_final: 0.7072 (mt0) REVERT: C 210 HIS cc_start: 0.7157 (m-70) cc_final: 0.6360 (t70) REVERT: C 262 ASN cc_start: 0.7166 (m110) cc_final: 0.6865 (m110) REVERT: C 293 ASP cc_start: 0.8160 (OUTLIER) cc_final: 0.7733 (m-30) REVERT: C 396 SER cc_start: 0.7837 (t) cc_final: 0.7529 (m) REVERT: C 407 LYS cc_start: 0.7970 (mttt) cc_final: 0.7564 (ttmt) REVERT: C 443 LYS cc_start: 0.7953 (pttt) cc_final: 0.6125 (tptt) REVERT: D 41 ASP cc_start: 0.7731 (m-30) cc_final: 0.7476 (m-30) REVERT: D 126 ARG cc_start: 0.7356 (mmp80) cc_final: 0.6702 (mtm-85) REVERT: D 130 GLN cc_start: 0.7236 (OUTLIER) cc_final: 0.6374 (mm110) REVERT: D 143 GLN cc_start: 0.7510 (mm-40) cc_final: 0.7302 (mm-40) REVERT: D 171 ARG cc_start: 0.7840 (ptm160) cc_final: 0.7581 (ptm-80) REVERT: D 227 ARG cc_start: 0.6204 (OUTLIER) cc_final: 0.5904 (tpt170) REVERT: D 296 PHE cc_start: 0.8071 (OUTLIER) cc_final: 0.7446 (p90) REVERT: D 371 ASP cc_start: 0.7908 (p0) cc_final: 0.7660 (p0) REVERT: D 372 GLU cc_start: 0.7367 (pm20) cc_final: 0.7049 (pm20) REVERT: D 380 MET cc_start: 0.8460 (mtt) cc_final: 0.8083 (mtm) REVERT: D 443 LYS cc_start: 0.7891 (mttt) cc_final: 0.7546 (mtpm) REVERT: D 451 GLN cc_start: 0.6993 (mm110) cc_final: 0.6576 (mm-40) REVERT: E 126 ARG cc_start: 0.7312 (mmp80) cc_final: 0.6624 (mtm-85) REVERT: E 314 GLN cc_start: 0.8697 (mt0) cc_final: 0.8466 (mt0) REVERT: E 371 ASP cc_start: 0.7926 (p0) cc_final: 0.7720 (p0) REVERT: E 372 GLU cc_start: 0.7272 (pm20) cc_final: 0.6975 (pm20) REVERT: E 443 LYS cc_start: 0.7862 (mttt) cc_final: 0.7521 (mtpm) REVERT: E 451 GLN cc_start: 0.6845 (mm110) cc_final: 0.6352 (mm-40) REVERT: F 1 MET cc_start: 0.8233 (OUTLIER) cc_final: 0.7941 (ttt) REVERT: F 84 GLU cc_start: 0.7253 (tt0) cc_final: 0.7033 (tt0) REVERT: F 110 ARG cc_start: 0.7054 (ttm-80) cc_final: 0.6754 (ttt-90) REVERT: F 126 ARG cc_start: 0.6722 (mmp80) cc_final: 0.5909 (mtt180) REVERT: F 195 GLN cc_start: 0.7465 (OUTLIER) cc_final: 0.7197 (mt0) REVERT: F 210 HIS cc_start: 0.7459 (m-70) cc_final: 0.6735 (t70) REVERT: F 262 ASN cc_start: 0.7608 (m110) cc_final: 0.7307 (m110) REVERT: F 267 MET cc_start: 0.8707 (mtt) cc_final: 0.8220 (mtp) REVERT: F 369 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.7974 (pm20) REVERT: F 396 SER cc_start: 0.7755 (t) cc_final: 0.7435 (m) REVERT: F 442 GLU cc_start: 0.7329 (tt0) cc_final: 0.7064 (mm-30) REVERT: F 443 LYS cc_start: 0.7910 (pttt) cc_final: 0.7673 (ptpp) REVERT: F 451 GLN cc_start: 0.7851 (mm-40) cc_final: 0.7613 (mm-40) REVERT: G 27 GLN cc_start: 0.7845 (mt0) cc_final: 0.7617 (mt0) REVERT: G 205 GLN cc_start: 0.7627 (mt0) cc_final: 0.7375 (mt0) REVERT: H 1 MET cc_start: 0.8332 (mtt) cc_final: 0.8112 (mtt) REVERT: H 31 ARG cc_start: 0.7514 (OUTLIER) cc_final: 0.6712 (mtm180) REVERT: H 71 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7648 (tp30) REVERT: H 191 ASP cc_start: 0.6875 (m-30) cc_final: 0.6523 (m-30) outliers start: 54 outliers final: 19 residues processed: 358 average time/residue: 1.6566 time to fit residues: 664.5245 Evaluate side-chains 356 residues out of total 2640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 326 time to evaluate : 2.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 MET Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 307 ASN Chi-restraints excluded: chain B residue 106 MET Chi-restraints excluded: chain B residue 110 ARG Chi-restraints excluded: chain B residue 116 HIS Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 370 GLN Chi-restraints excluded: chain C residue 195 GLN Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 293 ASP Chi-restraints excluded: chain C residue 324 MET Chi-restraints excluded: chain C residue 391 ASN Chi-restraints excluded: chain D residue 130 GLN Chi-restraints excluded: chain D residue 227 ARG Chi-restraints excluded: chain D residue 296 PHE Chi-restraints excluded: chain D residue 442 GLU Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 195 GLN Chi-restraints excluded: chain F residue 275 ILE Chi-restraints excluded: chain F residue 369 GLU Chi-restraints excluded: chain G residue 193 HIS Chi-restraints excluded: chain G residue 206 LEU Chi-restraints excluded: chain H residue 31 ARG Chi-restraints excluded: chain H residue 43 MET Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 193 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 267 optimal weight: 2.9990 chunk 203 optimal weight: 8.9990 chunk 140 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 129 optimal weight: 0.0270 chunk 182 optimal weight: 1.9990 chunk 272 optimal weight: 0.0060 chunk 288 optimal weight: 0.8980 chunk 142 optimal weight: 0.9990 chunk 257 optimal weight: 4.9990 chunk 77 optimal weight: 0.7980 overall best weight: 0.5456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 240 GLN C 174 ASN F 174 ASN F 373 ASN G 236 GLN H 50 GLN H 202 GLN H 236 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.1388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 24983 Z= 0.133 Angle : 0.442 7.044 33823 Z= 0.243 Chirality : 0.039 0.141 3706 Planarity : 0.004 0.050 4369 Dihedral : 6.576 69.988 3404 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.74 % Allowed : 10.91 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.78 (0.15), residues: 2979 helix: 1.81 (0.15), residues: 1160 sheet: -0.12 (0.21), residues: 572 loop : -0.34 (0.18), residues: 1247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 199 HIS 0.005 0.001 HIS A 352 PHE 0.020 0.001 PHE D 296 TYR 0.009 0.001 TYR A 272 ARG 0.004 0.000 ARG E 208 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 2640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 340 time to evaluate : 2.856 Fit side-chains REVERT: A 236 GLN cc_start: 0.8718 (OUTLIER) cc_final: 0.8476 (tm-30) REVERT: A 248 GLN cc_start: 0.8478 (tm-30) cc_final: 0.8103 (tm-30) REVERT: A 372 GLU cc_start: 0.7535 (pm20) cc_final: 0.7139 (mp0) REVERT: B 85 MET cc_start: 0.8830 (ttm) cc_final: 0.8344 (ttm) REVERT: B 134 ARG cc_start: 0.8041 (mtp180) cc_final: 0.7733 (mtp180) REVERT: B 248 GLN cc_start: 0.8349 (tm-30) cc_final: 0.8055 (tm-30) REVERT: C 1 MET cc_start: 0.8229 (OUTLIER) cc_final: 0.7931 (ttt) REVERT: C 18 ASP cc_start: 0.7509 (p0) cc_final: 0.7272 (p0) REVERT: C 110 ARG cc_start: 0.6992 (ttm-80) cc_final: 0.6698 (ttt-90) REVERT: C 126 ARG cc_start: 0.6928 (mmp80) cc_final: 0.6096 (mtm110) REVERT: C 195 GLN cc_start: 0.7207 (OUTLIER) cc_final: 0.6926 (mt0) REVERT: C 210 HIS cc_start: 0.7060 (m-70) cc_final: 0.6334 (t70) REVERT: C 293 ASP cc_start: 0.8132 (OUTLIER) cc_final: 0.7700 (m-30) REVERT: C 396 SER cc_start: 0.7763 (t) cc_final: 0.7469 (m) REVERT: C 407 LYS cc_start: 0.7907 (mttt) cc_final: 0.7511 (ttmt) REVERT: C 443 LYS cc_start: 0.7855 (pttt) cc_final: 0.7600 (ptpp) REVERT: D 41 ASP cc_start: 0.7702 (m-30) cc_final: 0.7421 (m-30) REVERT: D 126 ARG cc_start: 0.7399 (mmp80) cc_final: 0.6804 (mtm-85) REVERT: D 130 GLN cc_start: 0.7132 (OUTLIER) cc_final: 0.6280 (mm110) REVERT: D 171 ARG cc_start: 0.7839 (ptm160) cc_final: 0.7589 (ptm-80) REVERT: D 227 ARG cc_start: 0.6242 (OUTLIER) cc_final: 0.5964 (tpt170) REVERT: D 296 PHE cc_start: 0.8014 (OUTLIER) cc_final: 0.7398 (p90) REVERT: D 372 GLU cc_start: 0.7429 (pm20) cc_final: 0.7047 (pm20) REVERT: D 380 MET cc_start: 0.8371 (mtt) cc_final: 0.8015 (mtm) REVERT: D 443 LYS cc_start: 0.7903 (mttt) cc_final: 0.7531 (mtpm) REVERT: D 451 GLN cc_start: 0.6950 (mm110) cc_final: 0.6540 (mm-40) REVERT: E 126 ARG cc_start: 0.7301 (mmp80) cc_final: 0.6601 (mtm-85) REVERT: E 314 GLN cc_start: 0.8552 (mt0) cc_final: 0.8346 (mt0) REVERT: E 333 GLN cc_start: 0.7886 (OUTLIER) cc_final: 0.7150 (mt0) REVERT: E 372 GLU cc_start: 0.7438 (pm20) cc_final: 0.7044 (pm20) REVERT: E 443 LYS cc_start: 0.7871 (mttt) cc_final: 0.7515 (mtpm) REVERT: E 451 GLN cc_start: 0.6831 (mm110) cc_final: 0.6348 (mm-40) REVERT: F 18 ASP cc_start: 0.7972 (p0) cc_final: 0.7746 (p0) REVERT: F 84 GLU cc_start: 0.7223 (tt0) cc_final: 0.6989 (tt0) REVERT: F 110 ARG cc_start: 0.6989 (ttm-80) cc_final: 0.6647 (ttt-90) REVERT: F 126 ARG cc_start: 0.6713 (mmp80) cc_final: 0.5893 (mtt180) REVERT: F 195 GLN cc_start: 0.7185 (OUTLIER) cc_final: 0.6917 (mt0) REVERT: F 210 HIS cc_start: 0.7339 (m-70) cc_final: 0.6676 (t70) REVERT: F 262 ASN cc_start: 0.7588 (m110) cc_final: 0.7304 (m110) REVERT: F 267 MET cc_start: 0.8712 (mtt) cc_final: 0.8158 (mtp) REVERT: F 293 ASP cc_start: 0.8076 (OUTLIER) cc_final: 0.7618 (m-30) REVERT: F 369 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.8003 (pm20) REVERT: F 396 SER cc_start: 0.7760 (t) cc_final: 0.7429 (m) REVERT: F 442 GLU cc_start: 0.7341 (tt0) cc_final: 0.7099 (mm-30) REVERT: F 443 LYS cc_start: 0.7982 (pttt) cc_final: 0.7690 (ptpp) REVERT: G 27 GLN cc_start: 0.7801 (mt0) cc_final: 0.7489 (mt0) REVERT: G 36 ARG cc_start: 0.6801 (ptm160) cc_final: 0.6220 (ptm160) REVERT: G 205 GLN cc_start: 0.7556 (mt0) cc_final: 0.7300 (mt0) REVERT: H 71 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7611 (tp30) REVERT: H 191 ASP cc_start: 0.6658 (m-30) cc_final: 0.6335 (m-30) outliers start: 46 outliers final: 18 residues processed: 360 average time/residue: 1.6825 time to fit residues: 677.5294 Evaluate side-chains 359 residues out of total 2640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 329 time to evaluate : 2.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 229 GLN Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain B residue 116 HIS Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain B residue 229 GLN Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 370 GLN Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 106 MET Chi-restraints excluded: chain C residue 195 GLN Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 293 ASP Chi-restraints excluded: chain C residue 391 ASN Chi-restraints excluded: chain C residue 442 GLU Chi-restraints excluded: chain D residue 130 GLN Chi-restraints excluded: chain D residue 227 ARG Chi-restraints excluded: chain D residue 296 PHE Chi-restraints excluded: chain D residue 442 GLU Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 333 GLN Chi-restraints excluded: chain F residue 106 MET Chi-restraints excluded: chain F residue 195 GLN Chi-restraints excluded: chain F residue 293 ASP Chi-restraints excluded: chain F residue 369 GLU Chi-restraints excluded: chain G residue 193 HIS Chi-restraints excluded: chain G residue 206 LEU Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 193 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 239 optimal weight: 4.9990 chunk 163 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 214 optimal weight: 0.0870 chunk 118 optimal weight: 4.9990 chunk 245 optimal weight: 6.9990 chunk 199 optimal weight: 5.9990 chunk 0 optimal weight: 3.9990 chunk 147 optimal weight: 3.9990 chunk 258 optimal weight: 8.9990 chunk 72 optimal weight: 2.9990 overall best weight: 2.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 GLN B 253 HIS C 413 GLN F 373 ASN G 236 GLN H 236 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.1467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 24983 Z= 0.418 Angle : 0.654 7.699 33823 Z= 0.349 Chirality : 0.047 0.243 3706 Planarity : 0.006 0.058 4369 Dihedral : 7.042 78.887 3404 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.31 % Allowed : 11.44 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.23 (0.15), residues: 2979 helix: 1.24 (0.15), residues: 1165 sheet: -0.25 (0.21), residues: 539 loop : -0.61 (0.17), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 199 HIS 0.010 0.002 HIS B 352 PHE 0.028 0.003 PHE A 296 TYR 0.020 0.002 TYR B 193 ARG 0.010 0.001 ARG C 208 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 2640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 338 time to evaluate : 3.026 Fit side-chains REVERT: A 120 MET cc_start: 0.8569 (mmt) cc_final: 0.8369 (mmm) REVERT: A 134 ARG cc_start: 0.8284 (OUTLIER) cc_final: 0.8007 (mtp180) REVERT: A 372 GLU cc_start: 0.7557 (pm20) cc_final: 0.7317 (pm20) REVERT: B 85 MET cc_start: 0.8798 (ttm) cc_final: 0.8339 (ttm) REVERT: B 248 GLN cc_start: 0.8425 (tm-30) cc_final: 0.8129 (tm-30) REVERT: C 18 ASP cc_start: 0.7596 (p0) cc_final: 0.7325 (p0) REVERT: C 110 ARG cc_start: 0.7184 (ttm-80) cc_final: 0.6928 (ttt-90) REVERT: C 126 ARG cc_start: 0.6905 (mmp80) cc_final: 0.5981 (mtm180) REVERT: C 210 HIS cc_start: 0.7227 (m-70) cc_final: 0.6372 (t70) REVERT: C 262 ASN cc_start: 0.7149 (m110) cc_final: 0.6857 (m110) REVERT: C 396 SER cc_start: 0.7844 (t) cc_final: 0.7534 (m) REVERT: C 407 LYS cc_start: 0.8062 (mttt) cc_final: 0.7389 (mmtm) REVERT: C 456 ARG cc_start: 0.7226 (ttm110) cc_final: 0.6872 (mtt180) REVERT: D 126 ARG cc_start: 0.7437 (mmp80) cc_final: 0.6933 (mtm-85) REVERT: D 130 GLN cc_start: 0.7298 (OUTLIER) cc_final: 0.6452 (mm110) REVERT: D 296 PHE cc_start: 0.8136 (OUTLIER) cc_final: 0.7532 (p90) REVERT: D 443 LYS cc_start: 0.7880 (mttt) cc_final: 0.7530 (mtpm) REVERT: D 451 GLN cc_start: 0.6949 (mm110) cc_final: 0.6539 (mm-40) REVERT: E 126 ARG cc_start: 0.7296 (mmp80) cc_final: 0.6673 (mtm-85) REVERT: E 333 GLN cc_start: 0.8052 (OUTLIER) cc_final: 0.7394 (mt0) REVERT: E 372 GLU cc_start: 0.7239 (pm20) cc_final: 0.6992 (pm20) REVERT: E 443 LYS cc_start: 0.7875 (mttt) cc_final: 0.7517 (mtpm) REVERT: E 451 GLN cc_start: 0.6905 (mm110) cc_final: 0.6405 (mm-40) REVERT: F 18 ASP cc_start: 0.7924 (p0) cc_final: 0.7701 (p0) REVERT: F 84 GLU cc_start: 0.7237 (tt0) cc_final: 0.6993 (tt0) REVERT: F 110 ARG cc_start: 0.7177 (ttm-80) cc_final: 0.6744 (ttt-90) REVERT: F 126 ARG cc_start: 0.6742 (mmp80) cc_final: 0.5924 (mtt180) REVERT: F 210 HIS cc_start: 0.7455 (m-70) cc_final: 0.6644 (t70) REVERT: F 262 ASN cc_start: 0.7609 (m110) cc_final: 0.7320 (m110) REVERT: F 267 MET cc_start: 0.8742 (mtt) cc_final: 0.8195 (mtp) REVERT: F 293 ASP cc_start: 0.8169 (OUTLIER) cc_final: 0.7708 (m-30) REVERT: F 369 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7887 (pm20) REVERT: F 396 SER cc_start: 0.7764 (t) cc_final: 0.7461 (m) REVERT: F 411 ASP cc_start: 0.8258 (OUTLIER) cc_final: 0.7452 (t0) REVERT: F 442 GLU cc_start: 0.7311 (tt0) cc_final: 0.7093 (mm-30) REVERT: F 443 LYS cc_start: 0.8012 (pttt) cc_final: 0.7725 (ptpp) REVERT: G 27 GLN cc_start: 0.7835 (mt0) cc_final: 0.7545 (mt0) REVERT: G 31 ARG cc_start: 0.7602 (OUTLIER) cc_final: 0.6786 (mtm180) REVERT: G 36 ARG cc_start: 0.6881 (ptm160) cc_final: 0.6303 (ptm160) REVERT: G 205 GLN cc_start: 0.7569 (mt0) cc_final: 0.7332 (mt0) REVERT: H 1 MET cc_start: 0.8270 (mtt) cc_final: 0.8052 (mtt) REVERT: H 31 ARG cc_start: 0.7649 (OUTLIER) cc_final: 0.6896 (mtm180) REVERT: H 71 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.7678 (tp30) REVERT: H 191 ASP cc_start: 0.6994 (m-30) cc_final: 0.6641 (m-30) outliers start: 61 outliers final: 27 residues processed: 371 average time/residue: 1.6040 time to fit residues: 669.3374 Evaluate side-chains 365 residues out of total 2640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 328 time to evaluate : 2.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ARG Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain B residue 143 GLN Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain B residue 171 ARG Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 229 GLN Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 370 GLN Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 391 ASN Chi-restraints excluded: chain D residue 130 GLN Chi-restraints excluded: chain D residue 296 PHE Chi-restraints excluded: chain D residue 442 GLU Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 85 MET Chi-restraints excluded: chain E residue 296 PHE Chi-restraints excluded: chain E residue 333 GLN Chi-restraints excluded: chain E residue 407 LYS Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 275 ILE Chi-restraints excluded: chain F residue 293 ASP Chi-restraints excluded: chain F residue 324 MET Chi-restraints excluded: chain F residue 369 GLU Chi-restraints excluded: chain F residue 380 MET Chi-restraints excluded: chain F residue 411 ASP Chi-restraints excluded: chain G residue 31 ARG Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain G residue 193 HIS Chi-restraints excluded: chain H residue 31 ARG Chi-restraints excluded: chain H residue 43 MET Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 193 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 96 optimal weight: 2.9990 chunk 259 optimal weight: 10.0000 chunk 56 optimal weight: 0.3980 chunk 169 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 288 optimal weight: 5.9990 chunk 239 optimal weight: 4.9990 chunk 133 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 151 optimal weight: 0.6980 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 HIS C 174 ASN C 413 GLN D 373 ASN D 430 GLN E 430 GLN F 174 ASN F 373 ASN G 236 GLN H 236 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 24983 Z= 0.275 Angle : 0.552 7.509 33823 Z= 0.299 Chirality : 0.042 0.179 3706 Planarity : 0.005 0.057 4369 Dihedral : 6.854 76.160 3402 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.82 % Allowed : 12.88 % Favored : 85.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.28 (0.15), residues: 2979 helix: 1.29 (0.15), residues: 1165 sheet: -0.32 (0.21), residues: 559 loop : -0.55 (0.17), residues: 1255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP F 199 HIS 0.008 0.001 HIS B 352 PHE 0.020 0.002 PHE E 296 TYR 0.015 0.002 TYR B 193 ARG 0.006 0.000 ARG C 208 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 2640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 328 time to evaluate : 2.766 Fit side-chains REVERT: A 32 ASN cc_start: 0.9302 (OUTLIER) cc_final: 0.9091 (m110) REVERT: A 248 GLN cc_start: 0.8501 (tm-30) cc_final: 0.8177 (tm-30) REVERT: A 372 GLU cc_start: 0.7523 (pm20) cc_final: 0.7259 (pm20) REVERT: B 85 MET cc_start: 0.8739 (ttm) cc_final: 0.8282 (ttm) REVERT: B 134 ARG cc_start: 0.8046 (mtp180) cc_final: 0.7819 (mtp180) REVERT: B 248 GLN cc_start: 0.8392 (tm-30) cc_final: 0.8077 (tm-30) REVERT: C 18 ASP cc_start: 0.7491 (p0) cc_final: 0.7211 (p0) REVERT: C 110 ARG cc_start: 0.7077 (ttm-80) cc_final: 0.6825 (ttt-90) REVERT: C 126 ARG cc_start: 0.6917 (mmp80) cc_final: 0.6010 (mtm180) REVERT: C 195 GLN cc_start: 0.7536 (OUTLIER) cc_final: 0.7226 (mt0) REVERT: C 210 HIS cc_start: 0.7263 (m-70) cc_final: 0.6401 (t70) REVERT: C 293 ASP cc_start: 0.8201 (OUTLIER) cc_final: 0.7768 (m-30) REVERT: C 324 MET cc_start: 0.8085 (ttm) cc_final: 0.7860 (ttp) REVERT: C 396 SER cc_start: 0.7846 (t) cc_final: 0.7542 (m) REVERT: C 407 LYS cc_start: 0.7989 (mttt) cc_final: 0.7531 (ttmt) REVERT: D 126 ARG cc_start: 0.7332 (mmp80) cc_final: 0.6752 (mtm-85) REVERT: D 130 GLN cc_start: 0.7194 (OUTLIER) cc_final: 0.6374 (mm110) REVERT: D 296 PHE cc_start: 0.8111 (OUTLIER) cc_final: 0.7492 (p90) REVERT: D 333 GLN cc_start: 0.7980 (OUTLIER) cc_final: 0.7276 (mt0) REVERT: D 372 GLU cc_start: 0.7248 (pm20) cc_final: 0.6974 (pm20) REVERT: D 443 LYS cc_start: 0.7916 (mttt) cc_final: 0.7538 (mtpm) REVERT: D 451 GLN cc_start: 0.7079 (mm110) cc_final: 0.6673 (mm-40) REVERT: E 126 ARG cc_start: 0.7280 (mmp80) cc_final: 0.6673 (mtm-85) REVERT: E 130 GLN cc_start: 0.7167 (pt0) cc_final: 0.6671 (tp40) REVERT: E 314 GLN cc_start: 0.8601 (mt0) cc_final: 0.8364 (mt0) REVERT: E 371 ASP cc_start: 0.8019 (p0) cc_final: 0.7807 (p0) REVERT: E 372 GLU cc_start: 0.7251 (pm20) cc_final: 0.7002 (pm20) REVERT: E 443 LYS cc_start: 0.7867 (mttt) cc_final: 0.7507 (mtpm) REVERT: E 451 GLN cc_start: 0.6856 (mm110) cc_final: 0.6391 (mm-40) REVERT: F 84 GLU cc_start: 0.7211 (tt0) cc_final: 0.6984 (tt0) REVERT: F 110 ARG cc_start: 0.7184 (ttm-80) cc_final: 0.6735 (ttt-90) REVERT: F 126 ARG cc_start: 0.6729 (mmp80) cc_final: 0.5902 (mtt180) REVERT: F 195 GLN cc_start: 0.7481 (OUTLIER) cc_final: 0.7189 (mt0) REVERT: F 210 HIS cc_start: 0.7425 (m-70) cc_final: 0.6633 (t70) REVERT: F 262 ASN cc_start: 0.7602 (m110) cc_final: 0.7345 (m110) REVERT: F 267 MET cc_start: 0.8742 (mtt) cc_final: 0.8231 (mtp) REVERT: F 293 ASP cc_start: 0.8146 (OUTLIER) cc_final: 0.7695 (m-30) REVERT: F 369 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.7896 (pm20) REVERT: F 396 SER cc_start: 0.7748 (t) cc_final: 0.7463 (m) REVERT: F 443 LYS cc_start: 0.7985 (pttt) cc_final: 0.7705 (ptpp) REVERT: G 27 GLN cc_start: 0.7858 (mt0) cc_final: 0.7548 (mt0) REVERT: G 36 ARG cc_start: 0.6816 (ptm160) cc_final: 0.6264 (ptm160) REVERT: G 205 GLN cc_start: 0.7619 (mt0) cc_final: 0.7385 (mt0) REVERT: H 1 MET cc_start: 0.8278 (mtt) cc_final: 0.8045 (mtt) REVERT: H 71 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.7697 (tp30) REVERT: H 191 ASP cc_start: 0.6976 (m-30) cc_final: 0.6576 (m-30) outliers start: 48 outliers final: 26 residues processed: 357 average time/residue: 1.6579 time to fit residues: 663.3104 Evaluate side-chains 363 residues out of total 2640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 327 time to evaluate : 2.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ASN Chi-restraints excluded: chain A residue 85 MET Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 229 GLN Chi-restraints excluded: chain B residue 116 HIS Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain B residue 171 ARG Chi-restraints excluded: chain B residue 229 GLN Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 370 GLN Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 195 GLN Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 293 ASP Chi-restraints excluded: chain C residue 391 ASN Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 130 GLN Chi-restraints excluded: chain D residue 296 PHE Chi-restraints excluded: chain D residue 333 GLN Chi-restraints excluded: chain E residue 9 LEU Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 85 MET Chi-restraints excluded: chain E residue 144 VAL Chi-restraints excluded: chain E residue 296 PHE Chi-restraints excluded: chain E residue 407 LYS Chi-restraints excluded: chain F residue 174 ASN Chi-restraints excluded: chain F residue 195 GLN Chi-restraints excluded: chain F residue 275 ILE Chi-restraints excluded: chain F residue 293 ASP Chi-restraints excluded: chain F residue 324 MET Chi-restraints excluded: chain F residue 369 GLU Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain G residue 193 HIS Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 193 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 277 optimal weight: 0.0000 chunk 32 optimal weight: 1.9990 chunk 164 optimal weight: 1.9990 chunk 210 optimal weight: 0.9990 chunk 163 optimal weight: 3.9990 chunk 242 optimal weight: 1.9990 chunk 161 optimal weight: 0.0670 chunk 287 optimal weight: 0.0570 chunk 179 optimal weight: 0.9990 chunk 175 optimal weight: 3.9990 chunk 132 optimal weight: 5.9990 overall best weight: 0.4244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 373 ASN G 50 GLN G 236 GLN H 236 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 24983 Z= 0.135 Angle : 0.451 7.309 33823 Z= 0.248 Chirality : 0.039 0.143 3706 Planarity : 0.004 0.052 4369 Dihedral : 6.480 70.113 3402 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.52 % Allowed : 13.75 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.67 (0.15), residues: 2979 helix: 1.63 (0.15), residues: 1170 sheet: -0.10 (0.21), residues: 572 loop : -0.34 (0.18), residues: 1237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 199 HIS 0.006 0.001 HIS B 116 PHE 0.020 0.001 PHE D 296 TYR 0.011 0.001 TYR A 200 ARG 0.004 0.000 ARG D 208 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 2640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 343 time to evaluate : 2.936 Fit side-chains REVERT: A 120 MET cc_start: 0.8174 (mmt) cc_final: 0.7800 (mmt) REVERT: A 236 GLN cc_start: 0.8709 (OUTLIER) cc_final: 0.8468 (tm-30) REVERT: A 372 GLU cc_start: 0.7510 (pm20) cc_final: 0.7273 (pm20) REVERT: B 85 MET cc_start: 0.8774 (ttm) cc_final: 0.8251 (ttm) REVERT: B 248 GLN cc_start: 0.8315 (tm-30) cc_final: 0.7997 (tm-30) REVERT: C 1 MET cc_start: 0.8218 (OUTLIER) cc_final: 0.7934 (ttt) REVERT: C 18 ASP cc_start: 0.7413 (p0) cc_final: 0.7143 (p0) REVERT: C 110 ARG cc_start: 0.7001 (ttm-80) cc_final: 0.6720 (ttt-90) REVERT: C 126 ARG cc_start: 0.6909 (mmp80) cc_final: 0.6066 (mtm110) REVERT: C 210 HIS cc_start: 0.7037 (m-70) cc_final: 0.6288 (t70) REVERT: C 293 ASP cc_start: 0.8174 (OUTLIER) cc_final: 0.7760 (m-30) REVERT: C 324 MET cc_start: 0.8098 (ttm) cc_final: 0.7859 (ttp) REVERT: C 396 SER cc_start: 0.7757 (t) cc_final: 0.7471 (m) REVERT: C 407 LYS cc_start: 0.7919 (mttt) cc_final: 0.7482 (ttmt) REVERT: D 126 ARG cc_start: 0.7380 (mmp80) cc_final: 0.6851 (mtm-85) REVERT: D 130 GLN cc_start: 0.7099 (OUTLIER) cc_final: 0.6300 (mm110) REVERT: D 227 ARG cc_start: 0.6538 (OUTLIER) cc_final: 0.6262 (tpt170) REVERT: D 296 PHE cc_start: 0.8027 (OUTLIER) cc_final: 0.7413 (p90) REVERT: D 372 GLU cc_start: 0.7376 (pm20) cc_final: 0.7019 (pm20) REVERT: D 443 LYS cc_start: 0.7914 (mttt) cc_final: 0.7514 (mtpm) REVERT: D 451 GLN cc_start: 0.7028 (mm110) cc_final: 0.6631 (mm-40) REVERT: E 126 ARG cc_start: 0.7266 (mmp80) cc_final: 0.6628 (mtm-85) REVERT: E 130 GLN cc_start: 0.7073 (pt0) cc_final: 0.6614 (tp40) REVERT: E 371 ASP cc_start: 0.7801 (p0) cc_final: 0.7565 (p0) REVERT: E 372 GLU cc_start: 0.7285 (pm20) cc_final: 0.6973 (pm20) REVERT: E 443 LYS cc_start: 0.7859 (mttt) cc_final: 0.7495 (mtpm) REVERT: E 451 GLN cc_start: 0.6805 (mm110) cc_final: 0.6315 (mm-40) REVERT: F 110 ARG cc_start: 0.7070 (ttm-80) cc_final: 0.6625 (ttt-90) REVERT: F 126 ARG cc_start: 0.6709 (mmp80) cc_final: 0.5888 (mtt180) REVERT: F 210 HIS cc_start: 0.7362 (m-70) cc_final: 0.6667 (t70) REVERT: F 293 ASP cc_start: 0.8082 (OUTLIER) cc_final: 0.7623 (m-30) REVERT: F 369 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7922 (pm20) REVERT: F 396 SER cc_start: 0.7738 (t) cc_final: 0.7448 (m) REVERT: F 443 LYS cc_start: 0.7977 (pttt) cc_final: 0.7701 (ptpp) REVERT: G 27 GLN cc_start: 0.7776 (mt0) cc_final: 0.7481 (mt0) REVERT: G 36 ARG cc_start: 0.6783 (ptm160) cc_final: 0.6236 (ptm160) REVERT: G 205 GLN cc_start: 0.7490 (mt0) cc_final: 0.7275 (mt0) REVERT: H 1 MET cc_start: 0.8275 (mtt) cc_final: 0.8041 (mtt) REVERT: H 71 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7642 (tp30) REVERT: H 191 ASP cc_start: 0.6815 (m-30) cc_final: 0.6415 (m-30) REVERT: H 224 ARG cc_start: 0.7223 (ttp80) cc_final: 0.6819 (ttt180) outliers start: 40 outliers final: 17 residues processed: 367 average time/residue: 1.6336 time to fit residues: 673.7515 Evaluate side-chains 360 residues out of total 2640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 334 time to evaluate : 2.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 GLN Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain B residue 171 ARG Chi-restraints excluded: chain B residue 229 GLN Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 370 GLN Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 293 ASP Chi-restraints excluded: chain C residue 391 ASN Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 85 MET Chi-restraints excluded: chain D residue 130 GLN Chi-restraints excluded: chain D residue 227 ARG Chi-restraints excluded: chain D residue 296 PHE Chi-restraints excluded: chain D residue 442 GLU Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 144 VAL Chi-restraints excluded: chain F residue 293 ASP Chi-restraints excluded: chain F residue 369 GLU Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain G residue 193 HIS Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 193 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 177 optimal weight: 6.9990 chunk 114 optimal weight: 9.9990 chunk 171 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 55 optimal weight: 0.0970 chunk 182 optimal weight: 1.9990 chunk 195 optimal weight: 2.9990 chunk 142 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 chunk 225 optimal weight: 7.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 GLN C 174 ASN C 413 GLN G 236 GLN H 202 GLN H 236 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 24983 Z= 0.250 Angle : 0.534 8.349 33823 Z= 0.288 Chirality : 0.042 0.178 3706 Planarity : 0.005 0.057 4369 Dihedral : 6.708 76.338 3402 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 1.74 % Allowed : 14.39 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.15), residues: 2979 helix: 1.52 (0.15), residues: 1165 sheet: -0.21 (0.21), residues: 569 loop : -0.47 (0.17), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 199 HIS 0.008 0.001 HIS A 352 PHE 0.021 0.002 PHE A 296 TYR 0.013 0.001 TYR B 193 ARG 0.006 0.000 ARG C 208 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 2640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 339 time to evaluate : 2.825 Fit side-chains REVERT: A 32 ASN cc_start: 0.9309 (OUTLIER) cc_final: 0.9075 (m110) REVERT: A 203 LEU cc_start: 0.3203 (OUTLIER) cc_final: 0.2685 (mt) REVERT: A 372 GLU cc_start: 0.7504 (pm20) cc_final: 0.7254 (pm20) REVERT: B 32 ASN cc_start: 0.9351 (OUTLIER) cc_final: 0.9061 (m110) REVERT: B 85 MET cc_start: 0.8811 (ttm) cc_final: 0.8355 (ttm) REVERT: B 248 GLN cc_start: 0.8364 (tm-30) cc_final: 0.8037 (tm-30) REVERT: C 1 MET cc_start: 0.8254 (OUTLIER) cc_final: 0.7956 (ttt) REVERT: C 110 ARG cc_start: 0.7111 (ttm-80) cc_final: 0.6839 (ttt-90) REVERT: C 126 ARG cc_start: 0.6944 (mmp80) cc_final: 0.6045 (mtm180) REVERT: C 210 HIS cc_start: 0.7187 (m-70) cc_final: 0.6371 (t70) REVERT: C 293 ASP cc_start: 0.8190 (OUTLIER) cc_final: 0.7760 (m-30) REVERT: C 324 MET cc_start: 0.8126 (ttm) cc_final: 0.7894 (ttp) REVERT: C 396 SER cc_start: 0.7765 (t) cc_final: 0.7473 (m) REVERT: C 407 LYS cc_start: 0.7964 (mttt) cc_final: 0.7348 (mmtm) REVERT: D 126 ARG cc_start: 0.7432 (mmp80) cc_final: 0.6900 (mtm-85) REVERT: D 130 GLN cc_start: 0.7210 (OUTLIER) cc_final: 0.6392 (mm110) REVERT: D 227 ARG cc_start: 0.6594 (OUTLIER) cc_final: 0.6318 (tpt170) REVERT: D 296 PHE cc_start: 0.8100 (OUTLIER) cc_final: 0.7488 (p90) REVERT: D 372 GLU cc_start: 0.7303 (pm20) cc_final: 0.7034 (pm20) REVERT: D 443 LYS cc_start: 0.7939 (mttt) cc_final: 0.7535 (mtpm) REVERT: D 451 GLN cc_start: 0.7061 (mm110) cc_final: 0.6655 (mm-40) REVERT: E 126 ARG cc_start: 0.7281 (mmp80) cc_final: 0.6648 (mtm-85) REVERT: E 333 GLN cc_start: 0.8010 (OUTLIER) cc_final: 0.7337 (mt0) REVERT: E 371 ASP cc_start: 0.7882 (p0) cc_final: 0.7626 (p0) REVERT: E 372 GLU cc_start: 0.7279 (pm20) cc_final: 0.6969 (pm20) REVERT: E 443 LYS cc_start: 0.7861 (mttt) cc_final: 0.7497 (mtpm) REVERT: E 451 GLN cc_start: 0.6846 (mm110) cc_final: 0.6358 (mm-40) REVERT: F 110 ARG cc_start: 0.7158 (ttm-80) cc_final: 0.6702 (ttt-90) REVERT: F 126 ARG cc_start: 0.6752 (mmp80) cc_final: 0.5919 (mtt180) REVERT: F 210 HIS cc_start: 0.7424 (m-70) cc_final: 0.6701 (t70) REVERT: F 267 MET cc_start: 0.8688 (mtt) cc_final: 0.8265 (mtp) REVERT: F 293 ASP cc_start: 0.8119 (OUTLIER) cc_final: 0.7670 (m-30) REVERT: F 369 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.7917 (pm20) REVERT: F 396 SER cc_start: 0.7736 (t) cc_final: 0.7447 (m) REVERT: F 443 LYS cc_start: 0.8006 (pttt) cc_final: 0.7726 (ptpp) REVERT: G 27 GLN cc_start: 0.7777 (mt0) cc_final: 0.7468 (mt0) REVERT: G 36 ARG cc_start: 0.6839 (ptm160) cc_final: 0.6294 (ptm160) REVERT: G 200 LEU cc_start: 0.8289 (tp) cc_final: 0.8089 (mt) REVERT: G 205 GLN cc_start: 0.7575 (mt0) cc_final: 0.7357 (mt0) REVERT: H 1 MET cc_start: 0.8280 (mtt) cc_final: 0.8038 (mtt) REVERT: H 27 GLN cc_start: 0.7904 (mt0) cc_final: 0.7579 (mt0) REVERT: H 31 ARG cc_start: 0.7651 (OUTLIER) cc_final: 0.6887 (mtm180) REVERT: H 71 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.7663 (tp30) REVERT: H 191 ASP cc_start: 0.6842 (m-30) cc_final: 0.6440 (m-30) REVERT: H 224 ARG cc_start: 0.7210 (ttp80) cc_final: 0.6806 (ttt180) outliers start: 46 outliers final: 26 residues processed: 366 average time/residue: 1.6525 time to fit residues: 678.9357 Evaluate side-chains 368 residues out of total 2640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 329 time to evaluate : 3.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ASN Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 229 GLN Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain B residue 32 ASN Chi-restraints excluded: chain B residue 116 HIS Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain B residue 171 ARG Chi-restraints excluded: chain B residue 229 GLN Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 370 GLN Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 293 ASP Chi-restraints excluded: chain C residue 391 ASN Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 130 GLN Chi-restraints excluded: chain D residue 227 ARG Chi-restraints excluded: chain D residue 296 PHE Chi-restraints excluded: chain D residue 442 GLU Chi-restraints excluded: chain E residue 9 LEU Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 85 MET Chi-restraints excluded: chain E residue 144 VAL Chi-restraints excluded: chain E residue 333 GLN Chi-restraints excluded: chain F residue 18 ASP Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 275 ILE Chi-restraints excluded: chain F residue 293 ASP Chi-restraints excluded: chain F residue 324 MET Chi-restraints excluded: chain F residue 369 GLU Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain G residue 193 HIS Chi-restraints excluded: chain H residue 31 ARG Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 193 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 261 optimal weight: 10.0000 chunk 275 optimal weight: 7.9990 chunk 251 optimal weight: 1.9990 chunk 267 optimal weight: 0.9990 chunk 161 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 chunk 210 optimal weight: 0.6980 chunk 82 optimal weight: 5.9990 chunk 241 optimal weight: 1.9990 chunk 253 optimal weight: 9.9990 chunk 266 optimal weight: 3.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 GLN ** C 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 413 GLN F 373 ASN G 236 GLN H 202 GLN H 236 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 24983 Z= 0.294 Angle : 0.575 9.443 33823 Z= 0.309 Chirality : 0.043 0.196 3706 Planarity : 0.005 0.060 4369 Dihedral : 6.877 77.347 3402 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.89 % Allowed : 14.55 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.34 (0.15), residues: 2979 helix: 1.35 (0.15), residues: 1165 sheet: -0.29 (0.21), residues: 559 loop : -0.51 (0.17), residues: 1255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 199 HIS 0.008 0.001 HIS B 352 PHE 0.026 0.002 PHE E 296 TYR 0.016 0.002 TYR B 193 ARG 0.007 0.000 ARG C 208 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 2640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 334 time to evaluate : 2.945 Fit side-chains REVERT: A 203 LEU cc_start: 0.3210 (OUTLIER) cc_final: 0.2592 (mt) REVERT: A 372 GLU cc_start: 0.7492 (pm20) cc_final: 0.7259 (pm20) REVERT: B 32 ASN cc_start: 0.9367 (OUTLIER) cc_final: 0.9090 (m110) REVERT: B 85 MET cc_start: 0.8735 (ttm) cc_final: 0.8288 (ttm) REVERT: B 248 GLN cc_start: 0.8396 (tm-30) cc_final: 0.8071 (tm-30) REVERT: C 1 MET cc_start: 0.8325 (OUTLIER) cc_final: 0.7831 (ttt) REVERT: C 110 ARG cc_start: 0.7137 (ttm-80) cc_final: 0.6884 (ttt-90) REVERT: C 126 ARG cc_start: 0.6913 (mmp80) cc_final: 0.5990 (mtm180) REVERT: C 210 HIS cc_start: 0.7244 (m-70) cc_final: 0.6390 (t70) REVERT: C 293 ASP cc_start: 0.8208 (OUTLIER) cc_final: 0.7779 (m-30) REVERT: C 324 MET cc_start: 0.8124 (ttm) cc_final: 0.7891 (ttp) REVERT: C 396 SER cc_start: 0.7770 (t) cc_final: 0.7486 (m) REVERT: C 407 LYS cc_start: 0.7989 (mttt) cc_final: 0.7360 (mmtm) REVERT: C 456 ARG cc_start: 0.7260 (ttm170) cc_final: 0.6784 (mtt180) REVERT: D 126 ARG cc_start: 0.7430 (mmp80) cc_final: 0.6914 (mtm-85) REVERT: D 130 GLN cc_start: 0.7218 (OUTLIER) cc_final: 0.6420 (mm110) REVERT: D 227 ARG cc_start: 0.6662 (OUTLIER) cc_final: 0.6374 (tpt170) REVERT: D 296 PHE cc_start: 0.8100 (OUTLIER) cc_final: 0.7475 (p90) REVERT: D 333 GLN cc_start: 0.7982 (OUTLIER) cc_final: 0.7263 (mt0) REVERT: D 443 LYS cc_start: 0.7900 (mttt) cc_final: 0.7509 (mtpm) REVERT: D 451 GLN cc_start: 0.6901 (mm110) cc_final: 0.6494 (mm-40) REVERT: E 74 LEU cc_start: 0.8827 (mt) cc_final: 0.8619 (tp) REVERT: E 126 ARG cc_start: 0.7274 (mmp80) cc_final: 0.6677 (mtm-85) REVERT: E 130 GLN cc_start: 0.7188 (pt0) cc_final: 0.6647 (tp40) REVERT: E 333 GLN cc_start: 0.8074 (OUTLIER) cc_final: 0.7418 (mt0) REVERT: E 371 ASP cc_start: 0.7891 (p0) cc_final: 0.7652 (p0) REVERT: E 372 GLU cc_start: 0.7292 (pm20) cc_final: 0.6970 (pm20) REVERT: E 443 LYS cc_start: 0.7858 (mttt) cc_final: 0.7493 (mtpm) REVERT: E 451 GLN cc_start: 0.6870 (mm110) cc_final: 0.6374 (mm-40) REVERT: F 110 ARG cc_start: 0.7185 (ttm-80) cc_final: 0.6732 (ttt-90) REVERT: F 126 ARG cc_start: 0.6732 (mmp80) cc_final: 0.5926 (mtt180) REVERT: F 210 HIS cc_start: 0.7408 (m-70) cc_final: 0.6620 (t70) REVERT: F 267 MET cc_start: 0.8685 (mtt) cc_final: 0.8215 (mtp) REVERT: F 293 ASP cc_start: 0.8155 (OUTLIER) cc_final: 0.7690 (m-30) REVERT: F 369 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7918 (pm20) REVERT: F 396 SER cc_start: 0.7777 (t) cc_final: 0.7486 (m) REVERT: F 411 ASP cc_start: 0.8258 (OUTLIER) cc_final: 0.7457 (t0) REVERT: G 27 GLN cc_start: 0.7801 (mt0) cc_final: 0.7466 (mt0) REVERT: G 36 ARG cc_start: 0.6855 (ptm160) cc_final: 0.6324 (ptm160) REVERT: H 1 MET cc_start: 0.8261 (mtt) cc_final: 0.8043 (mtt) REVERT: H 27 GLN cc_start: 0.7902 (mt0) cc_final: 0.7561 (mt0) REVERT: H 71 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7660 (tp30) REVERT: H 191 ASP cc_start: 0.6959 (m-30) cc_final: 0.6538 (m-30) REVERT: H 224 ARG cc_start: 0.7234 (ttp80) cc_final: 0.6830 (ttt180) outliers start: 50 outliers final: 27 residues processed: 365 average time/residue: 1.7015 time to fit residues: 697.7608 Evaluate side-chains 366 residues out of total 2640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 326 time to evaluate : 2.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 MET Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 229 GLN Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain B residue 32 ASN Chi-restraints excluded: chain B residue 116 HIS Chi-restraints excluded: chain B residue 143 GLN Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain B residue 171 ARG Chi-restraints excluded: chain B residue 229 GLN Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 370 GLN Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 293 ASP Chi-restraints excluded: chain C residue 391 ASN Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 130 GLN Chi-restraints excluded: chain D residue 227 ARG Chi-restraints excluded: chain D residue 296 PHE Chi-restraints excluded: chain D residue 333 GLN Chi-restraints excluded: chain D residue 442 GLU Chi-restraints excluded: chain E residue 9 LEU Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 85 MET Chi-restraints excluded: chain E residue 144 VAL Chi-restraints excluded: chain E residue 333 GLN Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 173 ASP Chi-restraints excluded: chain F residue 293 ASP Chi-restraints excluded: chain F residue 324 MET Chi-restraints excluded: chain F residue 369 GLU Chi-restraints excluded: chain F residue 411 ASP Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain G residue 193 HIS Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 193 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 175 optimal weight: 2.9990 chunk 283 optimal weight: 8.9990 chunk 172 optimal weight: 0.8980 chunk 134 optimal weight: 0.6980 chunk 196 optimal weight: 2.9990 chunk 296 optimal weight: 5.9990 chunk 273 optimal weight: 3.9990 chunk 236 optimal weight: 0.6980 chunk 24 optimal weight: 0.3980 chunk 182 optimal weight: 1.9990 chunk 144 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 ASN A 229 GLN B 240 GLN C 413 GLN F 373 ASN G 236 GLN G 238 HIS H 202 GLN H 236 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 24983 Z= 0.160 Angle : 0.482 9.957 33823 Z= 0.263 Chirality : 0.040 0.147 3706 Planarity : 0.004 0.056 4369 Dihedral : 6.648 72.857 3402 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.36 % Allowed : 15.15 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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 (0.15), residues: 2979 helix: 1.59 (0.15), residues: 1165 sheet: -0.14 (0.21), residues: 564 loop : -0.39 (0.17), residues: 1250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP F 199 HIS 0.006 0.001 HIS B 352 PHE 0.020 0.001 PHE D 296 TYR 0.009 0.001 TYR B 193 ARG 0.006 0.000 ARG C 456 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 2640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 333 time to evaluate : 3.174 Fit side-chains REVERT: A 203 LEU cc_start: 0.3110 (OUTLIER) cc_final: 0.2615 (mt) REVERT: A 236 GLN cc_start: 0.8711 (OUTLIER) cc_final: 0.8477 (tm-30) REVERT: A 372 GLU cc_start: 0.7498 (pm20) cc_final: 0.7249 (pm20) REVERT: B 32 ASN cc_start: 0.9357 (OUTLIER) cc_final: 0.9055 (m110) REVERT: B 85 MET cc_start: 0.8754 (ttm) cc_final: 0.8255 (ttm) REVERT: B 248 GLN cc_start: 0.8337 (tm-30) cc_final: 0.8013 (tm-30) REVERT: C 1 MET cc_start: 0.8198 (OUTLIER) cc_final: 0.7951 (ttt) REVERT: C 110 ARG cc_start: 0.7011 (ttm-80) cc_final: 0.6747 (ttt-90) REVERT: C 126 ARG cc_start: 0.6932 (mmp80) cc_final: 0.6036 (mtm180) REVERT: C 210 HIS cc_start: 0.7129 (m-70) cc_final: 0.6323 (t70) REVERT: C 293 ASP cc_start: 0.8191 (OUTLIER) cc_final: 0.7761 (m-30) REVERT: C 324 MET cc_start: 0.8122 (ttm) cc_final: 0.7921 (ttp) REVERT: C 396 SER cc_start: 0.7751 (t) cc_final: 0.7468 (m) REVERT: C 407 LYS cc_start: 0.7941 (mttt) cc_final: 0.7336 (mmtm) REVERT: D 126 ARG cc_start: 0.7377 (mmp80) cc_final: 0.6862 (mtm-85) REVERT: D 130 GLN cc_start: 0.7125 (OUTLIER) cc_final: 0.6324 (mm110) REVERT: D 227 ARG cc_start: 0.6566 (OUTLIER) cc_final: 0.6288 (tpt170) REVERT: D 296 PHE cc_start: 0.8056 (OUTLIER) cc_final: 0.7390 (p90) REVERT: D 372 GLU cc_start: 0.7074 (pm20) cc_final: 0.6851 (pm20) REVERT: D 443 LYS cc_start: 0.7903 (mttt) cc_final: 0.7495 (mtpm) REVERT: D 451 GLN cc_start: 0.7018 (mm110) cc_final: 0.6622 (mm-40) REVERT: E 74 LEU cc_start: 0.8776 (mt) cc_final: 0.8547 (tp) REVERT: E 126 ARG cc_start: 0.7259 (mmp80) cc_final: 0.6640 (mtm-85) REVERT: E 130 GLN cc_start: 0.7090 (pt0) cc_final: 0.6620 (tp40) REVERT: E 333 GLN cc_start: 0.7999 (OUTLIER) cc_final: 0.7332 (mt0) REVERT: E 371 ASP cc_start: 0.7804 (p0) cc_final: 0.7602 (p0) REVERT: E 372 GLU cc_start: 0.7331 (pm20) cc_final: 0.7023 (pm20) REVERT: E 443 LYS cc_start: 0.7851 (mttt) cc_final: 0.7485 (mtpm) REVERT: E 451 GLN cc_start: 0.6823 (mm110) cc_final: 0.6342 (mm-40) REVERT: F 110 ARG cc_start: 0.7128 (ttm-80) cc_final: 0.6675 (ttt-90) REVERT: F 126 ARG cc_start: 0.6696 (mmp80) cc_final: 0.5893 (mtt180) REVERT: F 210 HIS cc_start: 0.7394 (m-70) cc_final: 0.6683 (t70) REVERT: F 267 MET cc_start: 0.8681 (mtt) cc_final: 0.8266 (mtp) REVERT: F 293 ASP cc_start: 0.8099 (OUTLIER) cc_final: 0.7644 (m-30) REVERT: F 369 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.7929 (pm20) REVERT: F 396 SER cc_start: 0.7760 (t) cc_final: 0.7477 (m) REVERT: G 27 GLN cc_start: 0.7783 (mt0) cc_final: 0.7455 (mt0) REVERT: G 36 ARG cc_start: 0.6817 (ptm160) cc_final: 0.6291 (ptm160) REVERT: H 1 MET cc_start: 0.8239 (mtt) cc_final: 0.8028 (mtt) REVERT: H 27 GLN cc_start: 0.7888 (mt0) cc_final: 0.7485 (mt0) REVERT: H 71 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7652 (tp30) REVERT: H 224 ARG cc_start: 0.7197 (ttp80) cc_final: 0.6806 (ttt180) outliers start: 36 outliers final: 17 residues processed: 352 average time/residue: 1.6806 time to fit residues: 662.8608 Evaluate side-chains 359 residues out of total 2640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 330 time to evaluate : 3.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain B residue 32 ASN Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain B residue 229 GLN Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 370 GLN Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 293 ASP Chi-restraints excluded: chain C residue 391 ASN Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 130 GLN Chi-restraints excluded: chain D residue 227 ARG Chi-restraints excluded: chain D residue 296 PHE Chi-restraints excluded: chain D residue 442 GLU Chi-restraints excluded: chain E residue 9 LEU Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 85 MET Chi-restraints excluded: chain E residue 144 VAL Chi-restraints excluded: chain E residue 333 GLN Chi-restraints excluded: chain F residue 293 ASP Chi-restraints excluded: chain F residue 369 GLU Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain G residue 193 HIS Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 193 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 187 optimal weight: 0.8980 chunk 251 optimal weight: 5.9990 chunk 72 optimal weight: 0.9980 chunk 217 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 chunk 65 optimal weight: 0.5980 chunk 236 optimal weight: 0.8980 chunk 99 optimal weight: 0.0980 chunk 243 optimal weight: 5.9990 chunk 29 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 GLN A 240 GLN B 240 GLN C 214 GLN F 373 ASN H 202 GLN H 236 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.185306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.125784 restraints weight = 24660.380| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 2.11 r_work: 0.3323 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 24983 Z= 0.153 Angle : 0.470 10.742 33823 Z= 0.256 Chirality : 0.039 0.148 3706 Planarity : 0.004 0.055 4369 Dihedral : 6.490 71.048 3402 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.25 % Allowed : 15.45 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.73 (0.15), residues: 2979 helix: 1.72 (0.15), residues: 1167 sheet: -0.07 (0.21), residues: 568 loop : -0.36 (0.17), residues: 1244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP F 199 HIS 0.006 0.001 HIS A 352 PHE 0.020 0.001 PHE D 296 TYR 0.009 0.001 TYR A 200 ARG 0.006 0.000 ARG E 227 =============================================================================== Job complete usr+sys time: 10693.94 seconds wall clock time: 188 minutes 10.45 seconds (11290.45 seconds total)