Starting phenix.real_space_refine on Mon Sep 30 08:12:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v4o_21043/09_2024/6v4o_21043_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v4o_21043/09_2024/6v4o_21043.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v4o_21043/09_2024/6v4o_21043.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v4o_21043/09_2024/6v4o_21043.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v4o_21043/09_2024/6v4o_21043_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v4o_21043/09_2024/6v4o_21043_neut.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 Ca 4 9.91 5 S 152 5.16 5 C 15628 2.51 5 N 4220 2.21 5 O 4792 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 24796 Number of models: 1 Model: "" Number of chains: 5 Chain: "I" Number of atoms: 2830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 2830 Classifications: {'peptide': 364} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 345} Chain breaks: 3 Chain: "A" Number of atoms: 1695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1695 Classifications: {'peptide': 223} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 209} Chain breaks: 1 Chain: "B" Number of atoms: 1634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1634 Classifications: {'peptide': 214} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 201} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 12 Unusual residues: {' CA': 1, 'BMA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: E, G, L, K, J, O, M, N, W, C, D, H Time building chain proxies: 12.52, per 1000 atoms: 0.50 Number of scatterers: 24796 At special positions: 0 Unit cell: (174.9, 174.9, 123.2, 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) Ca 4 19.99 S 152 16.00 O 4792 8.00 N 4220 7.00 C 15628 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS I 87 " - pdb=" SG CYS I 420 " distance=2.03 Simple disulfide: pdb=" SG CYS I 122 " - pdb=" SG CYS I 127 " distance=2.03 Simple disulfide: pdb=" SG CYS I 182 " - pdb=" SG CYS I 229 " distance=2.03 Simple disulfide: pdb=" SG CYS I 231 " - pdb=" SG CYS I 236 " distance=2.03 Simple disulfide: pdb=" SG CYS I 277 " - pdb=" SG CYS I 291 " distance=2.02 Simple disulfide: pdb=" SG CYS I 279 " - pdb=" SG CYS I 289 " distance=2.02 Simple disulfide: pdb=" SG CYS I 318 " - pdb=" SG CYS I 337 " distance=2.03 Simple disulfide: pdb=" SG CYS I 424 " - pdb=" SG CYS I 447 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA I 503 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA M 503 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA N 503 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA W 503 " NAG-ASN " NAG F 1 " - " ASN I 284 " " NAG J 1 " - " ASN M 284 " " NAG K 1 " - " ASN N 284 " " NAG O 1 " - " ASN W 284 " Time building additional restraints: 6.37 Conformation dependent library (CDL) restraints added in 3.5 seconds 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5856 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 68 sheets defined 5.2% alpha, 40.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.58 Creating SS restraints... Processing helix chain 'I' and resid 99 through 104 removed outlier: 3.594A pdb=" N GLY I 104 " --> pdb=" O HIS I 101 " (cutoff:3.500A) Processing helix chain 'I' and resid 386 through 390 removed outlier: 4.208A pdb=" N ASP I 390 " --> pdb=" O PRO I 387 " (cutoff:3.500A) Processing helix chain 'M' and resid 99 through 104 removed outlier: 3.595A pdb=" N GLY M 104 " --> pdb=" O HIS M 101 " (cutoff:3.500A) Processing helix chain 'M' and resid 386 through 390 removed outlier: 4.209A pdb=" N ASP M 390 " --> pdb=" O PRO M 387 " (cutoff:3.500A) Processing helix chain 'N' and resid 99 through 104 removed outlier: 3.594A pdb=" N GLY N 104 " --> pdb=" O HIS N 101 " (cutoff:3.500A) Processing helix chain 'N' and resid 386 through 390 removed outlier: 4.208A pdb=" N ASP N 390 " --> pdb=" O PRO N 387 " (cutoff:3.500A) Processing helix chain 'W' and resid 99 through 104 removed outlier: 3.594A pdb=" N GLY W 104 " --> pdb=" O HIS W 101 " (cutoff:3.500A) Processing helix chain 'W' and resid 386 through 390 removed outlier: 4.208A pdb=" N ASP W 390 " --> pdb=" O PRO W 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 32 removed outlier: 3.726A pdb=" N HIS A 32 " --> pdb=" O PHE A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 189 removed outlier: 3.673A pdb=" N LEU A 189 " --> pdb=" O SER A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 204 Processing helix chain 'C' and resid 28 through 32 removed outlier: 3.725A pdb=" N HIS C 32 " --> pdb=" O PHE C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 189 removed outlier: 3.672A pdb=" N LEU C 189 " --> pdb=" O SER C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 204 Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.725A pdb=" N HIS D 32 " --> pdb=" O PHE D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 185 through 189 removed outlier: 3.672A pdb=" N LEU D 189 " --> pdb=" O SER D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 200 through 204 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.725A pdb=" N HIS H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 185 through 189 removed outlier: 3.674A pdb=" N LEU H 189 " --> pdb=" O SER H 186 " (cutoff:3.500A) Processing helix chain 'H' and resid 200 through 204 Processing helix chain 'B' and resid 79 through 83 removed outlier: 4.244A pdb=" N PHE B 83 " --> pdb=" O PRO B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 128 removed outlier: 3.883A pdb=" N GLY B 128 " --> pdb=" O GLN B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 186 No H-bonds generated for 'chain 'B' and resid 184 through 186' Processing helix chain 'E' and resid 79 through 83 removed outlier: 4.243A pdb=" N PHE E 83 " --> pdb=" O PRO E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 128 removed outlier: 3.883A pdb=" N GLY E 128 " --> pdb=" O GLN E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 184 through 186 No H-bonds generated for 'chain 'E' and resid 184 through 186' Processing helix chain 'G' and resid 79 through 83 removed outlier: 4.243A pdb=" N PHE G 83 " --> pdb=" O PRO G 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 121 through 128 removed outlier: 3.883A pdb=" N GLY G 128 " --> pdb=" O GLN G 124 " (cutoff:3.500A) Processing helix chain 'G' and resid 184 through 186 No H-bonds generated for 'chain 'G' and resid 184 through 186' Processing helix chain 'L' and resid 79 through 83 removed outlier: 4.244A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 121 through 128 removed outlier: 3.882A pdb=" N GLY L 128 " --> pdb=" O GLN L 124 " (cutoff:3.500A) Processing helix chain 'L' and resid 184 through 186 No H-bonds generated for 'chain 'L' and resid 184 through 186' Processing sheet with id=AA1, first strand: chain 'I' and resid 92 through 98 removed outlier: 5.551A pdb=" N LYS I 94 " --> pdb=" O CYS I 447 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N CYS I 447 " --> pdb=" O LYS I 94 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'I' and resid 119 through 122 removed outlier: 3.929A pdb=" N MET I 174 " --> pdb=" O LEU I 156 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'I' and resid 178 through 183 removed outlier: 3.825A pdb=" N SER I 178 " --> pdb=" O VAL I 193 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ASP I 212 " --> pdb=" O ILE I 204 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N TYR I 206 " --> pdb=" O TYR I 210 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N TYR I 210 " --> pdb=" O TYR I 206 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'I' and resid 222 through 224 removed outlier: 3.583A pdb=" N ASN I 230 " --> pdb=" O TYR I 237 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'I' and resid 222 through 224 removed outlier: 3.646A pdb=" N ASP I 242 " --> pdb=" O GLU I 250 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLU I 250 " --> pdb=" O ASP I 242 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LYS I 263 " --> pdb=" O LYS I 255 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ARG I 257 " --> pdb=" O ILE I 261 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N ILE I 261 " --> pdb=" O ARG I 257 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'I' and resid 268 through 269 removed outlier: 6.558A pdb=" N THR I 268 " --> pdb=" O ILE I 314 " (cutoff:3.500A) removed outlier: 8.880A pdb=" N LEU I 316 " --> pdb=" O THR I 268 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N THR I 286 " --> pdb=" O ALA I 282 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'I' and resid 352 through 356 removed outlier: 8.173A pdb=" N MET I 375 " --> pdb=" O VAL I 401 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N VAL I 401 " --> pdb=" O MET I 375 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N MET I 377 " --> pdb=" O VAL I 399 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N VAL I 399 " --> pdb=" O MET I 377 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N LEU I 379 " --> pdb=" O SER I 397 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'M' and resid 92 through 98 removed outlier: 5.552A pdb=" N LYS M 94 " --> pdb=" O CYS M 447 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N CYS M 447 " --> pdb=" O LYS M 94 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'M' and resid 119 through 122 removed outlier: 3.928A pdb=" N MET M 174 " --> pdb=" O LEU M 156 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'M' and resid 178 through 183 removed outlier: 3.825A pdb=" N SER M 178 " --> pdb=" O VAL M 193 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ASP M 212 " --> pdb=" O ILE M 204 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N TYR M 206 " --> pdb=" O TYR M 210 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N TYR M 210 " --> pdb=" O TYR M 206 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'M' and resid 222 through 224 removed outlier: 3.582A pdb=" N ASN M 230 " --> pdb=" O TYR M 237 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'M' and resid 222 through 224 removed outlier: 3.646A pdb=" N ASP M 242 " --> pdb=" O GLU M 250 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLU M 250 " --> pdb=" O ASP M 242 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LYS M 263 " --> pdb=" O LYS M 255 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ARG M 257 " --> pdb=" O ILE M 261 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N ILE M 261 " --> pdb=" O ARG M 257 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'M' and resid 268 through 269 removed outlier: 6.558A pdb=" N THR M 268 " --> pdb=" O ILE M 314 " (cutoff:3.500A) removed outlier: 8.880A pdb=" N LEU M 316 " --> pdb=" O THR M 268 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N THR M 286 " --> pdb=" O ALA M 282 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'M' and resid 352 through 356 removed outlier: 8.172A pdb=" N MET M 375 " --> pdb=" O VAL M 401 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N VAL M 401 " --> pdb=" O MET M 375 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N MET M 377 " --> pdb=" O VAL M 399 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N VAL M 399 " --> pdb=" O MET M 377 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N LEU M 379 " --> pdb=" O SER M 397 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'N' and resid 92 through 98 removed outlier: 5.553A pdb=" N LYS N 94 " --> pdb=" O CYS N 447 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N CYS N 447 " --> pdb=" O LYS N 94 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'N' and resid 119 through 122 removed outlier: 3.928A pdb=" N MET N 174 " --> pdb=" O LEU N 156 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'N' and resid 178 through 183 removed outlier: 3.825A pdb=" N SER N 178 " --> pdb=" O VAL N 193 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ASP N 212 " --> pdb=" O ILE N 204 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N TYR N 206 " --> pdb=" O TYR N 210 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N TYR N 210 " --> pdb=" O TYR N 206 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'N' and resid 222 through 224 removed outlier: 3.582A pdb=" N ASN N 230 " --> pdb=" O TYR N 237 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'N' and resid 222 through 224 removed outlier: 3.647A pdb=" N ASP N 242 " --> pdb=" O GLU N 250 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLU N 250 " --> pdb=" O ASP N 242 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LYS N 263 " --> pdb=" O LYS N 255 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ARG N 257 " --> pdb=" O ILE N 261 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N ILE N 261 " --> pdb=" O ARG N 257 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'N' and resid 268 through 269 removed outlier: 6.559A pdb=" N THR N 268 " --> pdb=" O ILE N 314 " (cutoff:3.500A) removed outlier: 8.880A pdb=" N LEU N 316 " --> pdb=" O THR N 268 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N THR N 286 " --> pdb=" O ALA N 282 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'N' and resid 352 through 356 removed outlier: 8.172A pdb=" N MET N 375 " --> pdb=" O VAL N 401 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N VAL N 401 " --> pdb=" O MET N 375 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N MET N 377 " --> pdb=" O VAL N 399 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N VAL N 399 " --> pdb=" O MET N 377 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N LEU N 379 " --> pdb=" O SER N 397 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'W' and resid 92 through 98 removed outlier: 5.552A pdb=" N LYS W 94 " --> pdb=" O CYS W 447 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N CYS W 447 " --> pdb=" O LYS W 94 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'W' and resid 119 through 122 removed outlier: 3.928A pdb=" N MET W 174 " --> pdb=" O LEU W 156 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'W' and resid 178 through 183 removed outlier: 3.824A pdb=" N SER W 178 " --> pdb=" O VAL W 193 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ASP W 212 " --> pdb=" O ILE W 204 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N TYR W 206 " --> pdb=" O TYR W 210 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N TYR W 210 " --> pdb=" O TYR W 206 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'W' and resid 222 through 224 removed outlier: 3.583A pdb=" N ASN W 230 " --> pdb=" O TYR W 237 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'W' and resid 222 through 224 removed outlier: 3.646A pdb=" N ASP W 242 " --> pdb=" O GLU W 250 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLU W 250 " --> pdb=" O ASP W 242 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LYS W 263 " --> pdb=" O LYS W 255 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ARG W 257 " --> pdb=" O ILE W 261 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N ILE W 261 " --> pdb=" O ARG W 257 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'W' and resid 268 through 269 removed outlier: 6.559A pdb=" N THR W 268 " --> pdb=" O ILE W 314 " (cutoff:3.500A) removed outlier: 8.880A pdb=" N LEU W 316 " --> pdb=" O THR W 268 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N THR W 286 " --> pdb=" O ALA W 282 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'W' and resid 352 through 356 removed outlier: 8.172A pdb=" N MET W 375 " --> pdb=" O VAL W 401 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N VAL W 401 " --> pdb=" O MET W 375 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N MET W 377 " --> pdb=" O VAL W 399 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N VAL W 399 " --> pdb=" O MET W 377 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N LEU W 379 " --> pdb=" O SER W 397 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 3 through 6 Processing sheet with id=AD3, first strand: chain 'A' and resid 58 through 59 removed outlier: 6.775A pdb=" N TRP A 36 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N GLY A 50 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N LEU A 34 " --> pdb=" O GLY A 50 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N VAL A 102 " --> pdb=" O ARG A 94 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'A' and resid 58 through 59 removed outlier: 6.775A pdb=" N TRP A 36 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N GLY A 50 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N LEU A 34 " --> pdb=" O GLY A 50 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'A' and resid 120 through 124 removed outlier: 3.888A pdb=" N GLY A 139 " --> pdb=" O LEU A 124 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N GLY A 139 " --> pdb=" O VAL A 182 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N VAL A 182 " --> pdb=" O GLY A 139 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N LEU A 141 " --> pdb=" O SER A 180 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N SER A 180 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N LYS A 143 " --> pdb=" O LEU A 178 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LEU A 178 " --> pdb=" O LYS A 143 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU A 175 " --> pdb=" O GLN A 171 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL A 169 " --> pdb=" O SER A 177 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N SER A 179 " --> pdb=" O PRO A 167 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N VAL A 181 " --> pdb=" O THR A 165 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N THR A 165 " --> pdb=" O VAL A 181 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 3 through 6 Processing sheet with id=AD7, first strand: chain 'C' and resid 58 through 59 removed outlier: 6.775A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N GLY C 50 " --> pdb=" O LEU C 34 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N LEU C 34 " --> pdb=" O GLY C 50 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N VAL C 102 " --> pdb=" O ARG C 94 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 58 through 59 removed outlier: 6.775A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N GLY C 50 " --> pdb=" O LEU C 34 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N LEU C 34 " --> pdb=" O GLY C 50 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 120 through 124 removed outlier: 3.888A pdb=" N GLY C 139 " --> pdb=" O LEU C 124 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N GLY C 139 " --> pdb=" O VAL C 182 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N VAL C 182 " --> pdb=" O GLY C 139 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N LEU C 141 " --> pdb=" O SER C 180 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N SER C 180 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N LYS C 143 " --> pdb=" O LEU C 178 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LEU C 178 " --> pdb=" O LYS C 143 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU C 175 " --> pdb=" O GLN C 171 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL C 169 " --> pdb=" O SER C 177 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N SER C 179 " --> pdb=" O PRO C 167 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N VAL C 181 " --> pdb=" O THR C 165 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N THR C 165 " --> pdb=" O VAL C 181 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 3 through 6 Processing sheet with id=AE2, first strand: chain 'D' and resid 58 through 59 removed outlier: 6.775A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N GLY D 50 " --> pdb=" O LEU D 34 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N LEU D 34 " --> pdb=" O GLY D 50 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N VAL D 102 " --> pdb=" O ARG D 94 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 58 through 59 removed outlier: 6.775A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N GLY D 50 " --> pdb=" O LEU D 34 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N LEU D 34 " --> pdb=" O GLY D 50 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 120 through 124 removed outlier: 3.888A pdb=" N GLY D 139 " --> pdb=" O LEU D 124 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N GLY D 139 " --> pdb=" O VAL D 182 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N VAL D 182 " --> pdb=" O GLY D 139 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N LEU D 141 " --> pdb=" O SER D 180 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N SER D 180 " --> pdb=" O LEU D 141 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N LYS D 143 " --> pdb=" O LEU D 178 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LEU D 178 " --> pdb=" O LYS D 143 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU D 175 " --> pdb=" O GLN D 171 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL D 169 " --> pdb=" O SER D 177 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N SER D 179 " --> pdb=" O PRO D 167 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N VAL D 181 " --> pdb=" O THR D 165 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N THR D 165 " --> pdb=" O VAL D 181 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AE6, first strand: chain 'H' and resid 58 through 59 removed outlier: 6.775A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N GLY H 50 " --> pdb=" O LEU H 34 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N LEU H 34 " --> pdb=" O GLY H 50 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N VAL H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'H' and resid 58 through 59 removed outlier: 6.775A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N GLY H 50 " --> pdb=" O LEU H 34 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N LEU H 34 " --> pdb=" O GLY H 50 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 120 through 124 removed outlier: 3.888A pdb=" N GLY H 139 " --> pdb=" O LEU H 124 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N GLY H 139 " --> pdb=" O VAL H 182 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N VAL H 182 " --> pdb=" O GLY H 139 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N LEU H 141 " --> pdb=" O SER H 180 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N SER H 180 " --> pdb=" O LEU H 141 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N LYS H 143 " --> pdb=" O LEU H 178 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LEU H 178 " --> pdb=" O LYS H 143 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU H 175 " --> pdb=" O GLN H 171 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL H 169 " --> pdb=" O SER H 177 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N SER H 179 " --> pdb=" O PRO H 167 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N VAL H 181 " --> pdb=" O THR H 165 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N THR H 165 " --> pdb=" O VAL H 181 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 5 through 7 removed outlier: 3.516A pdb=" N ARG B 24 " --> pdb=" O THR B 5 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'B' and resid 10 through 13 removed outlier: 6.545A pdb=" N LEU B 11 " --> pdb=" O GLU B 105 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL B 85 " --> pdb=" O HIS B 38 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N LEU B 33 " --> pdb=" O ASN B 49 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N ASN B 49 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'B' and resid 10 through 13 removed outlier: 6.545A pdb=" N LEU B 11 " --> pdb=" O GLU B 105 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG B 90 " --> pdb=" O THR B 97 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N THR B 97 " --> pdb=" O ARG B 90 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'B' and resid 116 through 118 removed outlier: 4.049A pdb=" N THR B 178 " --> pdb=" O GLN B 160 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'B' and resid 116 through 118 removed outlier: 5.944A pdb=" N TYR B 173 " --> pdb=" O ASN B 138 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'B' and resid 145 through 149 removed outlier: 3.794A pdb=" N ALA B 193 " --> pdb=" O LYS B 149 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL B 196 " --> pdb=" O VAL B 205 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N VAL B 205 " --> pdb=" O VAL B 196 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'E' and resid 5 through 7 removed outlier: 3.516A pdb=" N ARG E 24 " --> pdb=" O THR E 5 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.545A pdb=" N LEU E 11 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LEU E 33 " --> pdb=" O ASN E 49 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N ASN E 49 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.545A pdb=" N LEU E 11 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG E 90 " --> pdb=" O THR E 97 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N THR E 97 " --> pdb=" O ARG E 90 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'E' and resid 116 through 118 removed outlier: 4.049A pdb=" N THR E 178 " --> pdb=" O GLN E 160 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'E' and resid 116 through 118 removed outlier: 5.944A pdb=" N TYR E 173 " --> pdb=" O ASN E 138 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'E' and resid 145 through 149 removed outlier: 3.794A pdb=" N ALA E 193 " --> pdb=" O LYS E 149 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL E 196 " --> pdb=" O VAL E 205 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N VAL E 205 " --> pdb=" O VAL E 196 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'G' and resid 5 through 7 removed outlier: 3.517A pdb=" N ARG G 24 " --> pdb=" O THR G 5 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'G' and resid 10 through 13 removed outlier: 6.545A pdb=" N LEU G 11 " --> pdb=" O GLU G 105 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL G 85 " --> pdb=" O HIS G 38 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LEU G 33 " --> pdb=" O ASN G 49 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N ASN G 49 " --> pdb=" O LEU G 33 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N TRP G 35 " --> pdb=" O LEU G 47 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'G' and resid 10 through 13 removed outlier: 6.545A pdb=" N LEU G 11 " --> pdb=" O GLU G 105 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ARG G 90 " --> pdb=" O THR G 97 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N THR G 97 " --> pdb=" O ARG G 90 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'G' and resid 116 through 118 removed outlier: 4.049A pdb=" N THR G 178 " --> pdb=" O GLN G 160 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'G' and resid 116 through 118 removed outlier: 5.944A pdb=" N TYR G 173 " --> pdb=" O ASN G 138 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'G' and resid 145 through 149 removed outlier: 3.795A pdb=" N ALA G 193 " --> pdb=" O LYS G 149 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL G 196 " --> pdb=" O VAL G 205 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N VAL G 205 " --> pdb=" O VAL G 196 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'L' and resid 5 through 7 removed outlier: 3.516A pdb=" N ARG L 24 " --> pdb=" O THR L 5 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.545A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N LEU L 33 " --> pdb=" O ASN L 49 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N ASN L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.545A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG L 90 " --> pdb=" O THR L 97 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N THR L 97 " --> pdb=" O ARG L 90 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'L' and resid 116 through 118 removed outlier: 4.049A pdb=" N THR L 178 " --> pdb=" O GLN L 160 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'L' and resid 116 through 118 removed outlier: 5.943A pdb=" N TYR L 173 " --> pdb=" O ASN L 138 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'L' and resid 145 through 149 removed outlier: 3.794A pdb=" N ALA L 193 " --> pdb=" O LYS L 149 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL L 196 " --> pdb=" O VAL L 205 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N VAL L 205 " --> pdb=" O VAL L 196 " (cutoff:3.500A) 782 hydrogen bonds defined for protein. 1932 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: 10.01 Time building geometry restraints manager: 7.42 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: 7952 1.34 - 1.46: 6422 1.46 - 1.58: 10798 1.58 - 1.70: 0 1.70 - 1.82: 204 Bond restraints: 25376 Sorted by residual: bond pdb=" CA LYS I 255 " pdb=" CB LYS I 255 " ideal model delta sigma weight residual 1.526 1.446 0.080 1.53e-02 4.27e+03 2.76e+01 bond pdb=" CA LYS M 255 " pdb=" CB LYS M 255 " ideal model delta sigma weight residual 1.526 1.446 0.080 1.53e-02 4.27e+03 2.75e+01 bond pdb=" CA LYS W 255 " pdb=" CB LYS W 255 " ideal model delta sigma weight residual 1.526 1.446 0.080 1.53e-02 4.27e+03 2.75e+01 bond pdb=" CA LYS N 255 " pdb=" CB LYS N 255 " ideal model delta sigma weight residual 1.526 1.446 0.080 1.53e-02 4.27e+03 2.75e+01 bond pdb=" C GLU I 404 " pdb=" N GLU I 405 " ideal model delta sigma weight residual 1.327 1.274 0.053 1.71e-02 3.42e+03 9.51e+00 ... (remaining 25371 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.76: 33957 2.76 - 5.51: 399 5.51 - 8.27: 20 8.27 - 11.03: 0 11.03 - 13.79: 8 Bond angle restraints: 34384 Sorted by residual: angle pdb=" C GLY I 145 " pdb=" N THR I 146 " pdb=" CA THR I 146 " ideal model delta sigma weight residual 120.95 134.29 -13.34 1.78e+00 3.16e-01 5.61e+01 angle pdb=" C GLY M 145 " pdb=" N THR M 146 " pdb=" CA THR M 146 " ideal model delta sigma weight residual 120.95 134.25 -13.30 1.78e+00 3.16e-01 5.58e+01 angle pdb=" C GLY W 145 " pdb=" N THR W 146 " pdb=" CA THR W 146 " ideal model delta sigma weight residual 120.95 134.21 -13.26 1.78e+00 3.16e-01 5.55e+01 angle pdb=" C GLY N 145 " pdb=" N THR N 146 " pdb=" CA THR N 146 " ideal model delta sigma weight residual 120.95 134.21 -13.26 1.78e+00 3.16e-01 5.55e+01 angle pdb=" C TRP I 408 " pdb=" N TYR I 409 " pdb=" CA TYR I 409 " ideal model delta sigma weight residual 121.54 135.33 -13.79 1.91e+00 2.74e-01 5.21e+01 ... (remaining 34379 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.54: 14117 21.54 - 43.08: 914 43.08 - 64.63: 193 64.63 - 86.17: 40 86.17 - 107.71: 20 Dihedral angle restraints: 15284 sinusoidal: 6116 harmonic: 9168 Sorted by residual: dihedral pdb=" CA THR C 183 " pdb=" C THR C 183 " pdb=" N VAL C 184 " pdb=" CA VAL C 184 " ideal model delta harmonic sigma weight residual 180.00 -145.98 -34.02 0 5.00e+00 4.00e-02 4.63e+01 dihedral pdb=" CA THR A 183 " pdb=" C THR A 183 " pdb=" N VAL A 184 " pdb=" CA VAL A 184 " ideal model delta harmonic sigma weight residual 180.00 -145.99 -34.01 0 5.00e+00 4.00e-02 4.63e+01 dihedral pdb=" CA THR H 183 " pdb=" C THR H 183 " pdb=" N VAL H 184 " pdb=" CA VAL H 184 " ideal model delta harmonic sigma weight residual -180.00 -146.00 -34.00 0 5.00e+00 4.00e-02 4.62e+01 ... (remaining 15281 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.336: 3804 0.336 - 0.671: 0 0.671 - 1.007: 0 1.007 - 1.343: 0 1.343 - 1.679: 4 Chirality restraints: 3808 Sorted by residual: chirality pdb=" C1 BMA W 503 " pdb=" O4 NAG O 2 " pdb=" C2 BMA W 503 " pdb=" O5 BMA W 503 " both_signs ideal model delta sigma weight residual False -2.40 -0.72 -1.68 2.00e-02 2.50e+03 7.04e+03 chirality pdb=" C1 BMA N 503 " pdb=" O4 NAG K 2 " pdb=" C2 BMA N 503 " pdb=" O5 BMA N 503 " both_signs ideal model delta sigma weight residual False -2.40 -0.72 -1.68 2.00e-02 2.50e+03 7.04e+03 chirality pdb=" C1 BMA I 503 " pdb=" O4 NAG F 2 " pdb=" C2 BMA I 503 " pdb=" O5 BMA I 503 " both_signs ideal model delta sigma weight residual False -2.40 -0.72 -1.68 2.00e-02 2.50e+03 7.03e+03 ... (remaining 3805 not shown) Planarity restraints: 4384 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE D 100C" -0.024 2.00e-02 2.50e+03 1.68e-02 4.92e+00 pdb=" CG PHE D 100C" 0.035 2.00e-02 2.50e+03 pdb=" CD1 PHE D 100C" 0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE D 100C" 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE D 100C" -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE D 100C" -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE D 100C" -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE H 100C" -0.024 2.00e-02 2.50e+03 1.67e-02 4.86e+00 pdb=" CG PHE H 100C" 0.035 2.00e-02 2.50e+03 pdb=" CD1 PHE H 100C" 0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE H 100C" 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE H 100C" -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE H 100C" -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE H 100C" -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 100C" 0.024 2.00e-02 2.50e+03 1.66e-02 4.85e+00 pdb=" CG PHE A 100C" -0.035 2.00e-02 2.50e+03 pdb=" CD1 PHE A 100C" -0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE A 100C" -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE A 100C" 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE A 100C" 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE A 100C" 0.009 2.00e-02 2.50e+03 ... (remaining 4381 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.26: 85 2.26 - 2.92: 11385 2.92 - 3.58: 32191 3.58 - 4.24: 58633 4.24 - 4.90: 99748 Nonbonded interactions: 202042 Sorted by model distance: nonbonded pdb=" OG1 THR H 135 " pdb=" O VAL H 184 " model vdw 1.602 3.040 nonbonded pdb=" OG1 THR C 135 " pdb=" O VAL C 184 " model vdw 1.602 3.040 nonbonded pdb=" OG1 THR A 135 " pdb=" O VAL A 184 " model vdw 1.603 3.040 nonbonded pdb=" OG1 THR D 135 " pdb=" O VAL D 184 " model vdw 1.603 3.040 nonbonded pdb=" O GLN B 124 " pdb=" OG SER B 127 " model vdw 2.002 3.040 ... (remaining 202037 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'F' selection = chain 'J' selection = chain 'K' selection = chain 'O' } ncs_group { reference = chain 'I' selection = chain 'M' selection = chain 'N' selection = chain 'W' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.05 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: 3.160 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 56.990 Find NCS groups from input model: 1.040 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 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 : 0.011 0.080 25376 Z= 0.719 Angle : 0.813 13.786 34384 Z= 0.462 Chirality : 0.075 1.679 3808 Planarity : 0.005 0.047 4380 Dihedral : 15.492 107.711 9404 Min Nonbonded Distance : 1.602 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.88 % Favored : 90.12 % Rotamer: Outliers : 2.95 % Allowed : 13.44 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.27 (0.12), residues: 3148 helix: -5.17 (0.18), residues: 28 sheet: -1.94 (0.13), residues: 1240 loop : -3.61 (0.10), residues: 1880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 154 HIS 0.006 0.001 HIS N 183 PHE 0.035 0.002 PHE D 100C TYR 0.012 0.001 TYR N 383 ARG 0.003 0.001 ARG N 154 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 2708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 426 time to evaluate : 2.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 ASP cc_start: 0.7668 (t70) cc_final: 0.7252 (t70) REVERT: A 100 TYR cc_start: 0.8902 (m-80) cc_final: 0.8688 (m-80) REVERT: A 145 TYR cc_start: 0.7152 (p90) cc_final: 0.6675 (p90) REVERT: A 176 TYR cc_start: 0.7568 (m-80) cc_final: 0.7269 (m-80) REVERT: C 72 ASP cc_start: 0.7394 (t70) cc_final: 0.6976 (t70) REVERT: C 100 TYR cc_start: 0.9134 (m-80) cc_final: 0.8930 (m-80) REVERT: D 72 ASP cc_start: 0.7472 (t70) cc_final: 0.7025 (t70) REVERT: D 100 TYR cc_start: 0.9096 (m-80) cc_final: 0.8811 (m-80) REVERT: D 145 TYR cc_start: 0.7000 (p90) cc_final: 0.6583 (p90) REVERT: D 176 TYR cc_start: 0.7769 (m-80) cc_final: 0.7160 (m-10) REVERT: H 72 ASP cc_start: 0.7403 (t70) cc_final: 0.6983 (t70) REVERT: H 100 TYR cc_start: 0.9104 (m-80) cc_final: 0.8902 (m-80) REVERT: H 145 TYR cc_start: 0.6776 (p90) cc_final: 0.6268 (p90) REVERT: H 176 TYR cc_start: 0.7588 (m-80) cc_final: 0.7346 (m-80) REVERT: B 116 PHE cc_start: 0.5661 (m-10) cc_final: 0.5444 (m-10) REVERT: B 143 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7334 (tm-30) REVERT: B 190 LYS cc_start: 0.8145 (mmmt) cc_final: 0.7677 (tptt) REVERT: E 143 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.7388 (tm-30) REVERT: E 190 LYS cc_start: 0.8123 (mmmt) cc_final: 0.7810 (tttp) REVERT: G 143 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7381 (tm-30) REVERT: L 143 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7312 (tm-30) outliers start: 80 outliers final: 30 residues processed: 490 average time/residue: 1.5142 time to fit residues: 841.8987 Evaluate side-chains 361 residues out of total 2708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 327 time to evaluate : 2.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 87 CYS Chi-restraints excluded: chain I residue 182 CYS Chi-restraints excluded: chain I residue 229 CYS Chi-restraints excluded: chain I residue 366 SER Chi-restraints excluded: chain I residue 420 CYS Chi-restraints excluded: chain M residue 87 CYS Chi-restraints excluded: chain M residue 182 CYS Chi-restraints excluded: chain M residue 229 CYS Chi-restraints excluded: chain M residue 366 SER Chi-restraints excluded: chain M residue 420 CYS Chi-restraints excluded: chain N residue 87 CYS Chi-restraints excluded: chain N residue 182 CYS Chi-restraints excluded: chain N residue 229 CYS Chi-restraints excluded: chain N residue 366 SER Chi-restraints excluded: chain N residue 420 CYS Chi-restraints excluded: chain W residue 87 CYS Chi-restraints excluded: chain W residue 182 CYS Chi-restraints excluded: chain W residue 229 CYS Chi-restraints excluded: chain W residue 366 SER Chi-restraints excluded: chain W residue 420 CYS Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 173 SER Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain D residue 173 SER Chi-restraints excluded: chain H residue 81 ASP Chi-restraints excluded: chain H residue 173 SER Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 49 ASN Chi-restraints excluded: chain B residue 143 GLU Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 143 GLU Chi-restraints excluded: chain G residue 32 SER Chi-restraints excluded: chain G residue 143 GLU Chi-restraints excluded: chain L residue 143 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 266 optimal weight: 40.0000 chunk 239 optimal weight: 7.9990 chunk 132 optimal weight: 0.9980 chunk 81 optimal weight: 0.9990 chunk 161 optimal weight: 6.9990 chunk 127 optimal weight: 4.9990 chunk 247 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 150 optimal weight: 2.9990 chunk 184 optimal weight: 20.0000 chunk 286 optimal weight: 0.0030 overall best weight: 0.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 431 HIS M 329 ASN M 431 HIS N 329 ASN N 431 HIS W 431 HIS A 39 GLN A 204 ASN ** C 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 204 ASN D 204 ASN H 155 ASN ** H 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 204 ASN ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 166 GLN ** B 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 199 GLN ** E 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 166 GLN ** G 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN L 166 GLN ** L 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25376 Z= 0.199 Angle : 0.668 7.309 34384 Z= 0.352 Chirality : 0.047 0.259 3808 Planarity : 0.005 0.049 4380 Dihedral : 8.555 58.490 3748 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 4.25 % Allowed : 18.17 % Favored : 77.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % 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: -3.06 (0.13), residues: 3148 helix: -4.62 (0.16), residues: 32 sheet: -1.39 (0.14), residues: 1264 loop : -2.54 (0.12), residues: 1852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP N 408 HIS 0.012 0.001 HIS A 164 PHE 0.017 0.002 PHE D 100C TYR 0.020 0.002 TYR G 186 ARG 0.006 0.001 ARG C 83 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 2708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 350 time to evaluate : 2.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 375 MET cc_start: 0.8775 (mmm) cc_final: 0.8313 (mmt) REVERT: I 390 ASP cc_start: 0.7287 (OUTLIER) cc_final: 0.6655 (m-30) REVERT: M 375 MET cc_start: 0.8671 (mmm) cc_final: 0.8382 (mmt) REVERT: M 390 ASP cc_start: 0.7310 (OUTLIER) cc_final: 0.6671 (m-30) REVERT: N 375 MET cc_start: 0.8734 (mmm) cc_final: 0.8439 (mmm) REVERT: N 390 ASP cc_start: 0.7302 (OUTLIER) cc_final: 0.6634 (m-30) REVERT: W 390 ASP cc_start: 0.7325 (OUTLIER) cc_final: 0.6678 (m-30) REVERT: A 72 ASP cc_start: 0.7859 (t70) cc_final: 0.7361 (t70) REVERT: A 145 TYR cc_start: 0.7125 (p90) cc_final: 0.6692 (p90) REVERT: C 30 ILE cc_start: 0.9016 (tt) cc_final: 0.8783 (tp) REVERT: C 72 ASP cc_start: 0.7499 (t70) cc_final: 0.7020 (t70) REVERT: D 30 ILE cc_start: 0.9106 (tt) cc_final: 0.8851 (tp) REVERT: D 72 ASP cc_start: 0.7610 (t70) cc_final: 0.7150 (t70) REVERT: D 100 TYR cc_start: 0.9025 (m-80) cc_final: 0.8750 (m-80) REVERT: D 145 TYR cc_start: 0.7032 (p90) cc_final: 0.6519 (p90) REVERT: D 176 TYR cc_start: 0.7577 (m-80) cc_final: 0.7038 (m-10) REVERT: H 30 ILE cc_start: 0.9021 (tt) cc_final: 0.8768 (tp) REVERT: H 72 ASP cc_start: 0.7611 (t70) cc_final: 0.7129 (t70) REVERT: H 100 TYR cc_start: 0.9045 (m-80) cc_final: 0.8836 (m-80) REVERT: H 145 TYR cc_start: 0.6815 (p90) cc_final: 0.6323 (p90) REVERT: H 176 TYR cc_start: 0.7574 (m-80) cc_final: 0.6988 (m-10) REVERT: E 190 LYS cc_start: 0.8073 (mmmt) cc_final: 0.7648 (tptt) REVERT: G 24 ARG cc_start: 0.8007 (OUTLIER) cc_final: 0.7754 (ttt-90) REVERT: G 108 ARG cc_start: 0.7535 (ptm160) cc_final: 0.6746 (ptm-80) REVERT: L 6 GLN cc_start: 0.8352 (OUTLIER) cc_final: 0.7455 (mt0) REVERT: L 18 ARG cc_start: 0.8523 (OUTLIER) cc_final: 0.7493 (ttm110) outliers start: 115 outliers final: 56 residues processed: 441 average time/residue: 1.2903 time to fit residues: 657.8251 Evaluate side-chains 377 residues out of total 2708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 314 time to evaluate : 2.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 182 CYS Chi-restraints excluded: chain I residue 198 SER Chi-restraints excluded: chain I residue 229 CYS Chi-restraints excluded: chain I residue 307 VAL Chi-restraints excluded: chain I residue 337 CYS Chi-restraints excluded: chain I residue 366 SER Chi-restraints excluded: chain I residue 390 ASP Chi-restraints excluded: chain I residue 410 SER Chi-restraints excluded: chain M residue 198 SER Chi-restraints excluded: chain M residue 307 VAL Chi-restraints excluded: chain M residue 366 SER Chi-restraints excluded: chain M residue 390 ASP Chi-restraints excluded: chain M residue 410 SER Chi-restraints excluded: chain N residue 198 SER Chi-restraints excluded: chain N residue 307 VAL Chi-restraints excluded: chain N residue 366 SER Chi-restraints excluded: chain N residue 390 ASP Chi-restraints excluded: chain N residue 410 SER Chi-restraints excluded: chain W residue 198 SER Chi-restraints excluded: chain W residue 307 VAL Chi-restraints excluded: chain W residue 366 SER Chi-restraints excluded: chain W residue 390 ASP Chi-restraints excluded: chain W residue 410 SER Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 100 ASP Chi-restraints excluded: chain H residue 184 VAL Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 182 SER Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 174 SER Chi-restraints excluded: chain G residue 24 ARG Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 76 SER Chi-restraints excluded: chain G residue 182 SER Chi-restraints excluded: chain G residue 206 THR Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 76 SER Chi-restraints excluded: chain L residue 150 VAL Chi-restraints excluded: chain L residue 206 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 159 optimal weight: 7.9990 chunk 89 optimal weight: 5.9990 chunk 238 optimal weight: 10.0000 chunk 195 optimal weight: 7.9990 chunk 79 optimal weight: 4.9990 chunk 287 optimal weight: 40.0000 chunk 310 optimal weight: 6.9990 chunk 256 optimal weight: 8.9990 chunk 285 optimal weight: 20.0000 chunk 98 optimal weight: 3.9990 chunk 230 optimal weight: 20.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 183 HIS I 225 GLN I 273 HIS M 183 HIS M 225 GLN M 273 HIS N 183 HIS N 225 GLN N 273 HIS W 183 HIS W 225 GLN W 273 HIS W 329 ASN ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 166 GLN E 27 GLN G 27 GLN ** G 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 166 GLN L 160 GLN L 166 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.072 25376 Z= 0.664 Angle : 0.775 8.632 34384 Z= 0.409 Chirality : 0.052 0.200 3808 Planarity : 0.006 0.060 4380 Dihedral : 7.172 59.917 3710 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 5.50 % Allowed : 18.69 % Favored : 75.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.51 (0.13), residues: 3148 helix: -4.43 (0.17), residues: 32 sheet: -0.97 (0.14), residues: 1284 loop : -2.20 (0.12), residues: 1832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 103 HIS 0.007 0.002 HIS I 215 PHE 0.048 0.003 PHE C 100C TYR 0.020 0.002 TYR B 173 ARG 0.006 0.001 ARG M 374 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 2708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 308 time to evaluate : 2.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 116 ARG cc_start: 0.8056 (OUTLIER) cc_final: 0.5915 (tmm160) REVERT: M 116 ARG cc_start: 0.7998 (OUTLIER) cc_final: 0.5888 (tmm160) REVERT: N 116 ARG cc_start: 0.7996 (OUTLIER) cc_final: 0.5863 (tmm160) REVERT: N 429 MET cc_start: 0.9127 (mtp) cc_final: 0.8916 (mtm) REVERT: W 116 ARG cc_start: 0.7994 (OUTLIER) cc_final: 0.5881 (tmm160) REVERT: W 429 MET cc_start: 0.9127 (mtp) cc_final: 0.8913 (mtm) REVERT: A 72 ASP cc_start: 0.8067 (t70) cc_final: 0.7595 (t70) REVERT: A 100 ASP cc_start: 0.7988 (OUTLIER) cc_final: 0.7753 (m-30) REVERT: A 100 PHE cc_start: 0.7809 (OUTLIER) cc_final: 0.7585 (p90) REVERT: A 145 TYR cc_start: 0.7354 (p90) cc_final: 0.6893 (p90) REVERT: A 176 TYR cc_start: 0.7436 (m-80) cc_final: 0.7018 (m-10) REVERT: C 30 ILE cc_start: 0.9134 (tt) cc_final: 0.8880 (tp) REVERT: C 72 ASP cc_start: 0.7939 (t70) cc_final: 0.7490 (t70) REVERT: C 100 ASP cc_start: 0.7811 (OUTLIER) cc_final: 0.7310 (m-30) REVERT: D 72 ASP cc_start: 0.7946 (t70) cc_final: 0.7494 (t70) REVERT: D 145 TYR cc_start: 0.7438 (p90) cc_final: 0.6889 (p90) REVERT: D 176 TYR cc_start: 0.7693 (m-80) cc_final: 0.7425 (m-80) REVERT: H 30 ILE cc_start: 0.9129 (tt) cc_final: 0.8872 (tp) REVERT: H 72 ASP cc_start: 0.7951 (t70) cc_final: 0.7516 (t70) REVERT: H 100 ASP cc_start: 0.7816 (OUTLIER) cc_final: 0.7290 (m-30) REVERT: H 145 TYR cc_start: 0.7365 (p90) cc_final: 0.6798 (p90) REVERT: H 176 TYR cc_start: 0.7748 (m-80) cc_final: 0.7477 (m-80) REVERT: B 108 ARG cc_start: 0.7772 (ptm160) cc_final: 0.7336 (ptm-80) REVERT: E 190 LYS cc_start: 0.8206 (mmmt) cc_final: 0.7850 (tptt) REVERT: E 191 VAL cc_start: 0.5356 (OUTLIER) cc_final: 0.5022 (t) REVERT: G 108 ARG cc_start: 0.7773 (ptm160) cc_final: 0.7002 (ptm-80) REVERT: G 165 GLU cc_start: 0.7969 (tp30) cc_final: 0.7427 (tp30) REVERT: G 166 GLN cc_start: 0.9032 (OUTLIER) cc_final: 0.8485 (tt0) REVERT: L 108 ARG cc_start: 0.7479 (ptm160) cc_final: 0.7163 (ptm-80) outliers start: 149 outliers final: 77 residues processed: 421 average time/residue: 1.3684 time to fit residues: 663.8093 Evaluate side-chains 361 residues out of total 2708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 274 time to evaluate : 2.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 116 ARG Chi-restraints excluded: chain I residue 146 THR Chi-restraints excluded: chain I residue 182 CYS Chi-restraints excluded: chain I residue 198 SER Chi-restraints excluded: chain I residue 229 CYS Chi-restraints excluded: chain I residue 307 VAL Chi-restraints excluded: chain I residue 337 CYS Chi-restraints excluded: chain I residue 359 SER Chi-restraints excluded: chain I residue 366 SER Chi-restraints excluded: chain M residue 116 ARG Chi-restraints excluded: chain M residue 146 THR Chi-restraints excluded: chain M residue 198 SER Chi-restraints excluded: chain M residue 307 VAL Chi-restraints excluded: chain M residue 359 SER Chi-restraints excluded: chain M residue 366 SER Chi-restraints excluded: chain M residue 420 CYS Chi-restraints excluded: chain N residue 116 ARG Chi-restraints excluded: chain N residue 146 THR Chi-restraints excluded: chain N residue 198 SER Chi-restraints excluded: chain N residue 307 VAL Chi-restraints excluded: chain N residue 366 SER Chi-restraints excluded: chain N residue 420 CYS Chi-restraints excluded: chain W residue 116 ARG Chi-restraints excluded: chain W residue 146 THR Chi-restraints excluded: chain W residue 198 SER Chi-restraints excluded: chain W residue 307 VAL Chi-restraints excluded: chain W residue 366 SER Chi-restraints excluded: chain W residue 420 CYS Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 100 ASP Chi-restraints excluded: chain H residue 100 ASP Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain H residue 184 VAL Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 79 GLU Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 182 SER Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 165 GLU Chi-restraints excluded: chain E residue 174 SER Chi-restraints excluded: chain E residue 182 SER Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 202 SER Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 76 SER Chi-restraints excluded: chain G residue 79 GLU Chi-restraints excluded: chain G residue 166 GLN Chi-restraints excluded: chain G residue 174 SER Chi-restraints excluded: chain G residue 202 SER Chi-restraints excluded: chain G residue 206 THR Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 76 SER Chi-restraints excluded: chain L residue 79 GLU Chi-restraints excluded: chain L residue 150 VAL Chi-restraints excluded: chain L residue 174 SER Chi-restraints excluded: chain L residue 182 SER Chi-restraints excluded: chain L residue 202 SER Chi-restraints excluded: chain L residue 206 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 284 optimal weight: 8.9990 chunk 216 optimal weight: 2.9990 chunk 149 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 137 optimal weight: 0.9980 chunk 193 optimal weight: 0.8980 chunk 288 optimal weight: 4.9990 chunk 305 optimal weight: 0.1980 chunk 150 optimal weight: 0.9980 chunk 273 optimal weight: 0.4980 chunk 82 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 329 ASN B 166 GLN E 27 GLN E 166 GLN ** G 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 166 GLN L 6 GLN L 166 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.2914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 25376 Z= 0.159 Angle : 0.581 7.764 34384 Z= 0.304 Chirality : 0.044 0.177 3808 Planarity : 0.005 0.055 4380 Dihedral : 5.684 39.139 3706 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 2.95 % Allowed : 22.19 % Favored : 74.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.14), residues: 3148 helix: -4.34 (0.17), residues: 32 sheet: -0.70 (0.14), residues: 1320 loop : -1.86 (0.13), residues: 1796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 148 HIS 0.003 0.001 HIS L 198 PHE 0.021 0.002 PHE B 116 TYR 0.023 0.001 TYR B 140 ARG 0.003 0.000 ARG E 24 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 2708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 321 time to evaluate : 2.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 375 MET cc_start: 0.8703 (mmm) cc_final: 0.8457 (mmt) REVERT: I 429 MET cc_start: 0.9128 (mtp) cc_final: 0.8895 (mtm) REVERT: M 375 MET cc_start: 0.8737 (mmm) cc_final: 0.8455 (mmm) REVERT: M 429 MET cc_start: 0.9132 (mtp) cc_final: 0.8897 (mtm) REVERT: N 371 LYS cc_start: 0.9189 (OUTLIER) cc_final: 0.8743 (ptpp) REVERT: N 375 MET cc_start: 0.8777 (mmm) cc_final: 0.8396 (mmt) REVERT: N 429 MET cc_start: 0.9113 (mtp) cc_final: 0.8852 (mtm) REVERT: W 371 LYS cc_start: 0.9187 (OUTLIER) cc_final: 0.8676 (ptpp) REVERT: W 429 MET cc_start: 0.9112 (mtp) cc_final: 0.8846 (mtm) REVERT: A 72 ASP cc_start: 0.8027 (t70) cc_final: 0.7507 (t70) REVERT: A 145 TYR cc_start: 0.7174 (p90) cc_final: 0.6690 (p90) REVERT: A 176 TYR cc_start: 0.7267 (m-80) cc_final: 0.6948 (m-10) REVERT: C 30 ILE cc_start: 0.9080 (tt) cc_final: 0.8847 (tp) REVERT: C 43 GLN cc_start: 0.8234 (mt0) cc_final: 0.8016 (tt0) REVERT: C 72 ASP cc_start: 0.7901 (t70) cc_final: 0.7392 (t70) REVERT: C 100 PHE cc_start: 0.7796 (OUTLIER) cc_final: 0.7532 (p90) REVERT: D 30 ILE cc_start: 0.9093 (tt) cc_final: 0.8870 (tp) REVERT: D 72 ASP cc_start: 0.7899 (t70) cc_final: 0.7393 (t70) REVERT: D 100 PHE cc_start: 0.7750 (OUTLIER) cc_final: 0.7493 (p90) REVERT: D 145 TYR cc_start: 0.7290 (p90) cc_final: 0.6681 (p90) REVERT: D 176 TYR cc_start: 0.7521 (m-80) cc_final: 0.7313 (m-80) REVERT: H 30 ILE cc_start: 0.9070 (tt) cc_final: 0.8836 (tp) REVERT: H 72 ASP cc_start: 0.7905 (t70) cc_final: 0.7394 (t70) REVERT: H 100 PHE cc_start: 0.7766 (OUTLIER) cc_final: 0.7492 (p90) REVERT: H 145 TYR cc_start: 0.7261 (p90) cc_final: 0.6672 (p90) REVERT: B 108 ARG cc_start: 0.7568 (ptm160) cc_final: 0.7322 (ptm-80) REVERT: E 190 LYS cc_start: 0.8183 (mmmt) cc_final: 0.7867 (tptt) REVERT: G 108 ARG cc_start: 0.7650 (ptm160) cc_final: 0.7397 (ptm-80) REVERT: L 108 ARG cc_start: 0.7554 (ptm160) cc_final: 0.7256 (ptm-80) outliers start: 80 outliers final: 30 residues processed: 386 average time/residue: 1.3521 time to fit residues: 601.5231 Evaluate side-chains 326 residues out of total 2708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 291 time to evaluate : 2.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 182 CYS Chi-restraints excluded: chain I residue 198 SER Chi-restraints excluded: chain I residue 229 CYS Chi-restraints excluded: chain I residue 337 CYS Chi-restraints excluded: chain M residue 198 SER Chi-restraints excluded: chain M residue 361 ILE Chi-restraints excluded: chain N residue 198 SER Chi-restraints excluded: chain N residue 361 ILE Chi-restraints excluded: chain N residue 371 LYS Chi-restraints excluded: chain W residue 198 SER Chi-restraints excluded: chain W residue 361 ILE Chi-restraints excluded: chain W residue 371 LYS Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 100 PHE Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain H residue 184 VAL Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain E residue 182 SER Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 33 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 254 optimal weight: 10.0000 chunk 173 optimal weight: 9.9990 chunk 4 optimal weight: 5.9990 chunk 227 optimal weight: 8.9990 chunk 126 optimal weight: 0.5980 chunk 260 optimal weight: 10.0000 chunk 211 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 chunk 155 optimal weight: 8.9990 chunk 274 optimal weight: 0.3980 chunk 77 optimal weight: 5.9990 overall best weight: 3.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 6 GLN B 27 GLN B 166 GLN E 6 GLN E 27 GLN E 166 GLN G 27 GLN G 42 GLN ** G 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 166 GLN L 6 GLN L 42 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.3123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 25376 Z= 0.443 Angle : 0.660 7.999 34384 Z= 0.345 Chirality : 0.047 0.146 3808 Planarity : 0.005 0.056 4380 Dihedral : 5.760 35.313 3702 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 3.69 % Allowed : 22.45 % Favored : 73.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.14), residues: 3148 helix: -4.19 (0.20), residues: 32 sheet: -0.46 (0.14), residues: 1308 loop : -1.89 (0.13), residues: 1808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 47 HIS 0.004 0.001 HIS I 129 PHE 0.038 0.002 PHE H 100C TYR 0.027 0.002 TYR L 140 ARG 0.005 0.001 ARG E 108 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 2708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 294 time to evaluate : 2.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 371 LYS cc_start: 0.9263 (OUTLIER) cc_final: 0.8801 (ptpp) REVERT: N 429 MET cc_start: 0.9177 (mtp) cc_final: 0.8902 (mtm) REVERT: W 371 LYS cc_start: 0.9276 (OUTLIER) cc_final: 0.8758 (ptpp) REVERT: W 429 MET cc_start: 0.9176 (mtp) cc_final: 0.8896 (mtm) REVERT: A 72 ASP cc_start: 0.8132 (t70) cc_final: 0.7683 (t70) REVERT: A 145 TYR cc_start: 0.7346 (p90) cc_final: 0.6706 (p90) REVERT: A 176 TYR cc_start: 0.7483 (m-80) cc_final: 0.7148 (m-80) REVERT: A 184 VAL cc_start: 0.8492 (OUTLIER) cc_final: 0.8271 (p) REVERT: C 30 ILE cc_start: 0.9133 (tt) cc_final: 0.8880 (tp) REVERT: C 43 GLN cc_start: 0.8299 (mt0) cc_final: 0.8061 (tt0) REVERT: C 46 GLU cc_start: 0.8000 (tt0) cc_final: 0.7738 (tt0) REVERT: C 72 ASP cc_start: 0.8054 (t70) cc_final: 0.7599 (t70) REVERT: C 184 VAL cc_start: 0.8420 (OUTLIER) cc_final: 0.8213 (p) REVERT: D 72 ASP cc_start: 0.8004 (t70) cc_final: 0.7552 (t70) REVERT: D 145 TYR cc_start: 0.7427 (p90) cc_final: 0.6793 (p90) REVERT: H 30 ILE cc_start: 0.9127 (tt) cc_final: 0.8872 (tp) REVERT: H 72 ASP cc_start: 0.8089 (t70) cc_final: 0.7603 (t70) REVERT: H 145 TYR cc_start: 0.7355 (p90) cc_final: 0.6737 (p90) REVERT: H 184 VAL cc_start: 0.8422 (OUTLIER) cc_final: 0.8190 (p) REVERT: B 108 ARG cc_start: 0.7773 (ptm160) cc_final: 0.7492 (ptm-80) REVERT: B 199 GLN cc_start: 0.8822 (tt0) cc_final: 0.8614 (tt0) REVERT: E 190 LYS cc_start: 0.8371 (mmmt) cc_final: 0.8061 (tptt) REVERT: G 108 ARG cc_start: 0.7731 (ptm160) cc_final: 0.7139 (ptm-80) REVERT: G 173 TYR cc_start: 0.8369 (m-10) cc_final: 0.8161 (m-10) REVERT: L 108 ARG cc_start: 0.7688 (ptm160) cc_final: 0.7449 (ptm-80) outliers start: 100 outliers final: 65 residues processed: 377 average time/residue: 1.3468 time to fit residues: 584.9620 Evaluate side-chains 350 residues out of total 2708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 280 time to evaluate : 2.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 146 THR Chi-restraints excluded: chain I residue 182 CYS Chi-restraints excluded: chain I residue 198 SER Chi-restraints excluded: chain I residue 229 CYS Chi-restraints excluded: chain I residue 307 VAL Chi-restraints excluded: chain I residue 337 CYS Chi-restraints excluded: chain I residue 359 SER Chi-restraints excluded: chain I residue 361 ILE Chi-restraints excluded: chain M residue 146 THR Chi-restraints excluded: chain M residue 198 SER Chi-restraints excluded: chain M residue 307 VAL Chi-restraints excluded: chain M residue 390 ASP Chi-restraints excluded: chain M residue 420 CYS Chi-restraints excluded: chain N residue 146 THR Chi-restraints excluded: chain N residue 198 SER Chi-restraints excluded: chain N residue 307 VAL Chi-restraints excluded: chain N residue 361 ILE Chi-restraints excluded: chain N residue 371 LYS Chi-restraints excluded: chain N residue 390 ASP Chi-restraints excluded: chain N residue 420 CYS Chi-restraints excluded: chain W residue 146 THR Chi-restraints excluded: chain W residue 198 SER Chi-restraints excluded: chain W residue 307 VAL Chi-restraints excluded: chain W residue 361 ILE Chi-restraints excluded: chain W residue 371 LYS Chi-restraints excluded: chain W residue 390 ASP Chi-restraints excluded: chain W residue 420 CYS Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 100 ASP Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain H residue 184 VAL Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 182 SER Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain E residue 27 GLN Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain E residue 174 SER Chi-restraints excluded: chain E residue 182 SER Chi-restraints excluded: chain E residue 202 SER Chi-restraints excluded: chain G residue 27 GLN Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 76 SER Chi-restraints excluded: chain G residue 79 GLU Chi-restraints excluded: chain G residue 202 SER Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 76 SER Chi-restraints excluded: chain L residue 202 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 102 optimal weight: 5.9990 chunk 275 optimal weight: 10.0000 chunk 60 optimal weight: 1.9990 chunk 179 optimal weight: 20.0000 chunk 75 optimal weight: 0.9990 chunk 305 optimal weight: 9.9990 chunk 253 optimal weight: 10.0000 chunk 141 optimal weight: 0.6980 chunk 25 optimal weight: 6.9990 chunk 101 optimal weight: 0.7980 chunk 160 optimal weight: 6.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 329 ASN ** I 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 6 GLN B 27 GLN B 166 GLN E 6 GLN E 27 GLN ** E 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 166 GLN ** G 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 160 GLN G 166 GLN L 6 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.3227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 25376 Z= 0.265 Angle : 0.596 7.540 34384 Z= 0.312 Chirality : 0.044 0.185 3808 Planarity : 0.005 0.055 4380 Dihedral : 5.453 37.058 3702 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 3.03 % Allowed : 23.71 % Favored : 73.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.14), residues: 3148 helix: -4.10 (0.22), residues: 32 sheet: -0.47 (0.14), residues: 1284 loop : -1.74 (0.13), residues: 1832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 47 HIS 0.003 0.001 HIS E 198 PHE 0.035 0.002 PHE A 100C TYR 0.025 0.002 TYR B 140 ARG 0.004 0.000 ARG L 24 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 2708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 294 time to evaluate : 2.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 371 LYS cc_start: 0.9258 (OUTLIER) cc_final: 0.8807 (ptpp) REVERT: N 429 MET cc_start: 0.9159 (mtp) cc_final: 0.8878 (mtm) REVERT: W 371 LYS cc_start: 0.9273 (OUTLIER) cc_final: 0.8771 (ptpp) REVERT: W 429 MET cc_start: 0.9159 (mtp) cc_final: 0.8873 (mtm) REVERT: A 72 ASP cc_start: 0.8116 (t70) cc_final: 0.7676 (t70) REVERT: A 184 VAL cc_start: 0.8540 (OUTLIER) cc_final: 0.8304 (p) REVERT: C 30 ILE cc_start: 0.9091 (tt) cc_final: 0.8843 (tp) REVERT: C 43 GLN cc_start: 0.8302 (mt0) cc_final: 0.8021 (tt0) REVERT: C 72 ASP cc_start: 0.8060 (t70) cc_final: 0.7579 (t70) REVERT: D 72 ASP cc_start: 0.8080 (t70) cc_final: 0.7591 (t70) REVERT: D 145 TYR cc_start: 0.7301 (p90) cc_final: 0.6614 (p90) REVERT: H 30 ILE cc_start: 0.9121 (tt) cc_final: 0.8876 (tp) REVERT: H 72 ASP cc_start: 0.8095 (t70) cc_final: 0.7644 (t70) REVERT: H 184 VAL cc_start: 0.8312 (OUTLIER) cc_final: 0.8103 (p) REVERT: B 108 ARG cc_start: 0.7745 (ptm160) cc_final: 0.7045 (ptm-80) REVERT: L 108 ARG cc_start: 0.7697 (ptm160) cc_final: 0.7098 (ptm-80) outliers start: 82 outliers final: 47 residues processed: 365 average time/residue: 1.3440 time to fit residues: 565.6138 Evaluate side-chains 333 residues out of total 2708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 282 time to evaluate : 3.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 182 CYS Chi-restraints excluded: chain I residue 198 SER Chi-restraints excluded: chain I residue 229 CYS Chi-restraints excluded: chain I residue 337 CYS Chi-restraints excluded: chain I residue 361 ILE Chi-restraints excluded: chain M residue 198 SER Chi-restraints excluded: chain M residue 361 ILE Chi-restraints excluded: chain M residue 390 ASP Chi-restraints excluded: chain N residue 198 SER Chi-restraints excluded: chain N residue 361 ILE Chi-restraints excluded: chain N residue 371 LYS Chi-restraints excluded: chain N residue 390 ASP Chi-restraints excluded: chain W residue 198 SER Chi-restraints excluded: chain W residue 361 ILE Chi-restraints excluded: chain W residue 371 LYS Chi-restraints excluded: chain W residue 390 ASP Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 100 ASP Chi-restraints excluded: chain H residue 184 VAL Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 79 GLU Chi-restraints excluded: chain B residue 182 SER Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain E residue 27 GLN Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 182 SER Chi-restraints excluded: chain E residue 202 SER Chi-restraints excluded: chain G residue 27 GLN Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 76 SER Chi-restraints excluded: chain G residue 202 SER Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 76 SER Chi-restraints excluded: chain L residue 202 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 294 optimal weight: 40.0000 chunk 34 optimal weight: 8.9990 chunk 174 optimal weight: 10.0000 chunk 223 optimal weight: 10.0000 chunk 172 optimal weight: 3.9990 chunk 257 optimal weight: 2.9990 chunk 170 optimal weight: 4.9990 chunk 304 optimal weight: 3.9990 chunk 190 optimal weight: 6.9990 chunk 185 optimal weight: 8.9990 chunk 140 optimal weight: 1.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 101 HIS ** M 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 6 GLN E 6 GLN E 27 GLN ** E 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 166 GLN ** G 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN L 160 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.3380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 25376 Z= 0.409 Angle : 0.648 12.360 34384 Z= 0.337 Chirality : 0.046 0.180 3808 Planarity : 0.005 0.053 4380 Dihedral : 5.530 35.730 3702 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 3.62 % Allowed : 23.60 % Favored : 72.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.14), residues: 3148 helix: -4.42 (0.20), residues: 56 sheet: -0.35 (0.14), residues: 1316 loop : -1.79 (0.13), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 47 HIS 0.008 0.001 HIS M 101 PHE 0.032 0.002 PHE H 100C TYR 0.024 0.002 TYR L 140 ARG 0.007 0.001 ARG G 108 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 2708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 281 time to evaluate : 2.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 116 ARG cc_start: 0.7842 (OUTLIER) cc_final: 0.5657 (tmm160) REVERT: M 116 ARG cc_start: 0.7840 (OUTLIER) cc_final: 0.5628 (tmm160) REVERT: N 371 LYS cc_start: 0.9290 (OUTLIER) cc_final: 0.8782 (ptpp) REVERT: N 429 MET cc_start: 0.9189 (mtp) cc_final: 0.8901 (mtm) REVERT: W 371 LYS cc_start: 0.9285 (OUTLIER) cc_final: 0.8769 (ptpp) REVERT: W 429 MET cc_start: 0.9188 (mtp) cc_final: 0.8891 (mtm) REVERT: A 72 ASP cc_start: 0.8170 (t70) cc_final: 0.7733 (t70) REVERT: A 184 VAL cc_start: 0.8557 (OUTLIER) cc_final: 0.8332 (p) REVERT: C 30 ILE cc_start: 0.9113 (tt) cc_final: 0.8854 (tp) REVERT: C 46 GLU cc_start: 0.8007 (tt0) cc_final: 0.7759 (tt0) REVERT: C 72 ASP cc_start: 0.8122 (t70) cc_final: 0.7687 (t70) REVERT: C 100 ASP cc_start: 0.7905 (OUTLIER) cc_final: 0.7423 (m-30) REVERT: D 72 ASP cc_start: 0.8122 (t70) cc_final: 0.7690 (t70) REVERT: D 145 TYR cc_start: 0.7407 (p90) cc_final: 0.6793 (p90) REVERT: H 30 ILE cc_start: 0.9108 (tt) cc_final: 0.8849 (tp) REVERT: H 72 ASP cc_start: 0.8143 (t70) cc_final: 0.7698 (t70) REVERT: H 184 VAL cc_start: 0.8253 (OUTLIER) cc_final: 0.8046 (p) REVERT: B 108 ARG cc_start: 0.7813 (ptm160) cc_final: 0.7135 (ptm-80) REVERT: L 108 ARG cc_start: 0.7691 (ptm160) cc_final: 0.7419 (ptt90) REVERT: L 140 TYR cc_start: 0.7276 (t80) cc_final: 0.6942 (t80) outliers start: 98 outliers final: 63 residues processed: 362 average time/residue: 1.3872 time to fit residues: 576.5859 Evaluate side-chains 345 residues out of total 2708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 275 time to evaluate : 2.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 116 ARG Chi-restraints excluded: chain I residue 146 THR Chi-restraints excluded: chain I residue 182 CYS Chi-restraints excluded: chain I residue 198 SER Chi-restraints excluded: chain I residue 229 CYS Chi-restraints excluded: chain I residue 337 CYS Chi-restraints excluded: chain I residue 359 SER Chi-restraints excluded: chain I residue 361 ILE Chi-restraints excluded: chain M residue 116 ARG Chi-restraints excluded: chain M residue 146 THR Chi-restraints excluded: chain M residue 198 SER Chi-restraints excluded: chain M residue 361 ILE Chi-restraints excluded: chain M residue 390 ASP Chi-restraints excluded: chain M residue 420 CYS Chi-restraints excluded: chain N residue 146 THR Chi-restraints excluded: chain N residue 198 SER Chi-restraints excluded: chain N residue 361 ILE Chi-restraints excluded: chain N residue 371 LYS Chi-restraints excluded: chain N residue 390 ASP Chi-restraints excluded: chain N residue 420 CYS Chi-restraints excluded: chain W residue 146 THR Chi-restraints excluded: chain W residue 198 SER Chi-restraints excluded: chain W residue 361 ILE Chi-restraints excluded: chain W residue 371 LYS Chi-restraints excluded: chain W residue 390 ASP Chi-restraints excluded: chain W residue 420 CYS Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 100 ASP Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain H residue 184 VAL Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 182 SER Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 182 SER Chi-restraints excluded: chain E residue 202 SER Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 76 SER Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 202 SER Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 76 SER Chi-restraints excluded: chain L residue 198 HIS Chi-restraints excluded: chain L residue 202 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 188 optimal weight: 5.9990 chunk 121 optimal weight: 0.9980 chunk 181 optimal weight: 10.0000 chunk 91 optimal weight: 2.9990 chunk 59 optimal weight: 0.6980 chunk 193 optimal weight: 0.8980 chunk 207 optimal weight: 6.9990 chunk 150 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 239 optimal weight: 9.9990 chunk 277 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 101 HIS M 101 HIS ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 166 GLN ** G 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.3529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25376 Z= 0.173 Angle : 0.579 10.084 34384 Z= 0.301 Chirality : 0.043 0.210 3808 Planarity : 0.005 0.083 4380 Dihedral : 4.995 38.432 3702 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.40 % Allowed : 25.22 % Favored : 72.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.14), residues: 3148 helix: -4.42 (0.19), residues: 56 sheet: -0.33 (0.14), residues: 1296 loop : -1.63 (0.13), residues: 1796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 148 HIS 0.008 0.001 HIS M 101 PHE 0.028 0.002 PHE B 116 TYR 0.023 0.001 TYR G 173 ARG 0.005 0.000 ARG G 108 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 2708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 292 time to evaluate : 3.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 429 MET cc_start: 0.9149 (mtp) cc_final: 0.8916 (mtm) REVERT: M 400 MET cc_start: 0.8858 (mtt) cc_final: 0.8526 (mtt) REVERT: N 371 LYS cc_start: 0.9256 (OUTLIER) cc_final: 0.8737 (ptpp) REVERT: W 400 MET cc_start: 0.8873 (mtt) cc_final: 0.8517 (mtt) REVERT: A 72 ASP cc_start: 0.8127 (t70) cc_final: 0.7663 (t70) REVERT: C 30 ILE cc_start: 0.9082 (tt) cc_final: 0.8832 (tp) REVERT: C 43 GLN cc_start: 0.8307 (mt0) cc_final: 0.8053 (tt0) REVERT: C 72 ASP cc_start: 0.8078 (t70) cc_final: 0.7650 (t70) REVERT: D 30 ILE cc_start: 0.9043 (tt) cc_final: 0.8823 (tp) REVERT: D 72 ASP cc_start: 0.8085 (t70) cc_final: 0.7646 (t70) REVERT: D 145 TYR cc_start: 0.7296 (p90) cc_final: 0.6605 (p90) REVERT: H 30 ILE cc_start: 0.9077 (tt) cc_final: 0.8828 (tp) REVERT: H 72 ASP cc_start: 0.8100 (t70) cc_final: 0.7661 (t70) REVERT: B 108 ARG cc_start: 0.7880 (OUTLIER) cc_final: 0.7644 (ptt90) REVERT: B 140 TYR cc_start: 0.7035 (t80) cc_final: 0.6833 (t80) REVERT: E 191 VAL cc_start: 0.5831 (OUTLIER) cc_final: 0.5381 (t) REVERT: L 108 ARG cc_start: 0.7639 (ptm160) cc_final: 0.7401 (ptt90) outliers start: 65 outliers final: 39 residues processed: 345 average time/residue: 1.4257 time to fit residues: 563.3465 Evaluate side-chains 319 residues out of total 2708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 277 time to evaluate : 2.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 182 CYS Chi-restraints excluded: chain I residue 198 SER Chi-restraints excluded: chain I residue 229 CYS Chi-restraints excluded: chain I residue 359 SER Chi-restraints excluded: chain I residue 361 ILE Chi-restraints excluded: chain I residue 419 LYS Chi-restraints excluded: chain M residue 198 SER Chi-restraints excluded: chain M residue 361 ILE Chi-restraints excluded: chain N residue 198 SER Chi-restraints excluded: chain N residue 371 LYS Chi-restraints excluded: chain N residue 390 ASP Chi-restraints excluded: chain W residue 198 SER Chi-restraints excluded: chain W residue 390 ASP Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 100 ASP Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain B residue 108 ARG Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 182 SER Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 202 SER Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 76 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 291 optimal weight: 20.0000 chunk 266 optimal weight: 50.0000 chunk 283 optimal weight: 0.0670 chunk 170 optimal weight: 9.9990 chunk 123 optimal weight: 5.9990 chunk 222 optimal weight: 10.0000 chunk 87 optimal weight: 5.9990 chunk 256 optimal weight: 8.9990 chunk 268 optimal weight: 9.9990 chunk 282 optimal weight: 0.9990 chunk 186 optimal weight: 9.9990 overall best weight: 4.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 101 HIS ** I 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 101 HIS ** M 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 101 HIS ** N 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 101 HIS ** W 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 6 GLN E 6 GLN ** E 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 166 GLN ** G 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.3594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.081 25376 Z= 0.479 Angle : 0.682 10.131 34384 Z= 0.354 Chirality : 0.047 0.181 3808 Planarity : 0.005 0.077 4380 Dihedral : 5.435 35.750 3702 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 2.77 % Allowed : 25.44 % Favored : 71.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.14), residues: 3148 helix: -4.29 (0.22), residues: 56 sheet: -0.31 (0.14), residues: 1312 loop : -1.71 (0.13), residues: 1780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 47 HIS 0.009 0.001 HIS N 101 PHE 0.038 0.002 PHE H 100C TYR 0.030 0.002 TYR E 173 ARG 0.005 0.001 ARG G 24 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 270 time to evaluate : 3.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 371 LYS cc_start: 0.9293 (OUTLIER) cc_final: 0.8790 (ptpp) REVERT: A 72 ASP cc_start: 0.8198 (t70) cc_final: 0.7773 (t70) REVERT: C 72 ASP cc_start: 0.8181 (t70) cc_final: 0.7750 (t70) REVERT: D 30 ILE cc_start: 0.9096 (tt) cc_final: 0.8867 (tp) REVERT: D 72 ASP cc_start: 0.8156 (t70) cc_final: 0.7766 (t70) REVERT: D 145 TYR cc_start: 0.7495 (p90) cc_final: 0.6836 (p90) REVERT: H 72 ASP cc_start: 0.8182 (t70) cc_final: 0.7753 (t70) REVERT: B 108 ARG cc_start: 0.7818 (OUTLIER) cc_final: 0.7578 (ptt90) REVERT: L 108 ARG cc_start: 0.7728 (ptm160) cc_final: 0.7527 (ptt90) outliers start: 75 outliers final: 50 residues processed: 334 average time/residue: 1.3872 time to fit residues: 533.7184 Evaluate side-chains 320 residues out of total 2708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 268 time to evaluate : 3.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 87 CYS Chi-restraints excluded: chain I residue 182 CYS Chi-restraints excluded: chain I residue 198 SER Chi-restraints excluded: chain I residue 229 CYS Chi-restraints excluded: chain I residue 307 VAL Chi-restraints excluded: chain I residue 359 SER Chi-restraints excluded: chain I residue 361 ILE Chi-restraints excluded: chain M residue 198 SER Chi-restraints excluded: chain M residue 307 VAL Chi-restraints excluded: chain M residue 361 ILE Chi-restraints excluded: chain N residue 198 SER Chi-restraints excluded: chain N residue 307 VAL Chi-restraints excluded: chain N residue 371 LYS Chi-restraints excluded: chain N residue 390 ASP Chi-restraints excluded: chain W residue 198 SER Chi-restraints excluded: chain W residue 307 VAL Chi-restraints excluded: chain W residue 390 ASP Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 100 ASP Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 108 ARG Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain E residue 27 GLN Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain E residue 182 SER Chi-restraints excluded: chain E residue 202 SER Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 202 SER Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 76 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 300 optimal weight: 5.9990 chunk 183 optimal weight: 8.9990 chunk 142 optimal weight: 0.6980 chunk 208 optimal weight: 10.0000 chunk 314 optimal weight: 7.9990 chunk 289 optimal weight: 9.9990 chunk 250 optimal weight: 30.0000 chunk 26 optimal weight: 0.9990 chunk 193 optimal weight: 2.9990 chunk 153 optimal weight: 2.9990 chunk 199 optimal weight: 1.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 101 HIS N 101 HIS W 101 HIS ** E 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 166 GLN ** G 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.3670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 25376 Z= 0.255 Angle : 0.610 9.795 34384 Z= 0.317 Chirality : 0.044 0.176 3808 Planarity : 0.005 0.085 4380 Dihedral : 5.145 37.040 3702 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.85 % Allowed : 26.18 % Favored : 71.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.14), residues: 3148 helix: -4.19 (0.24), residues: 56 sheet: -0.22 (0.14), residues: 1316 loop : -1.64 (0.13), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 47 HIS 0.010 0.001 HIS W 101 PHE 0.036 0.002 PHE D 100C TYR 0.022 0.001 TYR G 173 ARG 0.009 0.001 ARG G 108 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 282 time to evaluate : 2.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 371 LYS cc_start: 0.9263 (OUTLIER) cc_final: 0.8707 (ptpp) REVERT: A 72 ASP cc_start: 0.8161 (t70) cc_final: 0.7730 (t70) REVERT: C 43 GLN cc_start: 0.8323 (mt0) cc_final: 0.8056 (tt0) REVERT: C 72 ASP cc_start: 0.8148 (t70) cc_final: 0.7718 (t70) REVERT: D 30 ILE cc_start: 0.9076 (tt) cc_final: 0.8858 (tp) REVERT: D 72 ASP cc_start: 0.8151 (t70) cc_final: 0.7713 (t70) REVERT: H 72 ASP cc_start: 0.8168 (t70) cc_final: 0.7727 (t70) outliers start: 50 outliers final: 35 residues processed: 324 average time/residue: 1.3915 time to fit residues: 517.8262 Evaluate side-chains 309 residues out of total 2708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 273 time to evaluate : 3.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 87 CYS Chi-restraints excluded: chain I residue 182 CYS Chi-restraints excluded: chain I residue 198 SER Chi-restraints excluded: chain I residue 229 CYS Chi-restraints excluded: chain I residue 359 SER Chi-restraints excluded: chain M residue 198 SER Chi-restraints excluded: chain N residue 198 SER Chi-restraints excluded: chain N residue 371 LYS Chi-restraints excluded: chain W residue 198 SER Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 100 ASP Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 182 SER Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 202 SER Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 76 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 267 optimal weight: 7.9990 chunk 76 optimal weight: 4.9990 chunk 231 optimal weight: 8.9990 chunk 37 optimal weight: 0.4980 chunk 69 optimal weight: 4.9990 chunk 251 optimal weight: 20.0000 chunk 105 optimal weight: 4.9990 chunk 257 optimal weight: 0.9990 chunk 31 optimal weight: 6.9990 chunk 46 optimal weight: 1.9990 chunk 220 optimal weight: 4.9990 overall best weight: 2.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 101 HIS N 101 HIS W 101 HIS ** E 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.143078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.082303 restraints weight = 36130.736| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 2.36 r_work: 0.2869 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2735 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2726 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2726 r_free = 0.2726 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2726 r_free = 0.2726 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2726 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.3734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 25376 Z= 0.328 Angle : 0.638 9.549 34384 Z= 0.330 Chirality : 0.045 0.210 3808 Planarity : 0.005 0.075 4380 Dihedral : 5.181 36.485 3702 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 1.96 % Allowed : 26.81 % Favored : 71.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.14), residues: 3148 helix: -4.09 (0.27), residues: 56 sheet: -0.13 (0.14), residues: 1300 loop : -1.64 (0.13), residues: 1792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 47 HIS 0.009 0.001 HIS N 101 PHE 0.041 0.002 PHE A 100C TYR 0.021 0.002 TYR G 173 ARG 0.009 0.001 ARG G 108 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10194.58 seconds wall clock time: 180 minutes 9.11 seconds (10809.11 seconds total)