Starting phenix.real_space_refine on Sun Feb 18 09:42:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mcs_23757/02_2024/7mcs_23757_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mcs_23757/02_2024/7mcs_23757.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mcs_23757/02_2024/7mcs_23757.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mcs_23757/02_2024/7mcs_23757.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mcs_23757/02_2024/7mcs_23757_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mcs_23757/02_2024/7mcs_23757_updated.pdb" } resolution = 3.56 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= 0.003 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: 6 Type Number sf(0) Gaussians P 48 5.49 5 Mg 6 5.21 5 S 81 5.16 5 C 13494 2.51 5 N 3913 2.21 5 O 4058 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 12": "OD1" <-> "OD2" Residue "B GLU 182": "OE1" <-> "OE2" Residue "B ASP 278": "OD1" <-> "OD2" Residue "B ASP 294": "OD1" <-> "OD2" Residue "B GLU 307": "OE1" <-> "OE2" Residue "C GLU 118": "OE1" <-> "OE2" Residue "C GLU 200": "OE1" <-> "OE2" Residue "C TYR 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 387": "OE1" <-> "OE2" Residue "D GLU 25": "OE1" <-> "OE2" Residue "D TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 307": "OE1" <-> "OE2" Residue "E GLU 233": "OE1" <-> "OE2" Residue "F ASP 313": "OD1" <-> "OD2" Residue "F GLU 387": "OE1" <-> "OE2" Residue "G GLU 16": "OE1" <-> "OE2" Residue "G GLU 81": "OE1" <-> "OE2" Residue "G GLU 161": "OE1" <-> "OE2" Residue "G TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 276": "OE1" <-> "OE2" Residue "G TYR 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 377": "OD1" <-> "OD2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 21600 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 1967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1967 Classifications: {'peptide': 249} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 240} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 3196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3196 Classifications: {'peptide': 402} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 386} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 3208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 3208 Classifications: {'peptide': 404} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 388} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 3201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 3201 Classifications: {'peptide': 403} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 388} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 3196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3196 Classifications: {'peptide': 402} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 387} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "F" Number of atoms: 3183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3183 Classifications: {'peptide': 401} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 14, 'TRANS': 386} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 2842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2842 Classifications: {'peptide': 358} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 342} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "H" Number of atoms: 306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 306 Classifications: {'DNA': 15} Link IDs: {'rna3p': 14} Chain: "I" Number of atoms: 309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 309 Classifications: {'DNA': 15} Link IDs: {'rna3p': 14} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 11.35, per 1000 atoms: 0.53 Number of scatterers: 21600 At special positions: 0 Unit cell: (150.48, 153.9, 99.18, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 81 16.00 P 48 15.00 Mg 6 11.99 O 4058 8.00 N 3913 7.00 C 13494 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.22 Conformation dependent library (CDL) restraints added in 3.7 seconds 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4872 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 128 helices and 13 sheets defined 47.3% alpha, 5.3% beta 15 base pairs and 25 stacking pairs defined. Time for finding SS restraints: 7.94 Creating SS restraints... Processing helix chain 'A' and resid 22 through 25 No H-bonds generated for 'chain 'A' and resid 22 through 25' Processing helix chain 'A' and resid 76 through 94 removed outlier: 3.654A pdb=" N GLY A 93 " --> pdb=" O GLY A 89 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ARG A 94 " --> pdb=" O GLY A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 114 Processing helix chain 'A' and resid 142 through 152 removed outlier: 3.544A pdb=" N THR A 152 " --> pdb=" O ARG A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 194 removed outlier: 3.957A pdb=" N CYS A 184 " --> pdb=" O LEU A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 202 No H-bonds generated for 'chain 'A' and resid 199 through 202' Processing helix chain 'A' and resid 212 through 223 Processing helix chain 'A' and resid 234 through 239 removed outlier: 3.955A pdb=" N ARG A 239 " --> pdb=" O HIS A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 257 Processing helix chain 'A' and resid 269 through 276 removed outlier: 3.840A pdb=" N ARG A 272 " --> pdb=" O PRO A 269 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLU A 273 " --> pdb=" O LYS A 270 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ILE A 274 " --> pdb=" O ALA A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 284 Processing helix chain 'B' and resid 22 through 25 No H-bonds generated for 'chain 'B' and resid 22 through 25' Processing helix chain 'B' and resid 33 through 38 Processing helix chain 'B' and resid 48 through 51 Processing helix chain 'B' and resid 55 through 62 Processing helix chain 'B' and resid 65 through 68 No H-bonds generated for 'chain 'B' and resid 65 through 68' Processing helix chain 'B' and resid 75 through 90 removed outlier: 4.036A pdb=" N SER B 80 " --> pdb=" O LEU B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 113 Processing helix chain 'B' and resid 144 through 150 Processing helix chain 'B' and resid 180 through 194 removed outlier: 3.612A pdb=" N LEU B 185 " --> pdb=" O LYS B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 203 Processing helix chain 'B' and resid 210 through 223 removed outlier: 3.716A pdb=" N ALA B 215 " --> pdb=" O GLU B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 237 Processing helix chain 'B' and resid 242 through 255 removed outlier: 4.430A pdb=" N SER B 245 " --> pdb=" O SER B 242 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N GLN B 246 " --> pdb=" O GLY B 243 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N MET B 248 " --> pdb=" O SER B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 272 Processing helix chain 'B' and resid 280 through 285 removed outlier: 4.045A pdb=" N GLY B 285 " --> pdb=" O SER B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 317 removed outlier: 3.849A pdb=" N GLN B 317 " --> pdb=" O ASP B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 340 Processing helix chain 'B' and resid 344 through 361 Processing helix chain 'B' and resid 368 through 378 Processing helix chain 'B' and resid 383 through 391 removed outlier: 4.701A pdb=" N ALA B 388 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LEU B 389 " --> pdb=" O MET B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 399 Processing helix chain 'C' and resid 16 through 18 No H-bonds generated for 'chain 'C' and resid 16 through 18' Processing helix chain 'C' and resid 33 through 39 Processing helix chain 'C' and resid 48 through 51 No H-bonds generated for 'chain 'C' and resid 48 through 51' Processing helix chain 'C' and resid 55 through 62 Processing helix chain 'C' and resid 65 through 68 No H-bonds generated for 'chain 'C' and resid 65 through 68' Processing helix chain 'C' and resid 75 through 90 removed outlier: 3.559A pdb=" N LEU C 79 " --> pdb=" O HIS C 76 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N SER C 80 " --> pdb=" O LEU C 77 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU C 81 " --> pdb=" O LEU C 78 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE C 83 " --> pdb=" O SER C 80 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N MET C 86 " --> pdb=" O ILE C 83 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ILE C 87 " --> pdb=" O SER C 84 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG C 88 " --> pdb=" O VAL C 85 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLY C 89 " --> pdb=" O MET C 86 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY C 90 " --> pdb=" O ILE C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 113 Processing helix chain 'C' and resid 142 through 152 removed outlier: 4.184A pdb=" N THR C 152 " --> pdb=" O ARG C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 194 removed outlier: 4.011A pdb=" N CYS C 184 " --> pdb=" O LEU C 180 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N LEU C 185 " --> pdb=" O LYS C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 203 Processing helix chain 'C' and resid 211 through 223 removed outlier: 4.369A pdb=" N LEU C 216 " --> pdb=" O THR C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 236 No H-bonds generated for 'chain 'C' and resid 234 through 236' Processing helix chain 'C' and resid 246 through 258 Processing helix chain 'C' and resid 269 through 271 No H-bonds generated for 'chain 'C' and resid 269 through 271' Processing helix chain 'C' and resid 280 through 283 No H-bonds generated for 'chain 'C' and resid 280 through 283' Processing helix chain 'C' and resid 306 through 316 Processing helix chain 'C' and resid 330 through 340 removed outlier: 3.837A pdb=" N VAL C 335 " --> pdb=" O GLU C 331 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TRP C 336 " --> pdb=" O VAL C 332 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N TYR C 337 " --> pdb=" O ARG C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 344 through 361 removed outlier: 4.075A pdb=" N VAL C 348 " --> pdb=" O MET C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 378 removed outlier: 3.714A pdb=" N ARG C 372 " --> pdb=" O ALA C 368 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ASP C 377 " --> pdb=" O GLN C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 391 Proline residue: C 384 - end of helix removed outlier: 3.604A pdb=" N GLU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ALA C 388 " --> pdb=" O MET C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 394 through 399 removed outlier: 3.939A pdb=" N ARG C 399 " --> pdb=" O GLU C 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 40 removed outlier: 3.544A pdb=" N SER D 39 " --> pdb=" O ASN D 35 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LEU D 40 " --> pdb=" O SER D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 51 removed outlier: 3.730A pdb=" N LEU D 51 " --> pdb=" O SER D 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 48 through 51' Processing helix chain 'D' and resid 55 through 67 removed outlier: 3.652A pdb=" N ARG D 64 " --> pdb=" O HIS D 60 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ILE D 65 " --> pdb=" O THR D 61 " (cutoff:3.500A) Proline residue: D 66 - end of helix Processing helix chain 'D' and resid 74 through 89 removed outlier: 3.856A pdb=" N LEU D 77 " --> pdb=" O GLY D 74 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N LEU D 78 " --> pdb=" O THR D 75 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU D 79 " --> pdb=" O HIS D 76 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ILE D 87 " --> pdb=" O SER D 84 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLY D 89 " --> pdb=" O MET D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 94 No H-bonds generated for 'chain 'D' and resid 92 through 94' Processing helix chain 'D' and resid 102 through 112 Processing helix chain 'D' and resid 142 through 152 removed outlier: 4.038A pdb=" N ALA D 151 " --> pdb=" O HIS D 147 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N THR D 152 " --> pdb=" O ARG D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 194 removed outlier: 3.900A pdb=" N CYS D 184 " --> pdb=" O LEU D 180 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LEU D 185 " --> pdb=" O LYS D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 204 Processing helix chain 'D' and resid 210 through 223 removed outlier: 3.675A pdb=" N ALA D 215 " --> pdb=" O GLU D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 234 through 238 Processing helix chain 'D' and resid 245 through 257 Processing helix chain 'D' and resid 269 through 273 removed outlier: 3.966A pdb=" N GLU D 273 " --> pdb=" O LYS D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 285 Processing helix chain 'D' and resid 306 through 316 Processing helix chain 'D' and resid 330 through 340 removed outlier: 3.524A pdb=" N LEU D 339 " --> pdb=" O VAL D 335 " (cutoff:3.500A) Processing helix chain 'D' and resid 344 through 361 removed outlier: 3.812A pdb=" N VAL D 348 " --> pdb=" O MET D 344 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N PHE D 351 " --> pdb=" O VAL D 347 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 377 Processing helix chain 'D' and resid 383 through 391 Processing helix chain 'D' and resid 394 through 397 No H-bonds generated for 'chain 'D' and resid 394 through 397' Processing helix chain 'E' and resid 22 through 25 No H-bonds generated for 'chain 'E' and resid 22 through 25' Processing helix chain 'E' and resid 33 through 40 removed outlier: 4.009A pdb=" N ALA E 37 " --> pdb=" O SER E 33 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ALA E 38 " --> pdb=" O VAL E 34 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N SER E 39 " --> pdb=" O ASN E 35 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LEU E 40 " --> pdb=" O SER E 36 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 33 through 40' Processing helix chain 'E' and resid 48 through 51 removed outlier: 3.606A pdb=" N LEU E 51 " --> pdb=" O SER E 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 48 through 51' Processing helix chain 'E' and resid 55 through 68 removed outlier: 3.932A pdb=" N ARG E 64 " --> pdb=" O HIS E 60 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ILE E 65 " --> pdb=" O THR E 61 " (cutoff:3.500A) Proline residue: E 66 - end of helix Processing helix chain 'E' and resid 76 through 89 Processing helix chain 'E' and resid 102 through 113 removed outlier: 3.569A pdb=" N GLN E 106 " --> pdb=" O GLN E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 150 Processing helix chain 'E' and resid 180 through 194 removed outlier: 3.892A pdb=" N CYS E 184 " --> pdb=" O LEU E 180 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU E 185 " --> pdb=" O LYS E 181 " (cutoff:3.500A) Processing helix chain 'E' and resid 200 through 203 No H-bonds generated for 'chain 'E' and resid 200 through 203' Processing helix chain 'E' and resid 210 through 223 removed outlier: 4.091A pdb=" N ALA E 215 " --> pdb=" O GLU E 211 " (cutoff:3.500A) Processing helix chain 'E' and resid 234 through 238 removed outlier: 4.281A pdb=" N SER E 238 " --> pdb=" O GLN E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 246 through 257 removed outlier: 3.695A pdb=" N PHE E 251 " --> pdb=" O GLU E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 271 No H-bonds generated for 'chain 'E' and resid 269 through 271' Processing helix chain 'E' and resid 279 through 285 Processing helix chain 'E' and resid 306 through 318 removed outlier: 3.812A pdb=" N GLN E 317 " --> pdb=" O ASP E 313 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N LEU E 318 " --> pdb=" O ASN E 314 " (cutoff:3.500A) Processing helix chain 'E' and resid 330 through 340 Processing helix chain 'E' and resid 344 through 361 Processing helix chain 'E' and resid 368 through 378 removed outlier: 3.568A pdb=" N GLN E 376 " --> pdb=" O ARG E 372 " (cutoff:3.500A) Processing helix chain 'E' and resid 381 through 390 Proline residue: E 384 - end of helix removed outlier: 3.976A pdb=" N ARG E 390 " --> pdb=" O GLU E 387 " (cutoff:3.500A) Processing helix chain 'E' and resid 394 through 397 No H-bonds generated for 'chain 'E' and resid 394 through 397' Processing helix chain 'F' and resid 22 through 25 No H-bonds generated for 'chain 'F' and resid 22 through 25' Processing helix chain 'F' and resid 33 through 39 Processing helix chain 'F' and resid 48 through 51 No H-bonds generated for 'chain 'F' and resid 48 through 51' Processing helix chain 'F' and resid 55 through 64 removed outlier: 3.793A pdb=" N ILE F 62 " --> pdb=" O ARG F 58 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N CYS F 63 " --> pdb=" O ALA F 59 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ARG F 64 " --> pdb=" O HIS F 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 94 removed outlier: 3.510A pdb=" N LEU F 79 " --> pdb=" O THR F 75 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLY F 90 " --> pdb=" O MET F 86 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N TYR F 91 " --> pdb=" O ILE F 87 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N VAL F 92 " --> pdb=" O ARG F 88 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N GLY F 93 " --> pdb=" O GLY F 89 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ARG F 94 " --> pdb=" O GLY F 90 " (cutoff:3.500A) Processing helix chain 'F' and resid 101 through 113 removed outlier: 3.673A pdb=" N GLN F 113 " --> pdb=" O TYR F 109 " (cutoff:3.500A) Processing helix chain 'F' and resid 146 through 150 Processing helix chain 'F' and resid 182 through 194 removed outlier: 3.793A pdb=" N PHE F 188 " --> pdb=" O CYS F 184 " (cutoff:3.500A) Processing helix chain 'F' and resid 210 through 223 removed outlier: 3.632A pdb=" N ALA F 215 " --> pdb=" O GLU F 211 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER F 218 " --> pdb=" O LEU F 214 " (cutoff:3.500A) Processing helix chain 'F' and resid 234 through 237 removed outlier: 3.563A pdb=" N LEU F 237 " --> pdb=" O ILE F 234 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 234 through 237' Processing helix chain 'F' and resid 244 through 257 Processing helix chain 'F' and resid 269 through 275 removed outlier: 4.097A pdb=" N GLU F 273 " --> pdb=" O LYS F 270 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ILE F 274 " --> pdb=" O ALA F 271 " (cutoff:3.500A) Processing helix chain 'F' and resid 279 through 286 removed outlier: 3.878A pdb=" N ALA F 286 " --> pdb=" O ALA F 282 " (cutoff:3.500A) Processing helix chain 'F' and resid 306 through 317 removed outlier: 3.630A pdb=" N GLN F 317 " --> pdb=" O ASP F 313 " (cutoff:3.500A) Processing helix chain 'F' and resid 330 through 340 removed outlier: 3.741A pdb=" N GLU F 338 " --> pdb=" O ASP F 334 " (cutoff:3.500A) Processing helix chain 'F' and resid 344 through 359 removed outlier: 3.557A pdb=" N VAL F 348 " --> pdb=" O MET F 344 " (cutoff:3.500A) Processing helix chain 'F' and resid 368 through 378 Processing helix chain 'F' and resid 380 through 391 Proline residue: F 384 - end of helix removed outlier: 3.551A pdb=" N SER F 391 " --> pdb=" O ALA F 388 " (cutoff:3.500A) Processing helix chain 'F' and resid 394 through 399 Processing helix chain 'G' and resid 33 through 40 Processing helix chain 'G' and resid 48 through 51 No H-bonds generated for 'chain 'G' and resid 48 through 51' Processing helix chain 'G' and resid 55 through 63 Processing helix chain 'G' and resid 74 through 94 removed outlier: 3.544A pdb=" N LEU G 77 " --> pdb=" O GLY G 74 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ILE G 87 " --> pdb=" O SER G 84 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLY G 90 " --> pdb=" O ILE G 87 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLY G 93 " --> pdb=" O GLY G 90 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG G 94 " --> pdb=" O TYR G 91 " (cutoff:3.500A) Processing helix chain 'G' and resid 142 through 152 removed outlier: 3.917A pdb=" N LEU G 146 " --> pdb=" O LYS G 142 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N THR G 152 " --> pdb=" O ARG G 148 " (cutoff:3.500A) Processing helix chain 'G' and resid 180 through 194 removed outlier: 3.680A pdb=" N PHE G 187 " --> pdb=" O ILE G 183 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N PHE G 188 " --> pdb=" O CYS G 184 " (cutoff:3.500A) Processing helix chain 'G' and resid 199 through 202 No H-bonds generated for 'chain 'G' and resid 199 through 202' Processing helix chain 'G' and resid 213 through 223 Processing helix chain 'G' and resid 246 through 258 removed outlier: 3.506A pdb=" N PHE G 251 " --> pdb=" O GLU G 247 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N PHE G 252 " --> pdb=" O MET G 248 " (cutoff:3.500A) Processing helix chain 'G' and resid 269 through 273 removed outlier: 4.243A pdb=" N GLU G 273 " --> pdb=" O LYS G 270 " (cutoff:3.500A) Processing helix chain 'G' and resid 306 through 317 Processing helix chain 'G' and resid 330 through 340 removed outlier: 3.710A pdb=" N TRP G 336 " --> pdb=" O VAL G 332 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N TYR G 337 " --> pdb=" O ARG G 333 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLU G 338 " --> pdb=" O ASP G 334 " (cutoff:3.500A) Processing helix chain 'G' and resid 344 through 361 removed outlier: 3.746A pdb=" N VAL G 348 " --> pdb=" O MET G 344 " (cutoff:3.500A) Processing helix chain 'G' and resid 368 through 378 Processing helix chain 'G' and resid 380 through 391 Proline residue: G 384 - end of helix removed outlier: 3.609A pdb=" N ALA G 388 " --> pdb=" O PRO G 384 " (cutoff:3.500A) Processing helix chain 'G' and resid 394 through 399 removed outlier: 4.073A pdb=" N ARG G 399 " --> pdb=" O GLU G 395 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 133 through 135 removed outlier: 8.548A pdb=" N LEU A 134 " --> pdb=" O VAL A 263 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N LEU A 265 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N LEU A 229 " --> pdb=" O MET A 264 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N ILE A 266 " --> pdb=" O LEU A 229 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ILE A 231 " --> pdb=" O ILE A 266 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'B' and resid 290 through 293 removed outlier: 6.769A pdb=" N LEU B 133 " --> pdb=" O ILE B 291 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N TRP B 293 " --> pdb=" O LEU B 133 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N ILE B 135 " --> pdb=" O TRP B 293 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N LEU B 229 " --> pdb=" O MET B 264 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N ILE B 266 " --> pdb=" O LEU B 229 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ILE B 231 " --> pdb=" O ILE B 266 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LEU B 170 " --> pdb=" O VAL B 230 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N ASP B 232 " --> pdb=" O LEU B 170 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N ILE B 172 " --> pdb=" O ASP B 232 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 156 through 159 removed outlier: 3.554A pdb=" N HIS B 159 " --> pdb=" O VAL B 164 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N VAL B 164 " --> pdb=" O HIS B 159 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 290 through 293 removed outlier: 8.852A pdb=" N ILE C 291 " --> pdb=" O SER C 131 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N LEU C 133 " --> pdb=" O ILE C 291 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N TRP C 293 " --> pdb=" O LEU C 133 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ILE C 135 " --> pdb=" O TRP C 293 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N VAL C 263 " --> pdb=" O LEU C 132 " (cutoff:3.500A) removed outlier: 8.501A pdb=" N LEU C 134 " --> pdb=" O VAL C 263 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N LEU C 265 " --> pdb=" O LEU C 134 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N GLY C 136 " --> pdb=" O LEU C 265 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N GLY C 267 " --> pdb=" O GLY C 136 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N LEU C 229 " --> pdb=" O MET C 264 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N ILE C 266 " --> pdb=" O LEU C 229 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ILE C 231 " --> pdb=" O ILE C 266 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU C 170 " --> pdb=" O LEU C 228 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 290 through 292 removed outlier: 8.380A pdb=" N ILE D 291 " --> pdb=" O SER D 131 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N LEU D 133 " --> pdb=" O ILE D 291 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N VAL D 263 " --> pdb=" O LEU D 132 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N LEU D 134 " --> pdb=" O VAL D 263 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N LEU D 265 " --> pdb=" O LEU D 134 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N LEU D 170 " --> pdb=" O VAL D 230 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N ASP D 232 " --> pdb=" O LEU D 170 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ILE D 172 " --> pdb=" O ASP D 232 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'D' and resid 156 through 159 removed outlier: 3.846A pdb=" N VAL D 164 " --> pdb=" O HIS D 159 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'E' and resid 131 through 135 removed outlier: 6.678A pdb=" N VAL E 263 " --> pdb=" O LEU E 132 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N LEU E 134 " --> pdb=" O VAL E 263 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N LEU E 265 " --> pdb=" O LEU E 134 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N LEU E 170 " --> pdb=" O VAL E 230 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N ASP E 232 " --> pdb=" O LEU E 170 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ILE E 172 " --> pdb=" O ASP E 232 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'E' and resid 156 through 159 removed outlier: 3.819A pdb=" N VAL E 164 " --> pdb=" O HIS E 159 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'F' and resid 290 through 292 removed outlier: 8.531A pdb=" N ILE F 291 " --> pdb=" O SER F 131 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N LEU F 133 " --> pdb=" O ILE F 291 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N VAL F 263 " --> pdb=" O LEU F 132 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N LEU F 134 " --> pdb=" O VAL F 263 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LEU F 265 " --> pdb=" O LEU F 134 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU F 170 " --> pdb=" O LEU F 228 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'F' and resid 156 through 159 removed outlier: 4.430A pdb=" N VAL F 164 " --> pdb=" O HIS F 159 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'G' and resid 132 through 135 removed outlier: 4.191A pdb=" N LEU G 265 " --> pdb=" O LEU G 132 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'G' and resid 156 through 158 Processing sheet with id= M, first strand: chain 'G' and resid 170 through 173 661 hydrogen bonds defined for protein. 1767 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 45 hydrogen bonds 90 hydrogen bond angles 0 basepair planarities 15 basepair parallelities 25 stacking parallelities Total time for adding SS restraints: 5.70 Time building geometry restraints manager: 8.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3868 1.32 - 1.45: 5625 1.45 - 1.57: 12328 1.57 - 1.70: 95 1.70 - 1.82: 135 Bond restraints: 22051 Sorted by residual: bond pdb=" O3A ANP E 601 " pdb=" PB ANP E 601 " ideal model delta sigma weight residual 1.700 1.550 0.150 2.00e-02 2.50e+03 5.62e+01 bond pdb=" O3A ANP F 601 " pdb=" PB ANP F 601 " ideal model delta sigma weight residual 1.700 1.553 0.147 2.00e-02 2.50e+03 5.42e+01 bond pdb=" O3A ANP B 601 " pdb=" PB ANP B 601 " ideal model delta sigma weight residual 1.700 1.555 0.145 2.00e-02 2.50e+03 5.24e+01 bond pdb=" O3A ANP D 601 " pdb=" PB ANP D 601 " ideal model delta sigma weight residual 1.700 1.557 0.143 2.00e-02 2.50e+03 5.13e+01 bond pdb=" O3A ANP C 601 " pdb=" PB ANP C 601 " ideal model delta sigma weight residual 1.700 1.557 0.143 2.00e-02 2.50e+03 5.08e+01 ... (remaining 22046 not shown) Histogram of bond angle deviations from ideal: 97.98 - 105.19: 501 105.19 - 112.39: 11188 112.39 - 119.60: 7713 119.60 - 126.80: 10259 126.80 - 134.01: 337 Bond angle restraints: 29998 Sorted by residual: angle pdb=" CA PRO G 22 " pdb=" N PRO G 22 " pdb=" CD PRO G 22 " ideal model delta sigma weight residual 112.00 99.75 12.25 1.40e+00 5.10e-01 7.65e+01 angle pdb=" PB ANP G 601 " pdb=" N3B ANP G 601 " pdb=" PG ANP G 601 " ideal model delta sigma weight residual 126.95 108.00 18.95 3.00e+00 1.11e-01 3.99e+01 angle pdb=" PB ANP E 601 " pdb=" N3B ANP E 601 " pdb=" PG ANP E 601 " ideal model delta sigma weight residual 126.95 108.21 18.74 3.00e+00 1.11e-01 3.90e+01 angle pdb=" PB ANP C 601 " pdb=" N3B ANP C 601 " pdb=" PG ANP C 601 " ideal model delta sigma weight residual 126.95 108.44 18.51 3.00e+00 1.11e-01 3.81e+01 angle pdb=" PB ANP D 601 " pdb=" N3B ANP D 601 " pdb=" PG ANP D 601 " ideal model delta sigma weight residual 126.95 108.49 18.46 3.00e+00 1.11e-01 3.79e+01 ... (remaining 29993 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.08: 11688 18.08 - 36.16: 1192 36.16 - 54.24: 304 54.24 - 72.32: 97 72.32 - 90.40: 47 Dihedral angle restraints: 13328 sinusoidal: 5762 harmonic: 7566 Sorted by residual: dihedral pdb=" CA HIS D 147 " pdb=" C HIS D 147 " pdb=" N ARG D 148 " pdb=" CA ARG D 148 " ideal model delta harmonic sigma weight residual 180.00 154.43 25.57 0 5.00e+00 4.00e-02 2.61e+01 dihedral pdb=" C HIS C 224 " pdb=" N HIS C 224 " pdb=" CA HIS C 224 " pdb=" CB HIS C 224 " ideal model delta harmonic sigma weight residual -122.60 -109.95 -12.65 0 2.50e+00 1.60e-01 2.56e+01 dihedral pdb=" CA PRO C 269 " pdb=" C PRO C 269 " pdb=" N LYS C 270 " pdb=" CA LYS C 270 " ideal model delta harmonic sigma weight residual 180.00 158.35 21.65 0 5.00e+00 4.00e-02 1.87e+01 ... (remaining 13325 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 3092 0.084 - 0.167: 278 0.167 - 0.251: 10 0.251 - 0.334: 8 0.334 - 0.418: 1 Chirality restraints: 3389 Sorted by residual: chirality pdb=" CA HIS C 224 " pdb=" N HIS C 224 " pdb=" C HIS C 224 " pdb=" CB HIS C 224 " both_signs ideal model delta sigma weight residual False 2.51 2.93 -0.42 2.00e-01 2.50e+01 4.37e+00 chirality pdb=" C3' ANP C 601 " pdb=" C2' ANP C 601 " pdb=" C4' ANP C 601 " pdb=" O3' ANP C 601 " both_signs ideal model delta sigma weight residual False -2.36 -2.66 0.31 2.00e-01 2.50e+01 2.35e+00 chirality pdb=" C3' ANP F 601 " pdb=" C2' ANP F 601 " pdb=" C4' ANP F 601 " pdb=" O3' ANP F 601 " both_signs ideal model delta sigma weight residual False -2.36 -2.66 0.30 2.00e-01 2.50e+01 2.23e+00 ... (remaining 3386 not shown) Planarity restraints: 3747 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN G 21 " 0.079 5.00e-02 4.00e+02 1.10e-01 1.95e+01 pdb=" N PRO G 22 " -0.190 5.00e-02 4.00e+02 pdb=" CA PRO G 22 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO G 22 " 0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL F 261 " 0.041 5.00e-02 4.00e+02 6.27e-02 6.28e+00 pdb=" N PRO F 262 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO F 262 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO F 262 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN G 95 " -0.039 5.00e-02 4.00e+02 5.95e-02 5.67e+00 pdb=" N PRO G 96 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO G 96 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO G 96 " -0.033 5.00e-02 4.00e+02 ... (remaining 3744 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.58: 138 2.58 - 3.16: 17021 3.16 - 3.74: 32288 3.74 - 4.32: 44536 4.32 - 4.90: 73927 Nonbonded interactions: 167910 Sorted by model distance: nonbonded pdb=" OG1 THR D 143 " pdb="MG MG D 602 " model vdw 1.994 2.170 nonbonded pdb=" OG1 THR B 143 " pdb="MG MG B 602 " model vdw 2.031 2.170 nonbonded pdb=" OG1 THR G 143 " pdb="MG MG G 602 " model vdw 2.033 2.170 nonbonded pdb=" O1G ANP B 601 " pdb="MG MG B 602 " model vdw 2.061 2.170 nonbonded pdb=" O3G ANP D 601 " pdb="MG MG D 602 " model vdw 2.094 2.170 ... (remaining 167905 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'B' and ((resid 5 and (name N or name CA or name C or name O or name CB ) \ ) or resid 6 through 98 or resid 129 through 238 or resid 245 through 277 or res \ id 289 through 405 or resid 601 through 602)) selection = (chain 'C' and ((resid 5 and (name N or name CA or name C or name O or name CB ) \ ) or resid 6 through 98 or resid 129 through 238 or resid 245 through 277 or res \ id 289 through 405 or resid 601 through 602)) selection = (chain 'D' and ((resid 5 and (name N or name CA or name C or name O or name CB ) \ ) or resid 6 through 98 or resid 129 through 238 or resid 245 through 277 or res \ id 289 through 405 or resid 601 through 602)) selection = (chain 'E' and ((resid 5 and (name N or name CA or name C or name O or name CB ) \ ) or resid 6 through 98 or resid 129 through 238 or resid 245 through 277 or res \ id 289 through 405 or resid 601 through 602)) selection = (chain 'F' and (resid 5 through 98 or resid 129 through 238 or resid 245 through \ 277 or resid 289 through 405 or resid 601 through 602)) selection = (chain 'G' and ((resid 5 and (name N or name CA or name C or name O or name CB ) \ ) or resid 6 through 405 or resid 601 through 602)) } ncs_group { reference = (chain 'H' and resid 1 through 14) selection = (chain 'I' and resid 2 through 15) } 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=0.61 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.420 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: 0.010 Extract box with map and model: 7.160 Check model and map are aligned: 0.310 Set scattering table: 0.220 Process input model: 58.350 Find NCS groups from input model: 1.750 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 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 : 0.006 0.150 22051 Z= 0.330 Angle : 0.863 18.953 29998 Z= 0.418 Chirality : 0.048 0.418 3389 Planarity : 0.005 0.110 3747 Dihedral : 16.997 90.397 8456 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.27 % Favored : 95.65 % Rotamer: Outliers : 0.04 % Allowed : 0.53 % Favored : 99.42 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.15), residues: 2597 helix: -0.58 (0.15), residues: 1180 sheet: 0.22 (0.40), residues: 184 loop : -1.37 (0.15), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP G 316 HIS 0.009 0.001 HIS G 208 PHE 0.016 0.002 PHE D 288 TYR 0.015 0.001 TYR A 199 ARG 0.012 0.001 ARG D 111 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 2258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 501 time to evaluate : 2.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 LEU cc_start: 0.7066 (mt) cc_final: 0.6558 (mp) REVERT: B 330 ASP cc_start: 0.6698 (p0) cc_final: 0.6457 (p0) REVERT: D 327 LEU cc_start: 0.8863 (pp) cc_final: 0.8571 (mt) REVERT: F 248 MET cc_start: 0.8579 (ttm) cc_final: 0.8339 (ttt) REVERT: F 274 ILE cc_start: 0.8266 (pt) cc_final: 0.8049 (mt) REVERT: F 288 PHE cc_start: 0.7689 (t80) cc_final: 0.7138 (t80) REVERT: F 349 LYS cc_start: 0.8410 (ptpt) cc_final: 0.8201 (ptpt) REVERT: G 130 GLN cc_start: 0.1692 (mt0) cc_final: 0.0493 (mp10) REVERT: G 171 LYS cc_start: 0.7259 (pptt) cc_final: 0.5970 (mmmm) REVERT: G 180 LEU cc_start: 0.6879 (mp) cc_final: 0.6500 (tp) REVERT: G 385 MET cc_start: 0.7676 (mmp) cc_final: 0.7367 (mmp) outliers start: 1 outliers final: 0 residues processed: 502 average time/residue: 0.4464 time to fit residues: 311.8507 Evaluate side-chains 241 residues out of total 2258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 241 time to evaluate : 2.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 220 optimal weight: 9.9990 chunk 197 optimal weight: 0.8980 chunk 109 optimal weight: 0.8980 chunk 67 optimal weight: 7.9990 chunk 133 optimal weight: 2.9990 chunk 105 optimal weight: 4.9990 chunk 204 optimal weight: 8.9990 chunk 79 optimal weight: 5.9990 chunk 124 optimal weight: 3.9990 chunk 152 optimal weight: 3.9990 chunk 237 optimal weight: 10.0000 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 ASN ** A 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 HIS B 60 HIS B 159 HIS B 355 GLN D 102 GLN ** D 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 35 ASN E 222 ASN E 297 GLN F 35 ASN F 219 GLN G 45 GLN G 355 GLN ** G 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 22051 Z= 0.265 Angle : 0.625 8.774 29998 Z= 0.314 Chirality : 0.043 0.361 3389 Planarity : 0.005 0.053 3747 Dihedral : 13.420 58.991 3397 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.97 % Favored : 96.00 % Rotamer: Outliers : 2.36 % Allowed : 9.38 % Favored : 88.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.16), residues: 2597 helix: -0.38 (0.15), residues: 1189 sheet: 0.20 (0.40), residues: 183 loop : -1.32 (0.16), residues: 1225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP G 316 HIS 0.015 0.001 HIS B 60 PHE 0.024 0.002 PHE G 351 TYR 0.015 0.002 TYR G 375 ARG 0.007 0.001 ARG B 390 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 257 time to evaluate : 2.698 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 101 LEU cc_start: 0.7386 (mt) cc_final: 0.7036 (mp) REVERT: D 327 LEU cc_start: 0.8932 (pp) cc_final: 0.8557 (mt) REVERT: F 345 ASP cc_start: 0.7722 (t0) cc_final: 0.7395 (t0) REVERT: G 130 GLN cc_start: 0.1926 (mt0) cc_final: 0.0464 (mp10) REVERT: G 171 LYS cc_start: 0.7514 (pptt) cc_final: 0.6211 (mmmm) REVERT: G 248 MET cc_start: 0.7445 (tpt) cc_final: 0.7052 (tpt) REVERT: G 385 MET cc_start: 0.7808 (mmp) cc_final: 0.7377 (mmp) outliers start: 53 outliers final: 37 residues processed: 294 average time/residue: 0.4314 time to fit residues: 193.8022 Evaluate side-chains 248 residues out of total 2258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 211 time to evaluate : 2.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 107 ASN Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 176 HIS Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 278 ASP Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 232 ASP Chi-restraints excluded: chain D residue 273 GLU Chi-restraints excluded: chain E residue 6 ILE Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 222 ASN Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 387 GLU Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 273 GLU Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 184 CYS Chi-restraints excluded: chain G residue 191 LEU Chi-restraints excluded: chain G residue 198 ASN Chi-restraints excluded: chain G residue 206 LYS Chi-restraints excluded: chain G residue 230 VAL Chi-restraints excluded: chain G residue 245 SER Chi-restraints excluded: chain G residue 332 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 131 optimal weight: 5.9990 chunk 73 optimal weight: 7.9990 chunk 197 optimal weight: 4.9990 chunk 161 optimal weight: 4.9990 chunk 65 optimal weight: 0.0670 chunk 237 optimal weight: 20.0000 chunk 256 optimal weight: 6.9990 chunk 211 optimal weight: 7.9990 chunk 235 optimal weight: 10.0000 chunk 80 optimal weight: 7.9990 chunk 190 optimal weight: 0.3980 overall best weight: 3.2924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 HIS ** B 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 21 ASN ** D 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 35 ASN E 222 ASN ** F 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 257 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.2719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 22051 Z= 0.307 Angle : 0.629 10.913 29998 Z= 0.315 Chirality : 0.043 0.312 3389 Planarity : 0.005 0.050 3747 Dihedral : 12.293 59.126 3397 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.01 % Favored : 94.96 % Rotamer: Outliers : 2.76 % Allowed : 13.69 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.16), residues: 2597 helix: -0.39 (0.15), residues: 1188 sheet: 0.01 (0.38), residues: 196 loop : -1.38 (0.16), residues: 1213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 316 HIS 0.010 0.001 HIS D 147 PHE 0.021 0.002 PHE G 351 TYR 0.015 0.002 TYR E 153 ARG 0.005 0.000 ARG B 390 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 221 time to evaluate : 2.430 Fit side-chains revert: symmetry clash REVERT: A 101 LEU cc_start: 0.7355 (mt) cc_final: 0.7076 (mp) REVERT: B 220 ILE cc_start: 0.8751 (OUTLIER) cc_final: 0.8523 (mp) REVERT: B 241 ARG cc_start: 0.4085 (tpm170) cc_final: 0.3847 (ptp-110) REVERT: D 182 GLU cc_start: 0.7145 (OUTLIER) cc_final: 0.6902 (tp30) REVERT: D 327 LEU cc_start: 0.8952 (pp) cc_final: 0.8551 (mt) REVERT: F 102 GLN cc_start: 0.6643 (OUTLIER) cc_final: 0.5544 (tm-30) REVERT: F 121 ARG cc_start: 0.7115 (mmm-85) cc_final: 0.6817 (mmm-85) REVERT: F 210 ILE cc_start: 0.8363 (tt) cc_final: 0.8162 (tp) REVERT: G 130 GLN cc_start: 0.2280 (mt0) cc_final: 0.0707 (mp10) REVERT: G 146 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8249 (mm) REVERT: G 171 LYS cc_start: 0.7594 (pptt) cc_final: 0.6354 (mmmm) REVERT: G 248 MET cc_start: 0.7375 (tpt) cc_final: 0.7134 (tpt) REVERT: G 387 GLU cc_start: 0.7082 (OUTLIER) cc_final: 0.6518 (mp0) outliers start: 62 outliers final: 42 residues processed: 262 average time/residue: 0.3749 time to fit residues: 148.9961 Evaluate side-chains 247 residues out of total 2258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 200 time to evaluate : 2.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 161 GLU Chi-restraints excluded: chain B residue 176 HIS Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 278 ASP Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 147 HIS Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 182 GLU Chi-restraints excluded: chain D residue 273 GLU Chi-restraints excluded: chain E residue 6 ILE Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 350 LEU Chi-restraints excluded: chain E residue 387 GLU Chi-restraints excluded: chain F residue 102 GLN Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 195 LEU Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 146 LEU Chi-restraints excluded: chain G residue 180 LEU Chi-restraints excluded: chain G residue 184 CYS Chi-restraints excluded: chain G residue 191 LEU Chi-restraints excluded: chain G residue 198 ASN Chi-restraints excluded: chain G residue 206 LYS Chi-restraints excluded: chain G residue 230 VAL Chi-restraints excluded: chain G residue 332 VAL Chi-restraints excluded: chain G residue 387 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 234 optimal weight: 10.0000 chunk 178 optimal weight: 0.6980 chunk 123 optimal weight: 0.5980 chunk 26 optimal weight: 8.9990 chunk 113 optimal weight: 1.9990 chunk 159 optimal weight: 1.9990 chunk 238 optimal weight: 0.8980 chunk 252 optimal weight: 0.8980 chunk 124 optimal weight: 0.7980 chunk 225 optimal weight: 20.0000 chunk 67 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 21 ASN D 176 HIS E 222 ASN ** F 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 104 HIS ** F 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 113 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 22051 Z= 0.146 Angle : 0.510 12.069 29998 Z= 0.257 Chirality : 0.039 0.270 3389 Planarity : 0.004 0.047 3747 Dihedral : 11.709 59.737 3397 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.85 % Favored : 96.11 % Rotamer: Outliers : 2.13 % Allowed : 15.47 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.16), residues: 2597 helix: -0.05 (0.15), residues: 1199 sheet: 0.02 (0.38), residues: 198 loop : -1.17 (0.16), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 316 HIS 0.010 0.001 HIS D 147 PHE 0.014 0.001 PHE G 275 TYR 0.011 0.001 TYR D 337 ARG 0.012 0.000 ARG G 272 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 224 time to evaluate : 2.482 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 101 LEU cc_start: 0.7257 (mt) cc_final: 0.6964 (mp) REVERT: B 220 ILE cc_start: 0.8749 (OUTLIER) cc_final: 0.8502 (mp) REVERT: B 385 MET cc_start: 0.7015 (pmm) cc_final: 0.6803 (pmm) REVERT: D 182 GLU cc_start: 0.7005 (OUTLIER) cc_final: 0.6740 (tp30) REVERT: D 327 LEU cc_start: 0.8934 (pp) cc_final: 0.8538 (mt) REVERT: F 102 GLN cc_start: 0.6661 (OUTLIER) cc_final: 0.5498 (tm-30) REVERT: F 345 ASP cc_start: 0.7632 (t0) cc_final: 0.7410 (t0) REVERT: G 31 GLN cc_start: 0.4092 (pt0) cc_final: 0.3683 (mm-40) REVERT: G 146 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8185 (mm) REVERT: G 171 LYS cc_start: 0.7369 (pptt) cc_final: 0.6265 (mmmm) REVERT: G 387 GLU cc_start: 0.6998 (OUTLIER) cc_final: 0.6124 (tp30) outliers start: 48 outliers final: 29 residues processed: 257 average time/residue: 0.3697 time to fit residues: 142.8797 Evaluate side-chains 241 residues out of total 2258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 207 time to evaluate : 2.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 161 GLU Chi-restraints excluded: chain B residue 176 HIS Chi-restraints excluded: chain B residue 177 ASN Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain C residue 21 ASN Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 278 ASP Chi-restraints excluded: chain C residue 288 PHE Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 182 GLU Chi-restraints excluded: chain D residue 273 GLU Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 387 GLU Chi-restraints excluded: chain F residue 102 GLN Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 146 LEU Chi-restraints excluded: chain G residue 180 LEU Chi-restraints excluded: chain G residue 198 ASN Chi-restraints excluded: chain G residue 226 LEU Chi-restraints excluded: chain G residue 230 VAL Chi-restraints excluded: chain G residue 387 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 210 optimal weight: 0.9980 chunk 143 optimal weight: 6.9990 chunk 3 optimal weight: 7.9990 chunk 187 optimal weight: 8.9990 chunk 104 optimal weight: 1.9990 chunk 215 optimal weight: 9.9990 chunk 174 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 128 optimal weight: 9.9990 chunk 226 optimal weight: 8.9990 chunk 63 optimal weight: 6.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 HIS ** B 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 222 ASN G 355 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.3240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 22051 Z= 0.340 Angle : 0.638 11.069 29998 Z= 0.315 Chirality : 0.044 0.291 3389 Planarity : 0.005 0.046 3747 Dihedral : 11.751 59.902 3397 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.08 % Favored : 94.88 % Rotamer: Outliers : 3.29 % Allowed : 15.96 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.16), residues: 2597 helix: -0.43 (0.15), residues: 1224 sheet: -0.13 (0.38), residues: 194 loop : -1.34 (0.16), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP G 316 HIS 0.009 0.001 HIS D 147 PHE 0.020 0.002 PHE G 275 TYR 0.019 0.002 TYR E 153 ARG 0.005 0.000 ARG C 94 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 207 time to evaluate : 2.686 Fit side-chains revert: symmetry clash REVERT: A 105 LEU cc_start: 0.8158 (OUTLIER) cc_final: 0.7919 (mt) REVERT: B 220 ILE cc_start: 0.8768 (OUTLIER) cc_final: 0.8438 (mp) REVERT: D 182 GLU cc_start: 0.7238 (OUTLIER) cc_final: 0.6895 (tp30) REVERT: D 327 LEU cc_start: 0.8940 (pp) cc_final: 0.8542 (mt) REVERT: F 322 GLN cc_start: 0.8075 (OUTLIER) cc_final: 0.7799 (mm110) REVERT: G 146 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8304 (mm) REVERT: G 169 TYR cc_start: 0.8169 (p90) cc_final: 0.7716 (p90) REVERT: G 171 LYS cc_start: 0.7444 (pptt) cc_final: 0.6197 (mmmm) REVERT: G 248 MET cc_start: 0.7399 (tpt) cc_final: 0.7174 (tpt) outliers start: 74 outliers final: 54 residues processed: 264 average time/residue: 0.3661 time to fit residues: 145.1453 Evaluate side-chains 248 residues out of total 2258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 189 time to evaluate : 2.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 208 HIS Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 161 GLU Chi-restraints excluded: chain B residue 176 HIS Chi-restraints excluded: chain B residue 177 ASN Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 383 HIS Chi-restraints excluded: chain C residue 20 ASP Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 278 ASP Chi-restraints excluded: chain C residue 288 PHE Chi-restraints excluded: chain C residue 344 MET Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 147 HIS Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 182 GLU Chi-restraints excluded: chain D residue 213 MET Chi-restraints excluded: chain D residue 273 GLU Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 6 ILE Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 222 ASN Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 263 VAL Chi-restraints excluded: chain E residue 387 GLU Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 195 LEU Chi-restraints excluded: chain F residue 217 MET Chi-restraints excluded: chain F residue 322 GLN Chi-restraints excluded: chain G residue 146 LEU Chi-restraints excluded: chain G residue 180 LEU Chi-restraints excluded: chain G residue 191 LEU Chi-restraints excluded: chain G residue 198 ASN Chi-restraints excluded: chain G residue 206 LYS Chi-restraints excluded: chain G residue 230 VAL Chi-restraints excluded: chain G residue 265 LEU Chi-restraints excluded: chain G residue 332 VAL Chi-restraints excluded: chain G residue 356 LEU Chi-restraints excluded: chain G residue 387 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 84 optimal weight: 9.9990 chunk 227 optimal weight: 0.0970 chunk 49 optimal weight: 0.0870 chunk 148 optimal weight: 0.3980 chunk 62 optimal weight: 7.9990 chunk 252 optimal weight: 3.9990 chunk 209 optimal weight: 4.9990 chunk 116 optimal weight: 9.9990 chunk 20 optimal weight: 7.9990 chunk 83 optimal weight: 0.9980 chunk 132 optimal weight: 4.9990 overall best weight: 1.1158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 HIS ** B 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 21 ASN E 222 ASN F 104 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.3316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 22051 Z= 0.157 Angle : 0.518 11.878 29998 Z= 0.259 Chirality : 0.039 0.279 3389 Planarity : 0.004 0.046 3747 Dihedral : 11.504 59.996 3397 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.93 % Favored : 96.03 % Rotamer: Outliers : 2.62 % Allowed : 16.93 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.16), residues: 2597 helix: -0.11 (0.15), residues: 1225 sheet: 0.00 (0.38), residues: 192 loop : -1.16 (0.16), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G 316 HIS 0.011 0.001 HIS D 147 PHE 0.012 0.001 PHE C 251 TYR 0.015 0.001 TYR G 169 ARG 0.008 0.000 ARG G 272 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 2258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 208 time to evaluate : 2.505 Fit side-chains revert: symmetry clash REVERT: B 220 ILE cc_start: 0.8771 (OUTLIER) cc_final: 0.8510 (mp) REVERT: D 182 GLU cc_start: 0.7105 (OUTLIER) cc_final: 0.6824 (tp30) REVERT: D 327 LEU cc_start: 0.8941 (pp) cc_final: 0.8551 (mt) REVERT: F 24 ILE cc_start: 0.8451 (mt) cc_final: 0.8174 (mp) REVERT: F 322 GLN cc_start: 0.7991 (OUTLIER) cc_final: 0.7690 (mm110) REVERT: F 345 ASP cc_start: 0.7664 (t0) cc_final: 0.7454 (t0) REVERT: G 51 LEU cc_start: 0.6842 (OUTLIER) cc_final: 0.6337 (mp) REVERT: G 146 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8257 (mm) REVERT: G 171 LYS cc_start: 0.7333 (pptt) cc_final: 0.6150 (mmmm) REVERT: G 356 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8189 (mt) REVERT: G 375 TYR cc_start: 0.8492 (t80) cc_final: 0.8155 (t80) REVERT: G 387 GLU cc_start: 0.7019 (OUTLIER) cc_final: 0.6128 (tp30) outliers start: 59 outliers final: 42 residues processed: 249 average time/residue: 0.3568 time to fit residues: 134.2641 Evaluate side-chains 246 residues out of total 2258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 197 time to evaluate : 2.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 208 HIS Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 161 GLU Chi-restraints excluded: chain B residue 176 HIS Chi-restraints excluded: chain B residue 177 ASN Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 278 ASP Chi-restraints excluded: chain C residue 288 PHE Chi-restraints excluded: chain C residue 344 MET Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 182 GLU Chi-restraints excluded: chain D residue 213 MET Chi-restraints excluded: chain D residue 273 GLU Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 86 MET Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 387 GLU Chi-restraints excluded: chain F residue 45 GLN Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 217 MET Chi-restraints excluded: chain F residue 322 GLN Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 146 LEU Chi-restraints excluded: chain G residue 191 LEU Chi-restraints excluded: chain G residue 198 ASN Chi-restraints excluded: chain G residue 226 LEU Chi-restraints excluded: chain G residue 265 LEU Chi-restraints excluded: chain G residue 356 LEU Chi-restraints excluded: chain G residue 387 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 243 optimal weight: 20.0000 chunk 28 optimal weight: 1.9990 chunk 143 optimal weight: 9.9990 chunk 184 optimal weight: 6.9990 chunk 142 optimal weight: 0.9980 chunk 212 optimal weight: 9.9990 chunk 141 optimal weight: 1.9990 chunk 251 optimal weight: 5.9990 chunk 157 optimal weight: 2.9990 chunk 153 optimal weight: 10.0000 chunk 116 optimal weight: 10.0000 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 HIS ** B 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 21 ASN ** D 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 222 ASN ** F 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.3500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 22051 Z= 0.267 Angle : 0.577 12.134 29998 Z= 0.286 Chirality : 0.042 0.258 3389 Planarity : 0.004 0.046 3747 Dihedral : 11.495 59.211 3397 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.01 % Favored : 94.92 % Rotamer: Outliers : 3.60 % Allowed : 17.24 % Favored : 79.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.16), residues: 2597 helix: -0.20 (0.15), residues: 1215 sheet: -0.02 (0.38), residues: 196 loop : -1.26 (0.16), residues: 1186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 316 HIS 0.010 0.001 HIS D 147 PHE 0.018 0.002 PHE G 251 TYR 0.014 0.001 TYR E 153 ARG 0.005 0.000 ARG G 272 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 198 time to evaluate : 2.745 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 105 LEU cc_start: 0.8068 (OUTLIER) cc_final: 0.7860 (mt) REVERT: B 220 ILE cc_start: 0.8771 (OUTLIER) cc_final: 0.8464 (mp) REVERT: B 248 MET cc_start: 0.7800 (ttt) cc_final: 0.7578 (ttp) REVERT: D 182 GLU cc_start: 0.7217 (OUTLIER) cc_final: 0.6877 (tp30) REVERT: D 327 LEU cc_start: 0.8978 (pp) cc_final: 0.8581 (mt) REVERT: E 101 LEU cc_start: 0.6750 (OUTLIER) cc_final: 0.6543 (pp) REVERT: E 245 SER cc_start: 0.8254 (m) cc_final: 0.8020 (m) REVERT: F 102 GLN cc_start: 0.6801 (OUTLIER) cc_final: 0.5629 (tm-30) REVERT: F 322 GLN cc_start: 0.8092 (OUTLIER) cc_final: 0.7828 (mm110) REVERT: G 146 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8428 (mm) REVERT: G 171 LYS cc_start: 0.7327 (pptt) cc_final: 0.6166 (mmmm) REVERT: G 375 TYR cc_start: 0.8483 (t80) cc_final: 0.8081 (t80) outliers start: 81 outliers final: 59 residues processed: 258 average time/residue: 0.3743 time to fit residues: 145.9688 Evaluate side-chains 256 residues out of total 2258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 190 time to evaluate : 2.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 208 HIS Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 161 GLU Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 176 HIS Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 383 HIS Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 21 ASN Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 278 ASP Chi-restraints excluded: chain C residue 288 PHE Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 344 MET Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 147 HIS Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 182 GLU Chi-restraints excluded: chain D residue 213 MET Chi-restraints excluded: chain D residue 273 GLU Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain E residue 86 MET Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 222 ASN Chi-restraints excluded: chain E residue 231 ILE Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 330 ASP Chi-restraints excluded: chain E residue 387 GLU Chi-restraints excluded: chain F residue 45 GLN Chi-restraints excluded: chain F residue 102 GLN Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 195 LEU Chi-restraints excluded: chain F residue 217 MET Chi-restraints excluded: chain F residue 322 GLN Chi-restraints excluded: chain G residue 146 LEU Chi-restraints excluded: chain G residue 191 LEU Chi-restraints excluded: chain G residue 198 ASN Chi-restraints excluded: chain G residue 226 LEU Chi-restraints excluded: chain G residue 231 ILE Chi-restraints excluded: chain G residue 265 LEU Chi-restraints excluded: chain G residue 355 GLN Chi-restraints excluded: chain G residue 383 HIS Chi-restraints excluded: chain G residue 387 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 155 optimal weight: 0.7980 chunk 100 optimal weight: 0.9990 chunk 150 optimal weight: 7.9990 chunk 75 optimal weight: 8.9990 chunk 49 optimal weight: 0.0870 chunk 48 optimal weight: 0.9980 chunk 159 optimal weight: 2.9990 chunk 171 optimal weight: 6.9990 chunk 124 optimal weight: 0.9980 chunk 23 optimal weight: 10.0000 chunk 197 optimal weight: 2.9990 overall best weight: 0.7760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 HIS ** B 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 300 GLN E 222 ASN F 355 GLN G 355 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.3547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 22051 Z= 0.146 Angle : 0.516 13.527 29998 Z= 0.257 Chirality : 0.039 0.218 3389 Planarity : 0.004 0.047 3747 Dihedral : 11.356 59.881 3397 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.00 % Favored : 95.92 % Rotamer: Outliers : 2.84 % Allowed : 17.91 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.16), residues: 2597 helix: 0.02 (0.15), residues: 1227 sheet: 0.13 (0.39), residues: 192 loop : -1.15 (0.17), residues: 1178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP G 316 HIS 0.011 0.001 HIS D 147 PHE 0.025 0.001 PHE G 351 TYR 0.013 0.001 TYR G 169 ARG 0.004 0.000 ARG F 201 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 208 time to evaluate : 2.694 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 220 ILE cc_start: 0.8778 (OUTLIER) cc_final: 0.8507 (mp) REVERT: C 181 LYS cc_start: 0.8497 (tptt) cc_final: 0.7692 (tptm) REVERT: D 62 ILE cc_start: 0.8583 (OUTLIER) cc_final: 0.8269 (mt) REVERT: D 182 GLU cc_start: 0.7136 (OUTLIER) cc_final: 0.6817 (tp30) REVERT: F 102 GLN cc_start: 0.6707 (OUTLIER) cc_final: 0.5514 (tm-30) REVERT: F 322 GLN cc_start: 0.8000 (OUTLIER) cc_final: 0.7766 (mm110) REVERT: G 53 LYS cc_start: 0.6364 (ttpp) cc_final: 0.5913 (tttt) REVERT: G 146 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8496 (tp) REVERT: G 169 TYR cc_start: 0.8097 (p90) cc_final: 0.7578 (p90) REVERT: G 171 LYS cc_start: 0.7254 (pptt) cc_final: 0.6140 (mmmm) REVERT: G 375 TYR cc_start: 0.8474 (t80) cc_final: 0.8008 (t80) REVERT: G 387 GLU cc_start: 0.7001 (OUTLIER) cc_final: 0.6121 (tp30) outliers start: 64 outliers final: 47 residues processed: 254 average time/residue: 0.3551 time to fit residues: 137.3858 Evaluate side-chains 252 residues out of total 2258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 198 time to evaluate : 2.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 MET Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 208 HIS Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 161 GLU Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 20 ASP Chi-restraints excluded: chain C residue 21 ASN Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 278 ASP Chi-restraints excluded: chain C residue 288 PHE Chi-restraints excluded: chain C residue 344 MET Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 182 GLU Chi-restraints excluded: chain D residue 213 MET Chi-restraints excluded: chain D residue 273 GLU Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 86 MET Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 387 GLU Chi-restraints excluded: chain F residue 45 GLN Chi-restraints excluded: chain F residue 102 GLN Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 217 MET Chi-restraints excluded: chain F residue 322 GLN Chi-restraints excluded: chain G residue 146 LEU Chi-restraints excluded: chain G residue 191 LEU Chi-restraints excluded: chain G residue 198 ASN Chi-restraints excluded: chain G residue 226 LEU Chi-restraints excluded: chain G residue 231 ILE Chi-restraints excluded: chain G residue 265 LEU Chi-restraints excluded: chain G residue 355 GLN Chi-restraints excluded: chain G residue 383 HIS Chi-restraints excluded: chain G residue 387 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 228 optimal weight: 0.0770 chunk 241 optimal weight: 5.9990 chunk 219 optimal weight: 1.9990 chunk 234 optimal weight: 10.0000 chunk 240 optimal weight: 8.9990 chunk 141 optimal weight: 3.9990 chunk 102 optimal weight: 6.9990 chunk 184 optimal weight: 7.9990 chunk 71 optimal weight: 0.9990 chunk 211 optimal weight: 8.9990 chunk 221 optimal weight: 2.9990 overall best weight: 2.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 HIS C 21 ASN ** D 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 222 ASN ** F 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 166 GLN ** G 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.3632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 22051 Z= 0.218 Angle : 0.547 11.715 29998 Z= 0.271 Chirality : 0.040 0.238 3389 Planarity : 0.004 0.048 3747 Dihedral : 11.332 59.464 3397 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.62 % Favored : 95.30 % Rotamer: Outliers : 3.07 % Allowed : 18.22 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.16), residues: 2597 helix: -0.01 (0.15), residues: 1217 sheet: 0.09 (0.38), residues: 197 loop : -1.14 (0.17), residues: 1183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP G 316 HIS 0.011 0.001 HIS D 147 PHE 0.035 0.002 PHE G 351 TYR 0.012 0.001 TYR G 169 ARG 0.007 0.000 ARG F 121 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 206 time to evaluate : 2.617 Fit side-chains revert: symmetry clash REVERT: A 105 LEU cc_start: 0.8018 (OUTLIER) cc_final: 0.7812 (mt) REVERT: B 220 ILE cc_start: 0.8792 (OUTLIER) cc_final: 0.8464 (mp) REVERT: C 181 LYS cc_start: 0.8071 (tptt) cc_final: 0.7527 (tptm) REVERT: D 182 GLU cc_start: 0.7145 (OUTLIER) cc_final: 0.6832 (tp30) REVERT: F 102 GLN cc_start: 0.6738 (OUTLIER) cc_final: 0.5568 (tm-30) REVERT: F 322 GLN cc_start: 0.8091 (OUTLIER) cc_final: 0.7819 (mm110) REVERT: G 53 LYS cc_start: 0.6412 (ttpp) cc_final: 0.5990 (tttt) REVERT: G 146 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8457 (tp) REVERT: G 171 LYS cc_start: 0.7283 (pptt) cc_final: 0.6176 (mmmm) REVERT: G 355 GLN cc_start: 0.8106 (OUTLIER) cc_final: 0.7901 (mt0) REVERT: G 375 TYR cc_start: 0.8454 (t80) cc_final: 0.8041 (t80) outliers start: 69 outliers final: 50 residues processed: 258 average time/residue: 0.3667 time to fit residues: 145.4958 Evaluate side-chains 254 residues out of total 2258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 197 time to evaluate : 2.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 208 HIS Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 161 GLU Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 20 ASP Chi-restraints excluded: chain C residue 21 ASN Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 278 ASP Chi-restraints excluded: chain C residue 288 PHE Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 344 MET Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 182 GLU Chi-restraints excluded: chain D residue 213 MET Chi-restraints excluded: chain D residue 273 GLU Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 222 ASN Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 263 VAL Chi-restraints excluded: chain E residue 387 GLU Chi-restraints excluded: chain F residue 45 GLN Chi-restraints excluded: chain F residue 102 GLN Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 217 MET Chi-restraints excluded: chain F residue 322 GLN Chi-restraints excluded: chain G residue 146 LEU Chi-restraints excluded: chain G residue 191 LEU Chi-restraints excluded: chain G residue 198 ASN Chi-restraints excluded: chain G residue 206 LYS Chi-restraints excluded: chain G residue 226 LEU Chi-restraints excluded: chain G residue 231 ILE Chi-restraints excluded: chain G residue 265 LEU Chi-restraints excluded: chain G residue 355 GLN Chi-restraints excluded: chain G residue 383 HIS Chi-restraints excluded: chain G residue 387 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 233 optimal weight: 9.9990 chunk 153 optimal weight: 8.9990 chunk 247 optimal weight: 0.0980 chunk 151 optimal weight: 0.5980 chunk 117 optimal weight: 5.9990 chunk 172 optimal weight: 2.9990 chunk 260 optimal weight: 10.0000 chunk 239 optimal weight: 9.9990 chunk 207 optimal weight: 0.0670 chunk 21 optimal weight: 0.8980 chunk 159 optimal weight: 6.9990 overall best weight: 0.9320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 HIS C 21 ASN ** D 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 222 ASN ** G 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.3689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 22051 Z= 0.155 Angle : 0.522 13.164 29998 Z= 0.260 Chirality : 0.039 0.211 3389 Planarity : 0.004 0.050 3747 Dihedral : 11.256 59.553 3397 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.04 % Favored : 95.88 % Rotamer: Outliers : 2.36 % Allowed : 18.98 % Favored : 78.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.16), residues: 2597 helix: 0.13 (0.16), residues: 1209 sheet: 0.22 (0.38), residues: 196 loop : -1.07 (0.17), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP G 316 HIS 0.012 0.001 HIS E 224 PHE 0.020 0.001 PHE F 351 TYR 0.013 0.001 TYR G 400 ARG 0.010 0.000 ARG F 241 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 202 time to evaluate : 2.479 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 220 ILE cc_start: 0.8794 (OUTLIER) cc_final: 0.8501 (mp) REVERT: B 330 ASP cc_start: 0.6741 (p0) cc_final: 0.6403 (m-30) REVERT: C 181 LYS cc_start: 0.7985 (tptt) cc_final: 0.7523 (tptm) REVERT: D 182 GLU cc_start: 0.7150 (OUTLIER) cc_final: 0.6838 (tp30) REVERT: F 102 GLN cc_start: 0.6720 (OUTLIER) cc_final: 0.5511 (tm-30) REVERT: F 322 GLN cc_start: 0.8030 (OUTLIER) cc_final: 0.7778 (mm110) REVERT: G 146 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8463 (tp) REVERT: G 171 LYS cc_start: 0.7261 (pptt) cc_final: 0.6157 (mmmm) REVERT: G 375 TYR cc_start: 0.8502 (t80) cc_final: 0.8029 (t80) outliers start: 53 outliers final: 44 residues processed: 242 average time/residue: 0.3664 time to fit residues: 134.6434 Evaluate side-chains 247 residues out of total 2258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 198 time to evaluate : 2.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 208 HIS Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 161 GLU Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 176 HIS Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 278 ASP Chi-restraints excluded: chain C residue 288 PHE Chi-restraints excluded: chain C residue 344 MET Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 182 GLU Chi-restraints excluded: chain D residue 273 GLU Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 387 GLU Chi-restraints excluded: chain F residue 45 GLN Chi-restraints excluded: chain F residue 102 GLN Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 217 MET Chi-restraints excluded: chain F residue 322 GLN Chi-restraints excluded: chain G residue 146 LEU Chi-restraints excluded: chain G residue 191 LEU Chi-restraints excluded: chain G residue 198 ASN Chi-restraints excluded: chain G residue 226 LEU Chi-restraints excluded: chain G residue 231 ILE Chi-restraints excluded: chain G residue 265 LEU Chi-restraints excluded: chain G residue 383 HIS Chi-restraints excluded: chain G residue 387 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 126 optimal weight: 0.9990 chunk 164 optimal weight: 7.9990 chunk 220 optimal weight: 7.9990 chunk 63 optimal weight: 6.9990 chunk 190 optimal weight: 6.9990 chunk 30 optimal weight: 3.9990 chunk 57 optimal weight: 10.0000 chunk 207 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 212 optimal weight: 5.9990 chunk 26 optimal weight: 7.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 HIS ** D 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 222 ASN ** F 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 355 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.140349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.110541 restraints weight = 33118.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.111080 restraints weight = 29630.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.111253 restraints weight = 27888.724| |-----------------------------------------------------------------------------| r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3426 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3426 r_free = 0.3426 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.61 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3425 r_free = 0.3425 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3425 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.3822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 22051 Z= 0.310 Angle : 0.623 12.239 29998 Z= 0.307 Chirality : 0.043 0.244 3389 Planarity : 0.004 0.047 3747 Dihedral : 11.392 59.503 3397 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.97 % Favored : 94.96 % Rotamer: Outliers : 2.89 % Allowed : 18.36 % Favored : 78.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.16), residues: 2597 helix: -0.19 (0.15), residues: 1230 sheet: 0.01 (0.38), residues: 197 loop : -1.18 (0.17), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP G 316 HIS 0.011 0.001 HIS D 147 PHE 0.042 0.002 PHE G 351 TYR 0.016 0.002 TYR E 153 ARG 0.007 0.000 ARG F 121 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4089.06 seconds wall clock time: 75 minutes 20.86 seconds (4520.86 seconds total)