Starting phenix.real_space_refine (version: 1.21rc1) on Tue Jul 4 06:53:30 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dhr_30682/07_2023/7dhr_30682_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dhr_30682/07_2023/7dhr_30682.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dhr_30682/07_2023/7dhr_30682.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dhr_30682/07_2023/7dhr_30682.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dhr_30682/07_2023/7dhr_30682_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dhr_30682/07_2023/7dhr_30682_updated.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 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: 4 Type Number sf(0) Gaussians S 42 5.16 5 C 4538 2.51 5 N 1206 2.21 5 O 1271 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 16": "OE1" <-> "OE2" Residue "A GLU 27": "OE1" <-> "OE2" Residue "A PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 223": "OD1" <-> "OD2" Residue "A PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 295": "OD1" <-> "OD2" Residue "A GLU 299": "OE1" <-> "OE2" Residue "A ASP 343": "OD1" <-> "OD2" Residue "A TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 378": "OD1" <-> "OD2" Residue "B ARG 48": "NH1" <-> "NH2" Residue "B TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 247": "OD1" <-> "OD2" Residue "B ASP 258": "OD1" <-> "OD2" Residue "B GLU 260": "OE1" <-> "OE2" Residue "G GLU 22": "OE1" <-> "OE2" Residue "G ASP 26": "OD1" <-> "OD2" Residue "N PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 225": "OE1" <-> "OE2" Residue "R GLU 306": "OE1" <-> "OE2" Residue "R TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 331": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 7057 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1495 Classifications: {'peptide': 194} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 4, 'TRANS': 189} Chain breaks: 5 Unresolved non-hydrogen bonds: 168 Unresolved non-hydrogen angles: 204 Unresolved non-hydrogen dihedrals: 139 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 6, 'PHE:plan': 2, 'GLU:plan': 8, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 127 Chain: "B" Number of atoms: 2301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2301 Classifications: {'peptide': 327} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PTRANS': 5, 'TRANS': 321} Chain breaks: 1 Unresolved non-hydrogen bonds: 210 Unresolved non-hydrogen angles: 258 Unresolved non-hydrogen dihedrals: 162 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 6, 'GLU:plan': 6, 'ARG:plan': 14, 'ASN:plan1': 4, 'ASP:plan': 13} Unresolved non-hydrogen planarities: 169 Chain: "G" Number of atoms: 317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 317 Classifications: {'peptide': 49} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 4, 'TRANS': 44} Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "N" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 851 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 5, 'TRANS': 117} Chain breaks: 1 Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 113 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 3, 'ARG:plan': 3, 'PHE:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 58 Chain: "R" Number of atoms: 2093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2093 Unusual residues: {'5FW': 1} Classifications: {'peptide': 284, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 7, 'TRANS': 276, None: 1} Not linked: pdbres="LEU R 339 " pdbres="5FW R 601 " Chain breaks: 2 Unresolved non-hydrogen bonds: 229 Unresolved non-hydrogen angles: 292 Unresolved non-hydrogen dihedrals: 196 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 4, 'TRP:plan': 2, 'HIS:plan': 1, 'PHE:plan': 4, 'GLU:plan': 7, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 149 Time building chain proxies: 4.18, per 1000 atoms: 0.59 Number of scatterers: 7057 At special positions: 0 Unit cell: (82.134, 98.358, 120.666, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 42 16.00 O 1271 8.00 N 1206 7.00 C 4538 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 106 " - pdb=" SG CYS R 191 " distance=2.03 Simple disulfide: pdb=" SG CYS R 184 " - pdb=" SG CYS R 190 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.61 Conformation dependent library (CDL) restraints added in 1.3 seconds 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1844 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 32 helices and 9 sheets defined 23.3% alpha, 12.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'A' and resid 15 through 26 removed outlier: 3.592A pdb=" N GLN A 19 " --> pdb=" O GLU A 15 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU A 21 " --> pdb=" O LYS A 17 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ALA A 22 " --> pdb=" O ALA A 18 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS A 25 " --> pdb=" O GLU A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 30 through 37 removed outlier: 4.392A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 268 No H-bonds generated for 'chain 'A' and resid 265 through 268' Processing helix chain 'A' and resid 271 through 277 Processing helix chain 'A' and resid 296 through 299 No H-bonds generated for 'chain 'A' and resid 296 through 299' Processing helix chain 'A' and resid 313 through 315 No H-bonds generated for 'chain 'A' and resid 313 through 315' Processing helix chain 'A' and resid 332 through 349 removed outlier: 3.516A pdb=" N ARG A 336 " --> pdb=" O PRO A 332 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N ALA A 337 " --> pdb=" O ARG A 333 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR A 339 " --> pdb=" O THR A 335 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N PHE A 340 " --> pdb=" O ARG A 336 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ILE A 341 " --> pdb=" O ALA A 337 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG A 342 " --> pdb=" O LYS A 338 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU A 346 " --> pdb=" O ARG A 342 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N SER A 349 " --> pdb=" O PHE A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 389 removed outlier: 3.914A pdb=" N ASP A 378 " --> pdb=" O ARG A 374 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ASP A 381 " --> pdb=" O ASN A 377 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG A 389 " --> pdb=" O ARG A 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 24 removed outlier: 3.721A pdb=" N ILE B 18 " --> pdb=" O LEU B 14 " (cutoff:3.500A) Processing helix chain 'G' and resid 20 through 23 No H-bonds generated for 'chain 'G' and resid 20 through 23' Processing helix chain 'G' and resid 30 through 33 No H-bonds generated for 'chain 'G' and resid 30 through 33' Processing helix chain 'G' and resid 35 through 47 removed outlier: 3.697A pdb=" N ALA G 43 " --> pdb=" O ALA G 39 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N HIS G 44 " --> pdb=" O TYR G 40 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N ALA G 45 " --> pdb=" O CYS G 41 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N LYS G 46 " --> pdb=" O GLU G 42 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N GLU G 47 " --> pdb=" O ALA G 43 " (cutoff:3.500A) Processing helix chain 'R' and resid 32 through 48 removed outlier: 3.520A pdb=" N MET R 36 " --> pdb=" O TRP R 32 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ILE R 38 " --> pdb=" O VAL R 34 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL R 39 " --> pdb=" O GLY R 35 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N SER R 41 " --> pdb=" O GLY R 37 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE R 43 " --> pdb=" O VAL R 39 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N VAL R 44 " --> pdb=" O MET R 40 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LEU R 45 " --> pdb=" O SER R 41 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL R 48 " --> pdb=" O VAL R 44 " (cutoff:3.500A) Processing helix chain 'R' and resid 67 through 69 No H-bonds generated for 'chain 'R' and resid 67 through 69' Processing helix chain 'R' and resid 73 through 77 removed outlier: 4.398A pdb=" N VAL R 77 " --> pdb=" O SER R 74 " (cutoff:3.500A) Processing helix chain 'R' and resid 80 through 85 Processing helix chain 'R' and resid 89 through 95 removed outlier: 3.620A pdb=" N HIS R 93 " --> pdb=" O PHE R 89 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ILE R 94 " --> pdb=" O GLY R 90 " (cutoff:3.500A) Processing helix chain 'R' and resid 106 through 115 removed outlier: 3.634A pdb=" N THR R 110 " --> pdb=" O CYS R 106 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N SER R 111 " --> pdb=" O GLU R 107 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU R 115 " --> pdb=" O SER R 111 " (cutoff:3.500A) Processing helix chain 'R' and resid 122 through 135 removed outlier: 3.523A pdb=" N ALA R 128 " --> pdb=" O LEU R 124 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA R 134 " --> pdb=" O ASP R 130 " (cutoff:3.500A) Processing helix chain 'R' and resid 155 through 158 No H-bonds generated for 'chain 'R' and resid 155 through 158' Processing helix chain 'R' and resid 160 through 163 No H-bonds generated for 'chain 'R' and resid 160 through 163' Processing helix chain 'R' and resid 168 through 171 No H-bonds generated for 'chain 'R' and resid 168 through 171' Processing helix chain 'R' and resid 199 through 202 No H-bonds generated for 'chain 'R' and resid 199 through 202' Processing helix chain 'R' and resid 214 through 217 No H-bonds generated for 'chain 'R' and resid 214 through 217' Processing helix chain 'R' and resid 223 through 226 No H-bonds generated for 'chain 'R' and resid 223 through 226' Processing helix chain 'R' and resid 229 through 236 removed outlier: 4.395A pdb=" N ASP R 234 " --> pdb=" O LEU R 230 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N LYS R 235 " --> pdb=" O GLN R 231 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N SER R 236 " --> pdb=" O LYS R 232 " (cutoff:3.500A) Processing helix chain 'R' and resid 282 through 285 No H-bonds generated for 'chain 'R' and resid 282 through 285' Processing helix chain 'R' and resid 288 through 290 No H-bonds generated for 'chain 'R' and resid 288 through 290' Processing helix chain 'R' and resid 295 through 298 No H-bonds generated for 'chain 'R' and resid 295 through 298' Processing helix chain 'R' and resid 313 through 315 No H-bonds generated for 'chain 'R' and resid 313 through 315' Processing helix chain 'R' and resid 318 through 325 removed outlier: 3.698A pdb=" N ASN R 322 " --> pdb=" O ASN R 318 " (cutoff:3.500A) Proline residue: R 323 - end of helix No H-bonds generated for 'chain 'R' and resid 318 through 325' Processing helix chain 'R' and resid 330 through 335 removed outlier: 3.668A pdb=" N ILE R 334 " --> pdb=" O PRO R 330 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA R 335 " --> pdb=" O ASP R 331 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 330 through 335' Processing sheet with id= A, first strand: chain 'A' and resid 360 through 363 removed outlier: 3.730A pdb=" N LEU A 289 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU A 291 " --> pdb=" O HIS A 362 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU A 44 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ASN A 218 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N LEU A 43 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N HIS A 220 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N LEU A 45 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N PHE A 222 " --> pdb=" O LEU A 45 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 62 removed outlier: 7.541A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 103 through 105 removed outlier: 3.759A pdb=" N CYS B 121 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 262 through 264 removed outlier: 4.191A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU B 252 " --> pdb=" O MET B 262 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N PHE B 241 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 275 through 278 removed outlier: 3.619A pdb=" N SER B 277 " --> pdb=" O LEU B 286 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 327 through 329 removed outlier: 4.030A pdb=" N LEU B 336 " --> pdb=" O LEU B 51 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ILE B 338 " --> pdb=" O ARG B 49 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 165 through 170 removed outlier: 3.519A pdb=" N CYS B 166 " --> pdb=" O PHE B 180 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'N' and resid 17 through 21 Processing sheet with id= I, first strand: chain 'N' and resid 36 through 40 115 hydrogen bonds defined for protein. 324 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: 1.80 Time building geometry restraints manager: 2.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2272 1.34 - 1.46: 1719 1.46 - 1.58: 3153 1.58 - 1.70: 0 1.70 - 1.82: 58 Bond restraints: 7202 Sorted by residual: bond pdb=" C VAL R 210 " pdb=" N PRO R 211 " ideal model delta sigma weight residual 1.334 1.380 -0.046 2.34e-02 1.83e+03 3.89e+00 bond pdb=" C LEU R 167 " pdb=" N PRO R 168 " ideal model delta sigma weight residual 1.334 1.378 -0.044 2.34e-02 1.83e+03 3.53e+00 bond pdb=" CB TRP B 99 " pdb=" CG TRP B 99 " ideal model delta sigma weight residual 1.498 1.445 0.053 3.10e-02 1.04e+03 2.97e+00 bond pdb=" N THR R 189 " pdb=" CA THR R 189 " ideal model delta sigma weight residual 1.462 1.485 -0.023 1.54e-02 4.22e+03 2.23e+00 bond pdb=" N PHE B 292 " pdb=" CA PHE B 292 " ideal model delta sigma weight residual 1.458 1.476 -0.017 1.35e-02 5.49e+03 1.66e+00 ... (remaining 7197 not shown) Histogram of bond angle deviations from ideal: 100.30 - 107.09: 179 107.09 - 113.87: 4039 113.87 - 120.66: 2840 120.66 - 127.45: 2699 127.45 - 134.23: 84 Bond angle restraints: 9841 Sorted by residual: angle pdb=" N VAL R 152 " pdb=" CA VAL R 152 " pdb=" C VAL R 152 " ideal model delta sigma weight residual 111.81 107.54 4.27 8.60e-01 1.35e+00 2.47e+01 angle pdb=" C SER N 112 " pdb=" N THR N 113 " pdb=" CA THR N 113 " ideal model delta sigma weight residual 121.54 130.35 -8.81 1.91e+00 2.74e-01 2.13e+01 angle pdb=" N VAL R 31 " pdb=" CA VAL R 31 " pdb=" C VAL R 31 " ideal model delta sigma weight residual 113.42 108.46 4.96 1.17e+00 7.31e-01 1.80e+01 angle pdb=" C ARG R 304 " pdb=" N LYS R 305 " pdb=" CA LYS R 305 " ideal model delta sigma weight residual 121.54 128.97 -7.43 1.91e+00 2.74e-01 1.51e+01 angle pdb=" C ASP B 291 " pdb=" N PHE B 292 " pdb=" CA PHE B 292 " ideal model delta sigma weight residual 123.47 129.23 -5.76 1.53e+00 4.27e-01 1.42e+01 ... (remaining 9836 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.38: 3746 17.38 - 34.76: 336 34.76 - 52.14: 68 52.14 - 69.51: 8 69.51 - 86.89: 4 Dihedral angle restraints: 4162 sinusoidal: 1324 harmonic: 2838 Sorted by residual: dihedral pdb=" CB CYS R 184 " pdb=" SG CYS R 184 " pdb=" SG CYS R 190 " pdb=" CB CYS R 190 " ideal model delta sinusoidal sigma weight residual -86.00 -11.85 -74.15 1 1.00e+01 1.00e-02 6.98e+01 dihedral pdb=" CA ASN R 51 " pdb=" C ASN R 51 " pdb=" N VAL R 52 " pdb=" CA VAL R 52 " ideal model delta harmonic sigma weight residual 180.00 159.59 20.41 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" CA SER R 137 " pdb=" C SER R 137 " pdb=" N PRO R 138 " pdb=" CA PRO R 138 " ideal model delta harmonic sigma weight residual -180.00 -160.14 -19.86 0 5.00e+00 4.00e-02 1.58e+01 ... (remaining 4159 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 977 0.064 - 0.128: 175 0.128 - 0.191: 26 0.191 - 0.255: 1 0.255 - 0.319: 1 Chirality restraints: 1180 Sorted by residual: chirality pdb=" CB ILE R 303 " pdb=" CA ILE R 303 " pdb=" CG1 ILE R 303 " pdb=" CG2 ILE R 303 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.32 2.00e-01 2.50e+01 2.54e+00 chirality pdb=" CB ILE R 153 " pdb=" CA ILE R 153 " pdb=" CG1 ILE R 153 " pdb=" CG2 ILE R 153 " both_signs ideal model delta sigma weight residual False 2.64 2.86 -0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CB VAL A 248 " pdb=" CA VAL A 248 " pdb=" CG1 VAL A 248 " pdb=" CG2 VAL A 248 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 8.28e-01 ... (remaining 1177 not shown) Planarity restraints: 1240 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN R 322 " -0.049 5.00e-02 4.00e+02 7.25e-02 8.40e+00 pdb=" N PRO R 323 " 0.125 5.00e-02 4.00e+02 pdb=" CA PRO R 323 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO R 323 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " -0.047 5.00e-02 4.00e+02 7.14e-02 8.16e+00 pdb=" N PRO B 236 " 0.124 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL R 210 " -0.043 5.00e-02 4.00e+02 6.53e-02 6.82e+00 pdb=" N PRO R 211 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO R 211 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO R 211 " -0.037 5.00e-02 4.00e+02 ... (remaining 1237 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 2480 2.84 - 3.36: 5838 3.36 - 3.87: 10765 3.87 - 4.39: 11987 4.39 - 4.90: 21274 Nonbonded interactions: 52344 Sorted by model distance: nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.329 2.440 nonbonded pdb=" O SER B 84 " pdb=" OG SER B 84 " model vdw 2.336 2.440 nonbonded pdb=" OD2 ASP B 247 " pdb=" OG1 THR B 249 " model vdw 2.343 2.440 nonbonded pdb=" OG SER R 207 " pdb=" OAC 5FW R 601 " model vdw 2.349 2.440 nonbonded pdb=" O PHE R 133 " pdb=" OG SER R 137 " model vdw 2.352 2.440 ... (remaining 52339 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 1.950 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 21.700 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 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 : 0.004 0.058 7202 Z= 0.261 Angle : 0.858 9.691 9841 Z= 0.470 Chirality : 0.052 0.319 1180 Planarity : 0.006 0.072 1240 Dihedral : 14.180 86.892 2312 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.06 % Favored : 90.83 % Rotamer Outliers : 0.31 % 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: -6.33 (0.18), residues: 949 helix: -5.10 (0.08), residues: 306 sheet: -3.66 (0.31), residues: 191 loop : -3.70 (0.22), residues: 452 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 139 time to evaluate : 0.809 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 141 average time/residue: 0.2237 time to fit residues: 40.4306 Evaluate side-chains 112 residues out of total 841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 0.779 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 80 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 48 optimal weight: 0.0770 chunk 38 optimal weight: 5.9990 chunk 74 optimal weight: 0.7980 chunk 28 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 55 optimal weight: 0.0370 chunk 86 optimal weight: 1.9990 overall best weight: 0.7018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 ASN A 41 HIS A 390 GLN B 183 HIS B 239 ASN B 266 HIS B 295 ASN G 24 ASN N 123 GLN ** R 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 312 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.1343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 7202 Z= 0.139 Angle : 0.524 5.674 9841 Z= 0.282 Chirality : 0.042 0.157 1180 Planarity : 0.004 0.057 1240 Dihedral : 5.188 25.046 1028 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer Outliers : 2.77 % 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: -5.61 (0.20), residues: 949 helix: -4.35 (0.16), residues: 311 sheet: -3.53 (0.31), residues: 182 loop : -3.25 (0.24), residues: 456 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 116 time to evaluate : 0.813 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 7 residues processed: 128 average time/residue: 0.1978 time to fit residues: 33.9658 Evaluate side-chains 111 residues out of total 841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 104 time to evaluate : 0.808 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0659 time to fit residues: 1.9323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 47 optimal weight: 9.9990 chunk 26 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 86 optimal weight: 0.8980 chunk 93 optimal weight: 4.9990 chunk 76 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 chunk 29 optimal weight: 6.9990 chunk 69 optimal weight: 7.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 390 GLN B 183 HIS B 225 HIS G 24 ASN ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 7202 Z= 0.251 Angle : 0.576 6.813 9841 Z= 0.307 Chirality : 0.043 0.165 1180 Planarity : 0.004 0.054 1240 Dihedral : 5.427 29.446 1028 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.85 % Favored : 91.15 % Rotamer Outliers : 2.31 % 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: -5.24 (0.22), residues: 949 helix: -3.86 (0.20), residues: 316 sheet: -3.40 (0.32), residues: 179 loop : -3.14 (0.25), residues: 454 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 119 time to evaluate : 0.863 Fit side-chains outliers start: 15 outliers final: 8 residues processed: 126 average time/residue: 0.1875 time to fit residues: 31.9668 Evaluate side-chains 121 residues out of total 841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 113 time to evaluate : 0.780 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0644 time to fit residues: 2.0167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 85 optimal weight: 0.5980 chunk 64 optimal weight: 3.9990 chunk 44 optimal weight: 9.9990 chunk 9 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 91 optimal weight: 20.0000 chunk 45 optimal weight: 0.3980 chunk 82 optimal weight: 7.9990 chunk 24 optimal weight: 1.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 ASN ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 7202 Z= 0.204 Angle : 0.544 5.801 9841 Z= 0.291 Chirality : 0.042 0.145 1180 Planarity : 0.004 0.053 1240 Dihedral : 5.180 30.618 1028 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.75 % Favored : 91.25 % Rotamer Outliers : 2.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.96 (0.23), residues: 949 helix: -3.56 (0.22), residues: 318 sheet: -3.25 (0.34), residues: 176 loop : -3.01 (0.26), residues: 455 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 114 time to evaluate : 0.860 Fit side-chains outliers start: 19 outliers final: 9 residues processed: 128 average time/residue: 0.1896 time to fit residues: 32.7242 Evaluate side-chains 118 residues out of total 841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 109 time to evaluate : 0.797 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0664 time to fit residues: 2.1804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 76 optimal weight: 0.5980 chunk 52 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 68 optimal weight: 6.9990 chunk 37 optimal weight: 0.9980 chunk 78 optimal weight: 0.9980 chunk 63 optimal weight: 9.9990 chunk 0 optimal weight: 5.9990 chunk 46 optimal weight: 6.9990 chunk 82 optimal weight: 0.0970 chunk 23 optimal weight: 6.9990 overall best weight: 1.1380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 ASN ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 7202 Z= 0.183 Angle : 0.539 7.100 9841 Z= 0.285 Chirality : 0.042 0.143 1180 Planarity : 0.003 0.051 1240 Dihedral : 4.955 29.610 1028 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.38 % Favored : 90.62 % Rotamer Outliers : 1.85 % 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: -4.62 (0.24), residues: 949 helix: -3.30 (0.23), residues: 315 sheet: -3.07 (0.35), residues: 173 loop : -2.80 (0.26), residues: 461 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 113 time to evaluate : 0.799 Fit side-chains outliers start: 12 outliers final: 7 residues processed: 122 average time/residue: 0.1959 time to fit residues: 32.3759 Evaluate side-chains 116 residues out of total 841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 109 time to evaluate : 0.796 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0653 time to fit residues: 1.9378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 30 optimal weight: 2.9990 chunk 82 optimal weight: 0.0570 chunk 18 optimal weight: 0.9990 chunk 53 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 chunk 91 optimal weight: 3.9990 chunk 76 optimal weight: 0.3980 chunk 42 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 48 optimal weight: 0.0770 chunk 88 optimal weight: 5.9990 overall best weight: 0.5060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 ASN G 24 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 7202 Z= 0.126 Angle : 0.516 9.652 9841 Z= 0.268 Chirality : 0.042 0.147 1180 Planarity : 0.003 0.052 1240 Dihedral : 4.496 29.653 1028 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer Outliers : 1.85 % 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: -4.36 (0.24), residues: 949 helix: -2.95 (0.25), residues: 316 sheet: -3.13 (0.34), residues: 181 loop : -2.65 (0.27), residues: 452 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 114 time to evaluate : 0.731 Fit side-chains outliers start: 12 outliers final: 6 residues processed: 120 average time/residue: 0.1965 time to fit residues: 31.5466 Evaluate side-chains 111 residues out of total 841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 105 time to evaluate : 0.723 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0672 time to fit residues: 1.8210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 10 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 67 optimal weight: 20.0000 chunk 77 optimal weight: 0.9980 chunk 51 optimal weight: 8.9990 chunk 91 optimal weight: 5.9990 chunk 57 optimal weight: 0.2980 chunk 55 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 ASN ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 7202 Z= 0.189 Angle : 0.549 8.693 9841 Z= 0.286 Chirality : 0.043 0.139 1180 Planarity : 0.003 0.050 1240 Dihedral : 4.725 29.634 1028 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.75 % Favored : 91.25 % Rotamer Outliers : 1.08 % 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: -4.23 (0.25), residues: 949 helix: -2.78 (0.26), residues: 315 sheet: -3.08 (0.34), residues: 182 loop : -2.60 (0.28), residues: 452 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 113 time to evaluate : 0.805 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 117 average time/residue: 0.1939 time to fit residues: 30.5832 Evaluate side-chains 113 residues out of total 841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 109 time to evaluate : 0.796 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0738 time to fit residues: 1.5963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 54 optimal weight: 0.0170 chunk 27 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 62 optimal weight: 9.9990 chunk 45 optimal weight: 0.4980 chunk 8 optimal weight: 0.0870 chunk 71 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 87 optimal weight: 0.0980 chunk 80 optimal weight: 0.0970 overall best weight: 0.1594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 7202 Z= 0.115 Angle : 0.511 8.629 9841 Z= 0.263 Chirality : 0.041 0.141 1180 Planarity : 0.003 0.051 1240 Dihedral : 4.142 29.473 1028 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer Outliers : 0.46 % 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: -3.88 (0.25), residues: 949 helix: -2.46 (0.27), residues: 316 sheet: -2.88 (0.34), residues: 180 loop : -2.43 (0.28), residues: 453 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 120 time to evaluate : 0.736 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 122 average time/residue: 0.1834 time to fit residues: 30.6752 Evaluate side-chains 103 residues out of total 841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 102 time to evaluate : 0.780 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0711 time to fit residues: 1.2913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 85 optimal weight: 0.0010 chunk 87 optimal weight: 0.0870 chunk 51 optimal weight: 0.0570 chunk 37 optimal weight: 2.9990 chunk 67 optimal weight: 6.9990 chunk 26 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 80 optimal weight: 0.0070 chunk 56 optimal weight: 8.9990 chunk 90 optimal weight: 0.7980 chunk 55 optimal weight: 8.9990 overall best weight: 0.1900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN G 24 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 0.2821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.025 7202 Z= 0.112 Angle : 0.506 8.215 9841 Z= 0.260 Chirality : 0.041 0.136 1180 Planarity : 0.003 0.049 1240 Dihedral : 3.958 26.618 1028 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer Outliers : 0.46 % 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: -3.66 (0.25), residues: 949 helix: -2.34 (0.28), residues: 318 sheet: -2.51 (0.35), residues: 185 loop : -2.35 (0.28), residues: 446 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 103 time to evaluate : 0.729 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 105 average time/residue: 0.1637 time to fit residues: 24.3224 Evaluate side-chains 99 residues out of total 841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 97 time to evaluate : 0.736 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0646 time to fit residues: 1.2451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 42 optimal weight: 2.9990 chunk 62 optimal weight: 0.0170 chunk 94 optimal weight: 4.9990 chunk 87 optimal weight: 0.3980 chunk 75 optimal weight: 0.3980 chunk 7 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 46 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 80 optimal weight: 7.9990 chunk 23 optimal weight: 0.4980 overall best weight: 0.4218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 GLN ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 ASN ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 7202 Z= 0.122 Angle : 0.515 7.909 9841 Z= 0.263 Chirality : 0.041 0.135 1180 Planarity : 0.003 0.046 1240 Dihedral : 3.899 21.104 1028 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer Outliers : 0.15 % 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: -3.45 (0.26), residues: 949 helix: -2.17 (0.28), residues: 312 sheet: -2.31 (0.35), residues: 185 loop : -2.27 (0.28), residues: 452 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 102 time to evaluate : 0.725 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 103 average time/residue: 0.1663 time to fit residues: 24.1202 Evaluate side-chains 99 residues out of total 841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 0.802 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 69 optimal weight: 4.9990 chunk 11 optimal weight: 0.1980 chunk 20 optimal weight: 9.9990 chunk 75 optimal weight: 0.2980 chunk 31 optimal weight: 0.0070 chunk 77 optimal weight: 0.0980 chunk 9 optimal weight: 0.6980 chunk 13 optimal weight: 8.9990 chunk 66 optimal weight: 10.0000 chunk 4 optimal weight: 4.9990 chunk 54 optimal weight: 0.9990 overall best weight: 0.2598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 ASN ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.171300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.148790 restraints weight = 7580.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.145690 restraints weight = 12197.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.147055 restraints weight = 11632.797| |-----------------------------------------------------------------------------| r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.3058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.026 7202 Z= 0.110 Angle : 0.497 7.910 9841 Z= 0.254 Chirality : 0.041 0.135 1180 Planarity : 0.003 0.042 1240 Dihedral : 3.727 14.956 1028 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer Outliers : 0.46 % 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: -3.21 (0.26), residues: 949 helix: -1.92 (0.29), residues: 307 sheet: -2.21 (0.35), residues: 191 loop : -2.13 (0.28), residues: 451 =============================================================================== Job complete usr+sys time: 1603.06 seconds wall clock time: 29 minutes 42.02 seconds (1782.02 seconds total)