Starting phenix.real_space_refine on Fri Feb 16 07:04:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bti_30179/02_2024/7bti_30179_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bti_30179/02_2024/7bti_30179.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bti_30179/02_2024/7bti_30179.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bti_30179/02_2024/7bti_30179.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bti_30179/02_2024/7bti_30179_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bti_30179/02_2024/7bti_30179_updated.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.001 sd= 0.019 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 10 5.49 5 Mg 5 5.21 5 S 108 5.16 5 C 9239 2.51 5 N 2475 2.21 5 O 2813 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 167": "OE1" <-> "OE2" Residue "B GLU 241": "OE1" <-> "OE2" Residue "D PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 167": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 14650 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 2855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2855 Classifications: {'peptide': 366} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 19, 'TRANS': 346} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 2880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2880 Classifications: {'peptide': 369} Link IDs: {'PTRANS': 19, 'TRANS': 349} Chain: "C" Number of atoms: 2868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2868 Classifications: {'peptide': 369} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 19, 'TRANS': 349} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 2880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2880 Classifications: {'peptide': 369} Link IDs: {'PTRANS': 19, 'TRANS': 349} Chain: "E" Number of atoms: 2862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2862 Classifications: {'peptide': 366} Link IDs: {'PTRANS': 19, 'TRANS': 346} Chain breaks: 1 Chain: "X" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 55 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'HYP:plan-1': 1, 'ALO:plan-1': 1, 'G5G:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "Y" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 55 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'HYP:plan-1': 1, 'ALO:plan-1': 1, 'G5G:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "Z" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 55 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'HYP:plan-1': 1, 'ALO:plan-1': 1, 'G5G:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.69, per 1000 atoms: 0.52 Number of scatterers: 14650 At special positions: 0 Unit cell: (95.22, 95.22, 193.2, 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 108 16.00 P 10 15.00 Mg 5 11.99 O 2813 8.00 N 2475 7.00 C 9239 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.70 Conformation dependent library (CDL) restraints added in 2.9 seconds 3650 Ramachandran restraints generated. 1825 Oldfield, 0 Emsley, 1825 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3440 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 79 helices and 24 sheets defined 33.9% alpha, 9.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.92 Creating SS restraints... Processing helix chain 'A' and resid 56 through 60 Processing helix chain 'A' and resid 80 through 94 removed outlier: 4.046A pdb=" N GLU A 93 " --> pdb=" O THR A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 125 Processing helix chain 'A' and resid 137 through 145 removed outlier: 3.657A pdb=" N SER A 141 " --> pdb=" O GLN A 137 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU A 142 " --> pdb=" O ALA A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 192 removed outlier: 3.698A pdb=" N LYS A 191 " --> pdb=" O ASP A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 216 removed outlier: 3.792A pdb=" N ILE A 208 " --> pdb=" O ALA A 204 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ASP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LYS A 215 " --> pdb=" O ASP A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 230 Processing helix chain 'A' and resid 258 through 261 Processing helix chain 'A' and resid 264 through 266 No H-bonds generated for 'chain 'A' and resid 264 through 266' Processing helix chain 'A' and resid 274 through 283 removed outlier: 4.106A pdb=" N TYR A 279 " --> pdb=" O HIS A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 293 Processing helix chain 'A' and resid 309 through 318 removed outlier: 4.015A pdb=" N THR A 318 " --> pdb=" O GLN A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 348 removed outlier: 3.872A pdb=" N SER A 348 " --> pdb=" O SER A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 355 removed outlier: 3.981A pdb=" N GLN A 354 " --> pdb=" O SER A 350 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N MET A 355 " --> pdb=" O THR A 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 350 through 355' Processing helix chain 'A' and resid 359 through 363 Processing helix chain 'A' and resid 368 through 371 Processing helix chain 'B' and resid 56 through 60 Processing helix chain 'B' and resid 80 through 91 removed outlier: 4.125A pdb=" N ILE B 85 " --> pdb=" O ASP B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 125 Processing helix chain 'B' and resid 139 through 145 Processing helix chain 'B' and resid 182 through 195 removed outlier: 4.572A pdb=" N THR B 194 " --> pdb=" O MET B 190 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N GLU B 195 " --> pdb=" O LYS B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 216 removed outlier: 3.822A pdb=" N ILE B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASP B 211 " --> pdb=" O GLU B 207 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LYS B 215 " --> pdb=" O ASP B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 229 Processing helix chain 'B' and resid 274 through 283 removed outlier: 3.679A pdb=" N TYR B 279 " --> pdb=" O HIS B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 293 removed outlier: 3.943A pdb=" N LYS B 291 " --> pdb=" O ILE B 287 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N ASP B 292 " --> pdb=" O ASP B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 311 No H-bonds generated for 'chain 'B' and resid 309 through 311' Processing helix chain 'B' and resid 313 through 318 Processing helix chain 'B' and resid 338 through 348 Processing helix chain 'B' and resid 352 through 354 No H-bonds generated for 'chain 'B' and resid 352 through 354' Processing helix chain 'B' and resid 359 through 373 removed outlier: 3.699A pdb=" N ASP B 363 " --> pdb=" O LYS B 359 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU B 364 " --> pdb=" O GLN B 360 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA B 365 " --> pdb=" O GLU B 361 " (cutoff:3.500A) Proline residue: B 367 - end of helix removed outlier: 5.651A pdb=" N VAL B 370 " --> pdb=" O GLY B 366 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N HIS B 371 " --> pdb=" O PRO B 367 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ARG B 372 " --> pdb=" O SER B 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 60 No H-bonds generated for 'chain 'C' and resid 57 through 60' Processing helix chain 'C' and resid 79 through 91 Processing helix chain 'C' and resid 98 through 100 No H-bonds generated for 'chain 'C' and resid 98 through 100' Processing helix chain 'C' and resid 113 through 125 removed outlier: 3.659A pdb=" N GLU C 117 " --> pdb=" O LYS C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 145 removed outlier: 3.521A pdb=" N SER C 141 " --> pdb=" O GLN C 137 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N LEU C 142 " --> pdb=" O ALA C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 192 removed outlier: 3.647A pdb=" N LYS C 191 " --> pdb=" O ASP C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 216 removed outlier: 3.683A pdb=" N GLU C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LYS C 215 " --> pdb=" O ASP C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 229 removed outlier: 3.515A pdb=" N ALA C 228 " --> pdb=" O GLU C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 283 removed outlier: 3.533A pdb=" N ASN C 280 " --> pdb=" O GLU C 276 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N SER C 281 " --> pdb=" O THR C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 294 removed outlier: 4.075A pdb=" N LYS C 291 " --> pdb=" O ILE C 287 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N ASP C 292 " --> pdb=" O ASP C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 311 No H-bonds generated for 'chain 'C' and resid 309 through 311' Processing helix chain 'C' and resid 313 through 316 No H-bonds generated for 'chain 'C' and resid 313 through 316' Processing helix chain 'C' and resid 338 through 348 removed outlier: 3.684A pdb=" N GLY C 343 " --> pdb=" O VAL C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 368 removed outlier: 3.777A pdb=" N GLU C 364 " --> pdb=" O GLN C 360 " (cutoff:3.500A) Proline residue: C 367 - end of helix Processing helix chain 'D' and resid 57 through 60 No H-bonds generated for 'chain 'D' and resid 57 through 60' Processing helix chain 'D' and resid 79 through 91 removed outlier: 3.520A pdb=" N GLU D 83 " --> pdb=" O TRP D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 100 No H-bonds generated for 'chain 'D' and resid 98 through 100' Processing helix chain 'D' and resid 113 through 125 removed outlier: 3.554A pdb=" N THR D 120 " --> pdb=" O ARG D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 145 removed outlier: 3.815A pdb=" N LEU D 142 " --> pdb=" O ALA D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 192 removed outlier: 3.534A pdb=" N TYR D 188 " --> pdb=" O ASP D 184 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LYS D 191 " --> pdb=" O ASP D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 216 removed outlier: 3.971A pdb=" N ASP D 211 " --> pdb=" O GLU D 207 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LYS D 215 " --> pdb=" O ASP D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 229 removed outlier: 3.563A pdb=" N ALA D 228 " --> pdb=" O GLU D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 262 Processing helix chain 'D' and resid 264 through 267 removed outlier: 3.565A pdb=" N ILE D 267 " --> pdb=" O PRO D 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 264 through 267' Processing helix chain 'D' and resid 276 through 283 removed outlier: 4.162A pdb=" N SER D 281 " --> pdb=" O THR D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 293 removed outlier: 4.152A pdb=" N LYS D 291 " --> pdb=" O ILE D 287 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ASP D 292 " --> pdb=" O ASP D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 318 Processing helix chain 'D' and resid 338 through 348 removed outlier: 3.524A pdb=" N SER D 348 " --> pdb=" O SER D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 352 through 354 No H-bonds generated for 'chain 'D' and resid 352 through 354' Processing helix chain 'D' and resid 359 through 365 removed outlier: 3.797A pdb=" N GLU D 364 " --> pdb=" O GLN D 360 " (cutoff:3.500A) Processing helix chain 'D' and resid 369 through 373 Processing helix chain 'E' and resid 55 through 60 Processing helix chain 'E' and resid 79 through 91 removed outlier: 4.122A pdb=" N LYS E 84 " --> pdb=" O ASP E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 100 No H-bonds generated for 'chain 'E' and resid 98 through 100' Processing helix chain 'E' and resid 114 through 125 removed outlier: 3.659A pdb=" N THR E 120 " --> pdb=" O ARG E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 139 through 144 Processing helix chain 'E' and resid 182 through 195 removed outlier: 3.644A pdb=" N TYR E 188 " --> pdb=" O ASP E 184 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LYS E 191 " --> pdb=" O ASP E 187 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N THR E 194 " --> pdb=" O MET E 190 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N GLU E 195 " --> pdb=" O LYS E 191 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 216 removed outlier: 3.773A pdb=" N ASP E 211 " --> pdb=" O GLU E 207 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LYS E 215 " --> pdb=" O ASP E 211 " (cutoff:3.500A) Processing helix chain 'E' and resid 223 through 229 Processing helix chain 'E' and resid 258 through 260 No H-bonds generated for 'chain 'E' and resid 258 through 260' Processing helix chain 'E' and resid 264 through 267 removed outlier: 3.521A pdb=" N ILE E 267 " --> pdb=" O PRO E 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 264 through 267' Processing helix chain 'E' and resid 279 through 282 No H-bonds generated for 'chain 'E' and resid 279 through 282' Processing helix chain 'E' and resid 290 through 293 No H-bonds generated for 'chain 'E' and resid 290 through 293' Processing helix chain 'E' and resid 302 through 304 No H-bonds generated for 'chain 'E' and resid 302 through 304' Processing helix chain 'E' and resid 312 through 317 Processing helix chain 'E' and resid 338 through 346 Processing helix chain 'E' and resid 350 through 352 No H-bonds generated for 'chain 'E' and resid 350 through 352' Processing helix chain 'E' and resid 359 through 365 Processing helix chain 'E' and resid 367 through 372 removed outlier: 4.053A pdb=" N VAL E 370 " --> pdb=" O PRO E 367 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N HIS E 371 " --> pdb=" O SER E 368 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 8 through 11 removed outlier: 3.872A pdb=" N ALA A 19 " --> pdb=" O ALA A 29 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA A 29 " --> pdb=" O ALA A 19 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 35 through 38 removed outlier: 3.534A pdb=" N VAL A 35 " --> pdb=" O LYS A 68 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG A 37 " --> pdb=" O THR A 66 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 103 through 107 Processing sheet with id= D, first strand: chain 'A' and resid 297 through 299 removed outlier: 5.689A pdb=" N ILE A 151 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASN A 162 " --> pdb=" O MET A 176 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 239 through 241 Processing sheet with id= F, first strand: chain 'B' and resid 8 through 12 Processing sheet with id= G, first strand: chain 'B' and resid 103 through 105 Processing sheet with id= H, first strand: chain 'B' and resid 163 through 165 Processing sheet with id= I, first strand: chain 'B' and resid 160 through 162 Processing sheet with id= J, first strand: chain 'B' and resid 238 through 241 removed outlier: 3.573A pdb=" N LYS B 238 " --> pdb=" O ILE B 250 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 17 through 19 Processing sheet with id= L, first strand: chain 'C' and resid 52 through 54 Processing sheet with id= M, first strand: chain 'C' and resid 103 through 105 Processing sheet with id= N, first strand: chain 'C' and resid 297 through 299 removed outlier: 6.205A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 239 through 241 Processing sheet with id= P, first strand: chain 'D' and resid 8 through 12 removed outlier: 3.520A pdb=" N VAL D 9 " --> pdb=" O GLY D 20 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 52 through 54 Processing sheet with id= R, first strand: chain 'D' and resid 103 through 105 Processing sheet with id= S, first strand: chain 'D' and resid 297 through 299 removed outlier: 6.199A pdb=" N ILE D 151 " --> pdb=" O VAL D 298 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 238 through 241 removed outlier: 3.558A pdb=" N LYS D 238 " --> pdb=" O ILE D 250 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE D 250 " --> pdb=" O LYS D 238 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'E' and resid 8 through 12 removed outlier: 3.514A pdb=" N PHE E 31 " --> pdb=" O VAL E 17 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'E' and resid 52 through 54 removed outlier: 3.797A pdb=" N LYS E 68 " --> pdb=" O VAL E 35 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'E' and resid 103 through 105 Processing sheet with id= X, first strand: chain 'E' and resid 240 through 242 removed outlier: 3.852A pdb=" N GLN E 246 " --> pdb=" O LEU E 242 " (cutoff:3.500A) 375 hydrogen bonds defined for protein. 1029 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.09 Time building geometry restraints manager: 6.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 2443 1.30 - 1.43: 3806 1.43 - 1.56: 8510 1.56 - 1.68: 21 1.68 - 1.81: 189 Bond restraints: 14969 Sorted by residual: bond pdb=" C1' ADP D 402 " pdb=" C2' ADP D 402 " ideal model delta sigma weight residual 1.524 1.295 0.229 2.00e-02 2.50e+03 1.32e+02 bond pdb=" C1' ADP E 402 " pdb=" C2' ADP E 402 " ideal model delta sigma weight residual 1.524 1.295 0.229 2.00e-02 2.50e+03 1.32e+02 bond pdb=" C1' ADP C 402 " pdb=" C2' ADP C 402 " ideal model delta sigma weight residual 1.524 1.296 0.228 2.00e-02 2.50e+03 1.30e+02 bond pdb=" C1' ADP A 402 " pdb=" C2' ADP A 402 " ideal model delta sigma weight residual 1.524 1.298 0.226 2.00e-02 2.50e+03 1.28e+02 bond pdb=" C1' ADP B 402 " pdb=" C2' ADP B 402 " ideal model delta sigma weight residual 1.524 1.298 0.226 2.00e-02 2.50e+03 1.27e+02 ... (remaining 14964 not shown) Histogram of bond angle deviations from ideal: 99.57 - 106.47: 538 106.47 - 113.37: 8150 113.37 - 120.26: 5656 120.26 - 127.16: 5797 127.16 - 134.05: 178 Bond angle restraints: 20319 Sorted by residual: angle pdb=" C GLY C 308 " pdb=" N ILE C 309 " pdb=" CA ILE C 309 " ideal model delta sigma weight residual 121.97 131.32 -9.35 1.80e+00 3.09e-01 2.70e+01 angle pdb=" C GLY E 308 " pdb=" N ILE E 309 " pdb=" CA ILE E 309 " ideal model delta sigma weight residual 121.97 131.14 -9.17 1.80e+00 3.09e-01 2.60e+01 angle pdb=" C GLY B 308 " pdb=" N ILE B 309 " pdb=" CA ILE B 309 " ideal model delta sigma weight residual 121.97 131.11 -9.14 1.80e+00 3.09e-01 2.58e+01 angle pdb=" N HYP X 1 " pdb=" CA HYP X 1 " pdb=" CB HYP X 1 " ideal model delta sigma weight residual 103.00 108.56 -5.56 1.10e+00 8.26e-01 2.55e+01 angle pdb=" N HYP Z 1 " pdb=" CA HYP Z 1 " pdb=" CB HYP Z 1 " ideal model delta sigma weight residual 103.00 108.45 -5.45 1.10e+00 8.26e-01 2.46e+01 ... (remaining 20314 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.53: 8489 27.53 - 55.07: 468 55.07 - 82.60: 53 82.60 - 110.13: 8 110.13 - 137.66: 10 Dihedral angle restraints: 9028 sinusoidal: 3658 harmonic: 5370 Sorted by residual: dihedral pdb=" O2A ADP B 402 " pdb=" O3A ADP B 402 " pdb=" PA ADP B 402 " pdb=" PB ADP B 402 " ideal model delta sinusoidal sigma weight residual -60.00 77.67 -137.66 1 2.00e+01 2.50e-03 4.17e+01 dihedral pdb=" O2A ADP C 402 " pdb=" O3A ADP C 402 " pdb=" PA ADP C 402 " pdb=" PB ADP C 402 " ideal model delta sinusoidal sigma weight residual -60.00 77.62 -137.62 1 2.00e+01 2.50e-03 4.17e+01 dihedral pdb=" O2A ADP E 402 " pdb=" O3A ADP E 402 " pdb=" PA ADP E 402 " pdb=" PB ADP E 402 " ideal model delta sinusoidal sigma weight residual -60.00 75.56 -135.56 1 2.00e+01 2.50e-03 4.11e+01 ... (remaining 9025 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.143: 2242 0.143 - 0.287: 18 0.287 - 0.430: 0 0.430 - 0.574: 0 0.574 - 0.717: 3 Chirality restraints: 2263 Sorted by residual: chirality pdb=" CA G5G X 4 " pdb=" N G5G X 4 " pdb=" C G5G X 4 " pdb=" CB G5G X 4 " both_signs ideal model delta sigma weight residual False 2.51 1.79 0.72 2.00e-01 2.50e+01 1.29e+01 chirality pdb=" CA G5G Z 4 " pdb=" N G5G Z 4 " pdb=" C G5G Z 4 " pdb=" CB G5G Z 4 " both_signs ideal model delta sigma weight residual False 2.51 1.80 0.71 2.00e-01 2.50e+01 1.26e+01 chirality pdb=" CA G5G Y 4 " pdb=" N G5G Y 4 " pdb=" C G5G Y 4 " pdb=" CB G5G Y 4 " both_signs ideal model delta sigma weight residual False 2.51 1.81 0.70 2.00e-01 2.50e+01 1.23e+01 ... (remaining 2260 not shown) Planarity restraints: 2586 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR E 306 " 0.045 5.00e-02 4.00e+02 6.81e-02 7.43e+00 pdb=" N PRO E 307 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO E 307 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO E 307 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 242 " -0.045 5.00e-02 4.00e+02 6.79e-02 7.37e+00 pdb=" N PRO D 243 " 0.117 5.00e-02 4.00e+02 pdb=" CA PRO D 243 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO D 243 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 111 " 0.039 5.00e-02 4.00e+02 5.89e-02 5.56e+00 pdb=" N PRO B 112 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO B 112 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 112 " 0.033 5.00e-02 4.00e+02 ... (remaining 2583 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 244 2.65 - 3.21: 12316 3.21 - 3.77: 22646 3.77 - 4.34: 31368 4.34 - 4.90: 52510 Nonbonded interactions: 119084 Sorted by model distance: nonbonded pdb="MG MG B 401 " pdb=" O2B ADP B 402 " model vdw 2.083 2.170 nonbonded pdb="MG MG D 401 " pdb=" O2B ADP D 402 " model vdw 2.098 2.170 nonbonded pdb="MG MG E 401 " pdb=" O2B ADP E 402 " model vdw 2.109 2.170 nonbonded pdb="MG MG A 401 " pdb=" O3B ADP A 402 " model vdw 2.126 2.170 nonbonded pdb="MG MG C 401 " pdb=" O3B ADP C 402 " model vdw 2.127 2.170 ... (remaining 119079 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 6 through 48 or (resid 49 through 50 and (name N or name C \ A or name C or name O or name CB )) or resid 51 through 166 or (resid 167 and (n \ ame N or name CA or name C or name O or name CB )) or resid 168 through 374 or r \ esid 401 through 402)) selection = (chain 'B' and (resid 6 through 48 or (resid 49 through 50 and (name N or name C \ A or name C or name O or name CB )) or resid 51 through 166 or (resid 167 and (n \ ame N or name CA or name C or name O or name CB )) or resid 168 through 212 or ( \ resid 213 and (name N or name CA or name C or name O or name CB )) or resid 214 \ through 232 or resid 236 through 308 or (resid 309 through 310 and (name N or na \ me CA or name C or name O or name CB )) or resid 311 through 374 or resid 401 th \ rough 402)) selection = (chain 'C' and (resid 6 through 212 or (resid 213 and (name N or name CA or name \ C or name O or name CB )) or resid 214 through 232 or resid 236 through 308 or \ (resid 309 through 310 and (name N or name CA or name C or name O or name CB )) \ or resid 311 through 374 or resid 401 through 402)) selection = (chain 'D' and (resid 6 through 48 or (resid 49 through 50 and (name N or name C \ A or name C or name O or name CB )) or resid 51 through 166 or (resid 167 and (n \ ame N or name CA or name C or name O or name CB )) or resid 168 through 212 or ( \ resid 213 and (name N or name CA or name C or name O or name CB )) or resid 214 \ through 232 or resid 236 through 308 or (resid 309 through 310 and (name N or na \ me CA or name C or name O or name CB )) or resid 311 through 374 or resid 401 th \ rough 402)) selection = (chain 'E' and (resid 6 through 48 or (resid 49 through 50 and (name N or name C \ A or name C or name O or name CB )) or resid 51 through 166 or (resid 167 and (n \ ame N or name CA or name C or name O or name CB )) or resid 168 through 212 or ( \ resid 213 and (name N or name CA or name C or name O or name CB )) or resid 214 \ through 308 or (resid 309 through 310 and (name N or name CA or name C or name O \ or name CB )) or resid 311 through 374 or resid 401 through 402)) } ncs_group { reference = chain 'X' selection = chain 'Y' selection = chain 'Z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 4.460 Check model and map are aligned: 0.230 Set scattering table: 0.150 Process input model: 39.940 Find NCS groups from input model: 1.070 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 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 : 0.010 0.231 14969 Z= 0.624 Angle : 0.858 10.863 20319 Z= 0.439 Chirality : 0.057 0.717 2263 Planarity : 0.007 0.068 2586 Dihedral : 17.054 137.664 5588 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.70 % Favored : 94.08 % Rotamer: Outliers : 10.93 % Allowed : 11.06 % Favored : 78.01 % 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: -4.46 (0.16), residues: 1825 helix: -3.24 (0.13), residues: 687 sheet: -3.03 (0.24), residues: 312 loop : -2.51 (0.19), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP E 340 HIS 0.005 0.001 HIS D 87 PHE 0.015 0.002 PHE E 255 TYR 0.012 0.001 TYR C 143 ARG 0.004 0.000 ARG A 206 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3650 Ramachandran restraints generated. 1825 Oldfield, 0 Emsley, 1825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3650 Ramachandran restraints generated. 1825 Oldfield, 0 Emsley, 1825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 116 time to evaluate : 1.803 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.8615 (tpp) cc_final: 0.8371 (tpt) REVERT: A 291 LYS cc_start: 0.9228 (OUTLIER) cc_final: 0.8705 (mptt) REVERT: A 311 ASP cc_start: 0.8259 (OUTLIER) cc_final: 0.8034 (t0) REVERT: A 313 MET cc_start: 0.8224 (mmm) cc_final: 0.8015 (mmm) REVERT: A 369 ILE cc_start: 0.9149 (OUTLIER) cc_final: 0.8231 (tt) REVERT: B 49 GLN cc_start: 0.7817 (OUTLIER) cc_final: 0.7416 (pt0) REVERT: B 62 ARG cc_start: 0.8981 (OUTLIER) cc_final: 0.7742 (ptt180) REVERT: B 180 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8581 (tt) REVERT: B 291 LYS cc_start: 0.9226 (OUTLIER) cc_final: 0.8178 (mmtt) REVERT: B 328 LYS cc_start: 0.8464 (OUTLIER) cc_final: 0.8145 (tttm) REVERT: B 335 ARG cc_start: 0.9038 (OUTLIER) cc_final: 0.8717 (ptp-170) REVERT: C 51 ASP cc_start: 0.6253 (OUTLIER) cc_final: 0.6053 (m-30) REVERT: C 195 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.6888 (pp20) REVERT: C 370 VAL cc_start: 0.9206 (OUTLIER) cc_final: 0.9001 (p) REVERT: D 50 LYS cc_start: 0.7685 (OUTLIER) cc_final: 0.7441 (ttpp) REVERT: D 140 LEU cc_start: 0.9355 (OUTLIER) cc_final: 0.9123 (mt) REVERT: D 194 THR cc_start: 0.9298 (OUTLIER) cc_final: 0.9079 (p) REVERT: D 260 THR cc_start: 0.9157 (OUTLIER) cc_final: 0.8866 (p) REVERT: E 12 ASN cc_start: 0.8865 (t0) cc_final: 0.8533 (p0) REVERT: E 44 MET cc_start: 0.8939 (OUTLIER) cc_final: 0.8451 (mpt) REVERT: E 103 THR cc_start: 0.9229 (OUTLIER) cc_final: 0.8966 (m) REVERT: E 227 MET cc_start: 0.8545 (mmm) cc_final: 0.8263 (mmm) outliers start: 170 outliers final: 55 residues processed: 280 average time/residue: 0.2398 time to fit residues: 102.0401 Evaluate side-chains 162 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 89 time to evaluate : 1.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 291 LYS Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 326 LYS Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 49 GLN Chi-restraints excluded: chain B residue 62 ARG Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 253 GLU Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 291 LYS Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 328 LYS Chi-restraints excluded: chain B residue 335 ARG Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 111 ASN Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain C residue 246 GLN Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 50 LYS Chi-restraints excluded: chain D residue 56 ASP Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 141 SER Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 184 ASP Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain D residue 194 THR Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 246 GLN Chi-restraints excluded: chain D residue 253 GLU Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 286 ASP Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 335 ARG Chi-restraints excluded: chain D residue 369 ILE Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 44 MET Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 111 ASN Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 165 ILE Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 253 GLU Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 369 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 151 optimal weight: 4.9990 chunk 136 optimal weight: 0.0170 chunk 75 optimal weight: 0.1980 chunk 46 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 72 optimal weight: 8.9990 chunk 141 optimal weight: 0.7980 chunk 54 optimal weight: 4.9990 chunk 85 optimal weight: 0.7980 chunk 105 optimal weight: 2.9990 chunk 163 optimal weight: 5.9990 overall best weight: 0.7620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 GLN A 115 ASN A 137 GLN A 161 HIS A 353 GLN A 354 GLN B 49 GLN B 111 ASN B 115 ASN B 246 GLN C 12 ASN C 88 HIS ** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 ASN C 246 GLN C 314 GLN D 88 HIS D 92 ASN D 115 ASN D 137 GLN D 161 HIS D 162 ASN D 246 GLN D 314 GLN E 162 ASN E 314 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.1440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 14969 Z= 0.147 Angle : 0.599 7.395 20319 Z= 0.288 Chirality : 0.043 0.184 2263 Planarity : 0.004 0.050 2586 Dihedral : 13.711 133.177 2272 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 4.82 % Allowed : 14.98 % Favored : 80.19 % 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: -3.14 (0.18), residues: 1825 helix: -1.94 (0.18), residues: 671 sheet: -2.43 (0.24), residues: 337 loop : -1.88 (0.21), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 340 HIS 0.004 0.001 HIS E 101 PHE 0.008 0.001 PHE E 255 TYR 0.008 0.001 TYR C 69 ARG 0.011 0.000 ARG A 372 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3650 Ramachandran restraints generated. 1825 Oldfield, 0 Emsley, 1825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3650 Ramachandran restraints generated. 1825 Oldfield, 0 Emsley, 1825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 97 time to evaluate : 1.633 Fit side-chains REVERT: A 180 LEU cc_start: 0.9267 (OUTLIER) cc_final: 0.8916 (tp) REVERT: A 291 LYS cc_start: 0.9143 (OUTLIER) cc_final: 0.8734 (mttt) REVERT: A 313 MET cc_start: 0.8235 (mmm) cc_final: 0.8022 (mmm) REVERT: A 320 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8853 (pp) REVERT: B 328 LYS cc_start: 0.8351 (OUTLIER) cc_final: 0.8081 (tttm) REVERT: C 16 LEU cc_start: 0.9224 (OUTLIER) cc_final: 0.8970 (mt) REVERT: C 195 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.6935 (pp20) REVERT: D 50 LYS cc_start: 0.7199 (OUTLIER) cc_final: 0.6774 (tttm) REVERT: D 56 ASP cc_start: 0.8148 (OUTLIER) cc_final: 0.7888 (p0) REVERT: D 141 SER cc_start: 0.9411 (OUTLIER) cc_final: 0.9041 (t) REVERT: D 260 THR cc_start: 0.9277 (OUTLIER) cc_final: 0.9066 (p) REVERT: E 227 MET cc_start: 0.8526 (mmm) cc_final: 0.8231 (mmm) outliers start: 75 outliers final: 42 residues processed: 169 average time/residue: 0.2412 time to fit residues: 64.0689 Evaluate side-chains 147 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 95 time to evaluate : 1.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 291 LYS Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 326 LYS Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 253 GLU Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 328 LYS Chi-restraints excluded: chain B residue 335 ARG Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 50 LYS Chi-restraints excluded: chain D residue 56 ASP Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 141 SER Chi-restraints excluded: chain D residue 184 ASP Chi-restraints excluded: chain D residue 253 GLU Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 286 ASP Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 335 ARG Chi-restraints excluded: chain D residue 369 ILE Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 111 ASN Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 165 ILE Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 253 GLU Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain X residue 7 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 90 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 136 optimal weight: 0.8980 chunk 111 optimal weight: 6.9990 chunk 45 optimal weight: 0.0060 chunk 163 optimal weight: 2.9990 chunk 176 optimal weight: 4.9990 chunk 145 optimal weight: 8.9990 chunk 162 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 chunk 131 optimal weight: 2.9990 overall best weight: 2.1802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 GLN B 115 ASN B 162 ASN C 92 ASN C 137 GLN C 161 HIS D 115 ASN E 12 ASN E 111 ASN E 161 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14969 Z= 0.258 Angle : 0.607 7.173 20319 Z= 0.291 Chirality : 0.045 0.178 2263 Planarity : 0.004 0.050 2586 Dihedral : 12.569 135.712 2216 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 4.57 % Allowed : 15.11 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.61 (0.19), residues: 1825 helix: -1.32 (0.19), residues: 689 sheet: -2.18 (0.25), residues: 337 loop : -1.74 (0.22), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 340 HIS 0.004 0.001 HIS D 87 PHE 0.007 0.001 PHE E 255 TYR 0.009 0.001 TYR C 53 ARG 0.005 0.000 ARG B 372 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3650 Ramachandran restraints generated. 1825 Oldfield, 0 Emsley, 1825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3650 Ramachandran restraints generated. 1825 Oldfield, 0 Emsley, 1825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 91 time to evaluate : 1.849 Fit side-chains revert: symmetry clash REVERT: A 291 LYS cc_start: 0.9162 (OUTLIER) cc_final: 0.8746 (mttt) REVERT: A 320 LEU cc_start: 0.9192 (OUTLIER) cc_final: 0.8985 (pp) REVERT: B 328 LYS cc_start: 0.8341 (OUTLIER) cc_final: 0.8100 (tttm) REVERT: C 16 LEU cc_start: 0.9189 (OUTLIER) cc_final: 0.8899 (mt) REVERT: C 51 ASP cc_start: 0.6164 (OUTLIER) cc_final: 0.5913 (m-30) REVERT: C 195 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7020 (pp20) REVERT: D 330 ILE cc_start: 0.8768 (OUTLIER) cc_final: 0.8557 (pp) REVERT: E 45 VAL cc_start: 0.8438 (OUTLIER) cc_final: 0.8102 (t) REVERT: E 165 ILE cc_start: 0.9239 (OUTLIER) cc_final: 0.9004 (mm) REVERT: E 227 MET cc_start: 0.8526 (mmm) cc_final: 0.8232 (mmm) outliers start: 71 outliers final: 47 residues processed: 159 average time/residue: 0.2296 time to fit residues: 57.6142 Evaluate side-chains 144 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 88 time to evaluate : 1.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 283 MET Chi-restraints excluded: chain A residue 291 LYS Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 326 LYS Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 253 GLU Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 328 LYS Chi-restraints excluded: chain B residue 335 ARG Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 184 ASP Chi-restraints excluded: chain D residue 253 GLU Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain D residue 286 ASP Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 335 ARG Chi-restraints excluded: chain D residue 369 ILE Chi-restraints excluded: chain E residue 12 ASN Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 165 ILE Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 253 GLU Chi-restraints excluded: chain E residue 286 ASP Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 351 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 161 optimal weight: 7.9990 chunk 123 optimal weight: 4.9990 chunk 84 optimal weight: 7.9990 chunk 18 optimal weight: 5.9990 chunk 78 optimal weight: 5.9990 chunk 109 optimal weight: 8.9990 chunk 164 optimal weight: 5.9990 chunk 173 optimal weight: 3.9990 chunk 85 optimal weight: 5.9990 chunk 155 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 GLN ** A 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 162 ASN E 12 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 14969 Z= 0.483 Angle : 0.702 7.433 20319 Z= 0.341 Chirality : 0.049 0.197 2263 Planarity : 0.005 0.054 2586 Dihedral : 12.506 147.697 2204 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 5.79 % Allowed : 15.31 % Favored : 78.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.55 (0.19), residues: 1825 helix: -1.29 (0.19), residues: 704 sheet: -2.12 (0.26), residues: 339 loop : -1.70 (0.23), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 340 HIS 0.004 0.001 HIS D 87 PHE 0.011 0.002 PHE D 266 TYR 0.012 0.001 TYR D 198 ARG 0.004 0.001 ARG A 256 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3650 Ramachandran restraints generated. 1825 Oldfield, 0 Emsley, 1825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3650 Ramachandran restraints generated. 1825 Oldfield, 0 Emsley, 1825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 86 time to evaluate : 1.833 Fit side-chains REVERT: A 291 LYS cc_start: 0.9206 (OUTLIER) cc_final: 0.8745 (mttt) REVERT: A 320 LEU cc_start: 0.9220 (OUTLIER) cc_final: 0.9014 (pp) REVERT: B 328 LYS cc_start: 0.8307 (OUTLIER) cc_final: 0.8047 (tttm) REVERT: C 16 LEU cc_start: 0.9225 (OUTLIER) cc_final: 0.8928 (mt) REVERT: C 51 ASP cc_start: 0.6491 (OUTLIER) cc_final: 0.6200 (m-30) REVERT: C 195 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7155 (pp20) REVERT: D 50 LYS cc_start: 0.7757 (OUTLIER) cc_final: 0.7007 (tttm) REVERT: D 141 SER cc_start: 0.9402 (OUTLIER) cc_final: 0.9070 (t) REVERT: D 227 MET cc_start: 0.8234 (mmm) cc_final: 0.7831 (mmm) REVERT: D 330 ILE cc_start: 0.8812 (OUTLIER) cc_final: 0.8572 (pp) REVERT: E 12 ASN cc_start: 0.8733 (OUTLIER) cc_final: 0.8501 (t0) REVERT: E 227 MET cc_start: 0.8403 (mmm) cc_final: 0.8071 (mmm) REVERT: E 275 HIS cc_start: 0.9030 (OUTLIER) cc_final: 0.7778 (p-80) REVERT: E 305 MET cc_start: 0.8349 (OUTLIER) cc_final: 0.7888 (mmm) outliers start: 90 outliers final: 55 residues processed: 171 average time/residue: 0.2239 time to fit residues: 60.0824 Evaluate side-chains 153 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 86 time to evaluate : 1.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 283 MET Chi-restraints excluded: chain A residue 291 LYS Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 326 LYS Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 253 GLU Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 328 LYS Chi-restraints excluded: chain B residue 335 ARG Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 50 LYS Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 141 SER Chi-restraints excluded: chain D residue 184 ASP Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 253 GLU Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain D residue 286 ASP Chi-restraints excluded: chain D residue 297 ASN Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 335 ARG Chi-restraints excluded: chain D residue 369 ILE Chi-restraints excluded: chain E residue 12 ASN Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 253 GLU Chi-restraints excluded: chain E residue 275 HIS Chi-restraints excluded: chain E residue 286 ASP Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 305 MET Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 354 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 144 optimal weight: 10.0000 chunk 98 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 129 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 148 optimal weight: 7.9990 chunk 120 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 88 optimal weight: 4.9990 chunk 156 optimal weight: 7.9990 chunk 43 optimal weight: 1.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 ASN E 12 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14969 Z= 0.238 Angle : 0.606 8.682 20319 Z= 0.288 Chirality : 0.045 0.176 2263 Planarity : 0.004 0.052 2586 Dihedral : 11.996 145.745 2202 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 4.50 % Allowed : 16.91 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.20), residues: 1825 helix: -0.90 (0.20), residues: 686 sheet: -1.97 (0.26), residues: 339 loop : -1.56 (0.22), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 340 HIS 0.003 0.001 HIS B 101 PHE 0.009 0.001 PHE E 255 TYR 0.010 0.001 TYR E 166 ARG 0.003 0.000 ARG A 256 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3650 Ramachandran restraints generated. 1825 Oldfield, 0 Emsley, 1825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3650 Ramachandran restraints generated. 1825 Oldfield, 0 Emsley, 1825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 88 time to evaluate : 1.796 Fit side-chains revert: symmetry clash REVERT: A 82 MET cc_start: 0.9079 (tpt) cc_final: 0.8874 (tpt) REVERT: A 291 LYS cc_start: 0.9210 (OUTLIER) cc_final: 0.8745 (mttt) REVERT: B 328 LYS cc_start: 0.8330 (OUTLIER) cc_final: 0.8089 (tttm) REVERT: C 16 LEU cc_start: 0.9161 (OUTLIER) cc_final: 0.8878 (mt) REVERT: C 195 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7087 (pp20) REVERT: D 50 LYS cc_start: 0.7565 (OUTLIER) cc_final: 0.6831 (tmtt) REVERT: D 313 MET cc_start: 0.7774 (mmm) cc_final: 0.7271 (mtp) REVERT: E 45 VAL cc_start: 0.8457 (OUTLIER) cc_final: 0.8119 (t) REVERT: E 227 MET cc_start: 0.8405 (mmm) cc_final: 0.8091 (mmm) REVERT: E 275 HIS cc_start: 0.9010 (OUTLIER) cc_final: 0.7663 (p-80) REVERT: E 305 MET cc_start: 0.8231 (OUTLIER) cc_final: 0.7736 (mmm) REVERT: E 325 MET cc_start: 0.7501 (mtp) cc_final: 0.7127 (ttm) outliers start: 70 outliers final: 49 residues processed: 153 average time/residue: 0.2273 time to fit residues: 54.8956 Evaluate side-chains 144 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 87 time to evaluate : 1.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 283 MET Chi-restraints excluded: chain A residue 291 LYS Chi-restraints excluded: chain A residue 326 LYS Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 253 GLU Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 328 LYS Chi-restraints excluded: chain B residue 335 ARG Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 50 LYS Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 184 ASP Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 253 GLU Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 286 ASP Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 335 ARG Chi-restraints excluded: chain D residue 369 ILE Chi-restraints excluded: chain E residue 12 ASN Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 253 GLU Chi-restraints excluded: chain E residue 275 HIS Chi-restraints excluded: chain E residue 286 ASP Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 305 MET Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 354 GLN Chi-restraints excluded: chain E residue 355 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 58 optimal weight: 0.8980 chunk 156 optimal weight: 5.9990 chunk 34 optimal weight: 6.9990 chunk 102 optimal weight: 5.9990 chunk 42 optimal weight: 5.9990 chunk 174 optimal weight: 5.9990 chunk 144 optimal weight: 10.0000 chunk 80 optimal weight: 4.9990 chunk 14 optimal weight: 10.0000 chunk 57 optimal weight: 0.9980 chunk 91 optimal weight: 6.9990 overall best weight: 3.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 162 ASN D 162 ASN D 252 ASN E 12 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 14969 Z= 0.423 Angle : 0.670 7.930 20319 Z= 0.322 Chirality : 0.048 0.182 2263 Planarity : 0.004 0.055 2586 Dihedral : 12.024 146.922 2197 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 5.21 % Allowed : 16.91 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.27 (0.20), residues: 1825 helix: -1.01 (0.20), residues: 701 sheet: -1.95 (0.27), residues: 339 loop : -1.61 (0.23), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP E 340 HIS 0.003 0.001 HIS D 87 PHE 0.010 0.001 PHE E 255 TYR 0.012 0.001 TYR E 166 ARG 0.004 0.000 ARG A 256 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3650 Ramachandran restraints generated. 1825 Oldfield, 0 Emsley, 1825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3650 Ramachandran restraints generated. 1825 Oldfield, 0 Emsley, 1825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 86 time to evaluate : 1.691 Fit side-chains REVERT: A 47 MET cc_start: 0.7913 (pmm) cc_final: 0.7217 (tpt) REVERT: A 291 LYS cc_start: 0.9218 (OUTLIER) cc_final: 0.8757 (mttt) REVERT: B 103 THR cc_start: 0.9524 (OUTLIER) cc_final: 0.9322 (m) REVERT: B 328 LYS cc_start: 0.8381 (OUTLIER) cc_final: 0.8124 (tttm) REVERT: C 16 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.8931 (mt) REVERT: C 51 ASP cc_start: 0.6374 (OUTLIER) cc_final: 0.6141 (m-30) REVERT: C 195 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7179 (pp20) REVERT: D 50 LYS cc_start: 0.7543 (OUTLIER) cc_final: 0.6834 (tmmm) REVERT: D 93 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.8193 (tp30) REVERT: E 45 VAL cc_start: 0.8483 (OUTLIER) cc_final: 0.8148 (t) REVERT: E 227 MET cc_start: 0.8370 (mmm) cc_final: 0.8055 (mmm) REVERT: E 275 HIS cc_start: 0.9042 (OUTLIER) cc_final: 0.7786 (p-80) REVERT: E 305 MET cc_start: 0.8350 (OUTLIER) cc_final: 0.7878 (mmm) outliers start: 81 outliers final: 58 residues processed: 163 average time/residue: 0.2275 time to fit residues: 58.5704 Evaluate side-chains 155 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 86 time to evaluate : 1.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 283 MET Chi-restraints excluded: chain A residue 291 LYS Chi-restraints excluded: chain A residue 326 LYS Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 253 GLU Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 328 LYS Chi-restraints excluded: chain B residue 335 ARG Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 50 LYS Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 184 ASP Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 253 GLU Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain D residue 286 ASP Chi-restraints excluded: chain D residue 297 ASN Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 335 ARG Chi-restraints excluded: chain D residue 369 ILE Chi-restraints excluded: chain E residue 12 ASN Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 253 GLU Chi-restraints excluded: chain E residue 275 HIS Chi-restraints excluded: chain E residue 286 ASP Chi-restraints excluded: chain E residue 292 ASP Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 305 MET Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 354 GLN Chi-restraints excluded: chain E residue 355 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 167 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 127 optimal weight: 2.9990 chunk 98 optimal weight: 0.9990 chunk 146 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 173 optimal weight: 2.9990 chunk 108 optimal weight: 10.0000 chunk 105 optimal weight: 6.9990 chunk 80 optimal weight: 7.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 162 ASN E 12 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14969 Z= 0.241 Angle : 0.603 8.314 20319 Z= 0.286 Chirality : 0.045 0.175 2263 Planarity : 0.004 0.052 2586 Dihedral : 11.709 144.223 2194 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 4.76 % Allowed : 17.43 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (0.20), residues: 1825 helix: -0.73 (0.20), residues: 692 sheet: -1.85 (0.27), residues: 339 loop : -1.50 (0.23), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 340 HIS 0.003 0.001 HIS D 87 PHE 0.009 0.001 PHE E 255 TYR 0.010 0.001 TYR C 69 ARG 0.003 0.000 ARG A 256 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3650 Ramachandran restraints generated. 1825 Oldfield, 0 Emsley, 1825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3650 Ramachandran restraints generated. 1825 Oldfield, 0 Emsley, 1825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 88 time to evaluate : 1.665 Fit side-chains REVERT: A 47 MET cc_start: 0.7843 (pmm) cc_final: 0.7181 (tpt) REVERT: A 291 LYS cc_start: 0.9209 (OUTLIER) cc_final: 0.8755 (mttt) REVERT: B 30 VAL cc_start: 0.9022 (OUTLIER) cc_final: 0.8684 (p) REVERT: B 132 MET cc_start: 0.8950 (ppp) cc_final: 0.8646 (ppp) REVERT: B 328 LYS cc_start: 0.8325 (OUTLIER) cc_final: 0.8089 (tttm) REVERT: C 16 LEU cc_start: 0.9158 (OUTLIER) cc_final: 0.8870 (mt) REVERT: C 195 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7078 (pp20) REVERT: D 50 LYS cc_start: 0.7423 (OUTLIER) cc_final: 0.6730 (tmmm) REVERT: D 93 GLU cc_start: 0.8542 (OUTLIER) cc_final: 0.8199 (tp30) REVERT: D 141 SER cc_start: 0.9367 (OUTLIER) cc_final: 0.9079 (t) REVERT: D 313 MET cc_start: 0.7760 (mmm) cc_final: 0.7281 (mtp) REVERT: E 227 MET cc_start: 0.8350 (mmm) cc_final: 0.8028 (mmm) REVERT: E 275 HIS cc_start: 0.9030 (OUTLIER) cc_final: 0.7682 (p-80) REVERT: E 305 MET cc_start: 0.8260 (OUTLIER) cc_final: 0.7771 (mmm) outliers start: 74 outliers final: 57 residues processed: 157 average time/residue: 0.2240 time to fit residues: 55.6926 Evaluate side-chains 155 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 88 time to evaluate : 1.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 283 MET Chi-restraints excluded: chain A residue 291 LYS Chi-restraints excluded: chain A residue 326 LYS Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 253 GLU Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 328 LYS Chi-restraints excluded: chain B residue 335 ARG Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 50 LYS Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 141 SER Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 253 GLU Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain D residue 286 ASP Chi-restraints excluded: chain D residue 297 ASN Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 335 ARG Chi-restraints excluded: chain D residue 369 ILE Chi-restraints excluded: chain E residue 12 ASN Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 253 GLU Chi-restraints excluded: chain E residue 275 HIS Chi-restraints excluded: chain E residue 286 ASP Chi-restraints excluded: chain E residue 292 ASP Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 305 MET Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 354 GLN Chi-restraints excluded: chain E residue 355 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 107 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 34 optimal weight: 10.0000 chunk 33 optimal weight: 2.9990 chunk 110 optimal weight: 0.8980 chunk 118 optimal weight: 6.9990 chunk 85 optimal weight: 0.0030 chunk 16 optimal weight: 0.3980 chunk 136 optimal weight: 0.2980 overall best weight: 0.4790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 GLN A 162 ASN C 162 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 14969 Z= 0.125 Angle : 0.561 7.298 20319 Z= 0.263 Chirality : 0.043 0.169 2263 Planarity : 0.003 0.050 2586 Dihedral : 11.185 135.355 2191 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 3.92 % Allowed : 18.26 % Favored : 77.81 % 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: -1.69 (0.20), residues: 1825 helix: -0.40 (0.21), residues: 680 sheet: -1.72 (0.27), residues: 339 loop : -1.35 (0.23), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 340 HIS 0.003 0.000 HIS B 161 PHE 0.008 0.001 PHE E 255 TYR 0.008 0.001 TYR C 69 ARG 0.002 0.000 ARG A 256 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3650 Ramachandran restraints generated. 1825 Oldfield, 0 Emsley, 1825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3650 Ramachandran restraints generated. 1825 Oldfield, 0 Emsley, 1825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 89 time to evaluate : 1.780 Fit side-chains REVERT: A 47 MET cc_start: 0.7686 (pmm) cc_final: 0.7043 (tpt) REVERT: A 291 LYS cc_start: 0.9158 (OUTLIER) cc_final: 0.8742 (mttt) REVERT: B 103 THR cc_start: 0.9583 (OUTLIER) cc_final: 0.9376 (m) REVERT: B 132 MET cc_start: 0.8910 (ppp) cc_final: 0.8598 (ppp) REVERT: B 140 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8904 (mp) REVERT: B 305 MET cc_start: 0.8733 (mmm) cc_final: 0.8406 (tpp) REVERT: D 50 LYS cc_start: 0.7371 (OUTLIER) cc_final: 0.6646 (tmtt) REVERT: D 93 GLU cc_start: 0.8509 (OUTLIER) cc_final: 0.8189 (tp30) REVERT: D 313 MET cc_start: 0.7700 (mmm) cc_final: 0.7235 (mtp) REVERT: D 355 MET cc_start: 0.8351 (mmm) cc_final: 0.7730 (mmm) REVERT: E 45 VAL cc_start: 0.8407 (OUTLIER) cc_final: 0.8051 (t) REVERT: E 227 MET cc_start: 0.8427 (mmm) cc_final: 0.8096 (mmm) outliers start: 61 outliers final: 43 residues processed: 146 average time/residue: 0.2406 time to fit residues: 55.3457 Evaluate side-chains 137 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 88 time to evaluate : 1.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 283 MET Chi-restraints excluded: chain A residue 291 LYS Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 253 GLU Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 335 ARG Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 50 LYS Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 253 GLU Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 335 ARG Chi-restraints excluded: chain D residue 369 ILE Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 253 GLU Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 354 GLN Chi-restraints excluded: chain E residue 355 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 157 optimal weight: 4.9990 chunk 166 optimal weight: 8.9990 chunk 151 optimal weight: 0.8980 chunk 161 optimal weight: 9.9990 chunk 97 optimal weight: 0.1980 chunk 70 optimal weight: 5.9990 chunk 126 optimal weight: 6.9990 chunk 49 optimal weight: 2.9990 chunk 146 optimal weight: 4.9990 chunk 152 optimal weight: 0.8980 chunk 106 optimal weight: 8.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 GLN A 162 ASN D 162 ASN E 12 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14969 Z= 0.242 Angle : 0.583 6.966 20319 Z= 0.274 Chirality : 0.045 0.172 2263 Planarity : 0.003 0.052 2586 Dihedral : 11.063 134.480 2175 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 3.79 % Allowed : 18.14 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.20), residues: 1825 helix: -0.32 (0.21), residues: 680 sheet: -1.66 (0.27), residues: 339 loop : -1.32 (0.23), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 340 HIS 0.003 0.001 HIS D 87 PHE 0.008 0.001 PHE E 255 TYR 0.008 0.001 TYR C 69 ARG 0.003 0.000 ARG A 256 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3650 Ramachandran restraints generated. 1825 Oldfield, 0 Emsley, 1825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3650 Ramachandran restraints generated. 1825 Oldfield, 0 Emsley, 1825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 88 time to evaluate : 1.745 Fit side-chains REVERT: A 47 MET cc_start: 0.7731 (pmm) cc_final: 0.7027 (tpt) REVERT: A 291 LYS cc_start: 0.9183 (OUTLIER) cc_final: 0.8746 (mttt) REVERT: B 103 THR cc_start: 0.9567 (OUTLIER) cc_final: 0.9331 (m) REVERT: B 132 MET cc_start: 0.8942 (ppp) cc_final: 0.8638 (ppp) REVERT: B 305 MET cc_start: 0.8789 (mmm) cc_final: 0.8475 (tpp) REVERT: D 50 LYS cc_start: 0.7440 (OUTLIER) cc_final: 0.6748 (tmmm) REVERT: D 93 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.8229 (tp30) REVERT: D 355 MET cc_start: 0.8412 (mmm) cc_final: 0.7754 (mmm) REVERT: E 45 VAL cc_start: 0.8426 (OUTLIER) cc_final: 0.8065 (t) REVERT: E 227 MET cc_start: 0.8390 (mmm) cc_final: 0.8053 (mmm) outliers start: 59 outliers final: 48 residues processed: 143 average time/residue: 0.2215 time to fit residues: 50.4269 Evaluate side-chains 141 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 88 time to evaluate : 1.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 283 MET Chi-restraints excluded: chain A residue 291 LYS Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 253 GLU Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 335 ARG Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 50 LYS Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 253 GLU Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 335 ARG Chi-restraints excluded: chain D residue 369 ILE Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 253 GLU Chi-restraints excluded: chain E residue 287 ILE Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 354 GLN Chi-restraints excluded: chain E residue 355 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 170 optimal weight: 7.9990 chunk 104 optimal weight: 7.9990 chunk 81 optimal weight: 6.9990 chunk 118 optimal weight: 3.9990 chunk 179 optimal weight: 6.9990 chunk 165 optimal weight: 2.9990 chunk 142 optimal weight: 8.9990 chunk 14 optimal weight: 7.9990 chunk 110 optimal weight: 0.8980 chunk 87 optimal weight: 8.9990 chunk 113 optimal weight: 2.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 12 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 14969 Z= 0.397 Angle : 0.653 6.903 20319 Z= 0.313 Chirality : 0.048 0.178 2263 Planarity : 0.004 0.053 2586 Dihedral : 11.363 140.283 2175 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 3.92 % Allowed : 18.01 % Favored : 78.07 % 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: -1.80 (0.20), residues: 1825 helix: -0.55 (0.20), residues: 695 sheet: -1.68 (0.27), residues: 339 loop : -1.42 (0.23), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP E 340 HIS 0.004 0.001 HIS D 87 PHE 0.009 0.001 PHE E 255 TYR 0.011 0.001 TYR C 69 ARG 0.005 0.001 ARG A 256 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3650 Ramachandran restraints generated. 1825 Oldfield, 0 Emsley, 1825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3650 Ramachandran restraints generated. 1825 Oldfield, 0 Emsley, 1825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 87 time to evaluate : 1.582 Fit side-chains REVERT: A 47 MET cc_start: 0.7914 (pmm) cc_final: 0.7167 (tpt) REVERT: A 291 LYS cc_start: 0.9200 (OUTLIER) cc_final: 0.8810 (mptt) REVERT: B 103 THR cc_start: 0.9541 (OUTLIER) cc_final: 0.9311 (m) REVERT: B 132 MET cc_start: 0.9011 (ppp) cc_final: 0.8711 (ppp) REVERT: C 16 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8882 (tp) REVERT: C 195 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7110 (pp20) REVERT: D 50 LYS cc_start: 0.7334 (OUTLIER) cc_final: 0.6697 (tmmm) REVERT: D 141 SER cc_start: 0.9362 (OUTLIER) cc_final: 0.9081 (t) REVERT: D 313 MET cc_start: 0.7778 (mmm) cc_final: 0.7315 (mtp) REVERT: E 45 VAL cc_start: 0.8462 (OUTLIER) cc_final: 0.8109 (t) REVERT: E 227 MET cc_start: 0.8325 (mmm) cc_final: 0.7997 (mmm) outliers start: 61 outliers final: 51 residues processed: 143 average time/residue: 0.2274 time to fit residues: 52.0685 Evaluate side-chains 144 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 86 time to evaluate : 1.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 283 MET Chi-restraints excluded: chain A residue 291 LYS Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 253 GLU Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 335 ARG Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 50 LYS Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 141 SER Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 253 GLU Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 335 ARG Chi-restraints excluded: chain D residue 369 ILE Chi-restraints excluded: chain E residue 12 ASN Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 253 GLU Chi-restraints excluded: chain E residue 286 ASP Chi-restraints excluded: chain E residue 287 ILE Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 354 GLN Chi-restraints excluded: chain E residue 355 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 152 optimal weight: 7.9990 chunk 43 optimal weight: 0.7980 chunk 131 optimal weight: 0.1980 chunk 21 optimal weight: 0.4980 chunk 39 optimal weight: 0.0040 chunk 143 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 146 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 26 optimal weight: 9.9990 chunk 125 optimal weight: 0.9990 overall best weight: 0.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.054684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2586 r_free = 0.2586 target = 0.045935 restraints weight = 44236.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2628 r_free = 0.2628 target = 0.047455 restraints weight = 22500.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.2653 r_free = 0.2653 target = 0.048420 restraints weight = 14092.584| |-----------------------------------------------------------------------------| r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.153 14969 Z= 0.346 Angle : 0.873 59.172 20319 Z= 0.484 Chirality : 0.046 0.176 2263 Planarity : 0.004 0.053 2586 Dihedral : 11.366 140.349 2175 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 4.05 % Allowed : 18.01 % Favored : 77.94 % Cbeta Deviations : 0.06 % 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: -1.80 (0.20), residues: 1825 helix: -0.54 (0.20), residues: 695 sheet: -1.68 (0.27), residues: 339 loop : -1.42 (0.23), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 340 HIS 0.003 0.001 HIS D 87 PHE 0.009 0.001 PHE E 255 TYR 0.011 0.001 TYR C 69 ARG 0.004 0.000 ARG A 256 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2417.75 seconds wall clock time: 45 minutes 30.87 seconds (2730.87 seconds total)