Starting phenix.real_space_refine on Fri Dec 8 13:50:34 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jol_36459/12_2023/8jol_36459_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jol_36459/12_2023/8jol_36459.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jol_36459/12_2023/8jol_36459.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jol_36459/12_2023/8jol_36459.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jol_36459/12_2023/8jol_36459_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jol_36459/12_2023/8jol_36459_updated.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 6 5.49 5 Mg 2 5.21 5 S 58 5.16 5 C 5388 2.51 5 N 1439 2.21 5 O 1620 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 4": "OE1" <-> "OE2" Residue "A GLU 38": "OE1" <-> "OE2" Residue "A GLU 88": "OE1" <-> "OE2" Residue "A GLU 255": "OE1" <-> "OE2" Residue "A GLU 289": "OE1" <-> "OE2" Residue "A GLU 324": "OE1" <-> "OE2" Residue "A GLU 341": "OE1" <-> "OE2" Residue "A GLU 383": "OE1" <-> "OE2" Residue "A GLU 424": "OE1" <-> "OE2" Residue "A ARG 436": "NH1" <-> "NH2" Residue "A ARG 440": "NH1" <-> "NH2" Residue "A ARG 448": "NH1" <-> "NH2" Residue "A ARG 483": "NH1" <-> "NH2" Residue "A GLU 486": "OE1" <-> "OE2" Residue "B GLU 4": "OE1" <-> "OE2" Residue "B GLU 88": "OE1" <-> "OE2" Residue "B GLU 255": "OE1" <-> "OE2" Residue "B GLU 289": "OE1" <-> "OE2" Residue "B GLU 324": "OE1" <-> "OE2" Residue "B GLU 383": "OE1" <-> "OE2" Residue "B ARG 436": "NH1" <-> "NH2" Residue "B ARG 440": "NH1" <-> "NH2" Residue "B ARG 448": "NH1" <-> "NH2" Residue "B ARG 483": "NH1" <-> "NH2" Residue "B GLU 486": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 8513 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 503, 4039 Classifications: {'peptide': 503} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 481} Chain breaks: 2 Chain: "B" Number of atoms: 3965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 3965 Classifications: {'peptide': 494} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 473} Chain breaks: 3 Chain: "C" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 445 Classifications: {'peptide': 90} Incomplete info: {'truncation_to_alanine': 78} Link IDs: {'PTRANS': 1, 'TRANS': 88} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 278 Unresolved non-hydrogen angles: 349 Unresolved non-hydrogen dihedrals: 221 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 4, 'ASP:plan': 7, 'PHE:plan': 3, 'GLU:plan': 8, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 162 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.91, per 1000 atoms: 0.58 Number of scatterers: 8513 At special positions: 0 Unit cell: (95.04, 114.84, 137.28, 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 58 16.00 P 6 15.00 Mg 2 11.99 O 1620 8.00 N 1439 7.00 C 5388 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.49 Conformation dependent library (CDL) restraints added in 1.8 seconds 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2096 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 57 helices and 3 sheets defined 55.7% alpha, 5.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.60 Creating SS restraints... Processing helix chain 'A' and resid 4 through 17 removed outlier: 3.630A pdb=" N LEU A 10 " --> pdb=" O GLU A 6 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N HIS A 14 " --> pdb=" O LEU A 10 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N THR A 15 " --> pdb=" O SER A 11 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N ARG A 16 " --> pdb=" O THR A 12 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU A 17 " --> pdb=" O ALA A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 23 through 32 removed outlier: 4.419A pdb=" N THR A 28 " --> pdb=" O ARG A 24 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N TYR A 29 " --> pdb=" O ASP A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 45 Processing helix chain 'A' and resid 50 through 64 removed outlier: 3.833A pdb=" N ARG A 63 " --> pdb=" O ARG A 59 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLN A 64 " --> pdb=" O ILE A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 77 Processing helix chain 'A' and resid 81 through 95 removed outlier: 3.881A pdb=" N PHE A 86 " --> pdb=" O HIS A 82 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ALA A 94 " --> pdb=" O TYR A 90 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ILE A 95 " --> pdb=" O ILE A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 104 Processing helix chain 'A' and resid 107 through 109 No H-bonds generated for 'chain 'A' and resid 107 through 109' Processing helix chain 'A' and resid 112 through 121 Processing helix chain 'A' and resid 134 through 147 removed outlier: 3.952A pdb=" N MET A 147 " --> pdb=" O LYS A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 172 Processing helix chain 'A' and resid 199 through 211 removed outlier: 4.023A pdb=" N PHE A 204 " --> pdb=" O THR A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 241 removed outlier: 3.692A pdb=" N ALA A 238 " --> pdb=" O MET A 234 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N ASP A 241 " --> pdb=" O ASN A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 263 removed outlier: 3.653A pdb=" N ALA A 261 " --> pdb=" O THR A 257 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLN A 262 " --> pdb=" O ILE A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 280 Processing helix chain 'A' and resid 295 through 305 removed outlier: 3.648A pdb=" N TYR A 299 " --> pdb=" O ILE A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 326 removed outlier: 4.885A pdb=" N VAL A 318 " --> pdb=" O LYS A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 339 Processing helix chain 'A' and resid 345 through 354 Processing helix chain 'A' and resid 359 through 362 Processing helix chain 'A' and resid 374 through 383 removed outlier: 4.498A pdb=" N ARG A 380 " --> pdb=" O MET A 376 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N CYS A 381 " --> pdb=" O ALA A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 398 removed outlier: 3.738A pdb=" N SER A 391 " --> pdb=" O ASP A 387 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA A 396 " --> pdb=" O ALA A 392 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N VAL A 397 " --> pdb=" O LEU A 393 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N VAL A 398 " --> pdb=" O ALA A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 411 Processing helix chain 'A' and resid 429 through 439 Processing helix chain 'A' and resid 459 through 467 removed outlier: 3.654A pdb=" N PHE A 463 " --> pdb=" O ILE A 459 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LEU A 464 " --> pdb=" O ILE A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 485 removed outlier: 3.768A pdb=" N ALA A 474 " --> pdb=" O ALA A 470 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLN A 482 " --> pdb=" O SER A 478 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG A 483 " --> pdb=" O ILE A 479 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU A 485 " --> pdb=" O GLU A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 541 removed outlier: 4.526A pdb=" N LYS A 538 " --> pdb=" O LEU A 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 17 removed outlier: 3.630A pdb=" N LEU B 10 " --> pdb=" O GLU B 6 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N HIS B 14 " --> pdb=" O LEU B 10 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N THR B 15 " --> pdb=" O SER B 11 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N ARG B 16 " --> pdb=" O THR B 12 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU B 17 " --> pdb=" O ALA B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 32 removed outlier: 4.377A pdb=" N THR B 28 " --> pdb=" O ARG B 24 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N TYR B 29 " --> pdb=" O ASP B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 45 Processing helix chain 'B' and resid 50 through 64 removed outlier: 3.541A pdb=" N ARG B 62 " --> pdb=" O LEU B 58 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ARG B 63 " --> pdb=" O ARG B 59 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN B 64 " --> pdb=" O ILE B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 77 Processing helix chain 'B' and resid 81 through 95 removed outlier: 3.836A pdb=" N PHE B 86 " --> pdb=" O HIS B 82 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ALA B 94 " --> pdb=" O TYR B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 121 removed outlier: 3.891A pdb=" N MET B 114 " --> pdb=" O PHE B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 147 removed outlier: 3.897A pdb=" N MET B 147 " --> pdb=" O LYS B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 172 Processing helix chain 'B' and resid 199 through 211 removed outlier: 4.015A pdb=" N PHE B 204 " --> pdb=" O THR B 200 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU B 208 " --> pdb=" O PHE B 204 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU B 209 " --> pdb=" O THR B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 241 removed outlier: 3.929A pdb=" N ASP B 241 " --> pdb=" O ASN B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 263 Processing helix chain 'B' and resid 275 through 280 Processing helix chain 'B' and resid 295 through 305 removed outlier: 3.591A pdb=" N TYR B 299 " --> pdb=" O ILE B 295 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR B 305 " --> pdb=" O PHE B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 326 removed outlier: 4.890A pdb=" N VAL B 318 " --> pdb=" O LYS B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 339 Processing helix chain 'B' and resid 345 through 362 removed outlier: 3.791A pdb=" N GLU B 356 " --> pdb=" O ASN B 352 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N LEU B 360 " --> pdb=" O GLU B 356 " (cutoff:3.500A) removed outlier: 8.202A pdb=" N VAL B 361 " --> pdb=" O SER B 357 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLY B 362 " --> pdb=" O ARG B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 383 removed outlier: 4.531A pdb=" N ARG B 380 " --> pdb=" O MET B 376 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N CYS B 381 " --> pdb=" O ALA B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 398 removed outlier: 3.533A pdb=" N ALA B 396 " --> pdb=" O ALA B 392 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N VAL B 397 " --> pdb=" O LEU B 393 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N VAL B 398 " --> pdb=" O ALA B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 411 No H-bonds generated for 'chain 'B' and resid 408 through 411' Processing helix chain 'B' and resid 429 through 439 Processing helix chain 'B' and resid 458 through 467 Processing helix chain 'B' and resid 470 through 484 removed outlier: 3.793A pdb=" N ALA B 474 " --> pdb=" O ALA B 470 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ARG B 483 " --> pdb=" O ILE B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 541 removed outlier: 4.491A pdb=" N LYS B 538 " --> pdb=" O LEU B 535 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 17 removed outlier: 4.065A pdb=" N ILE C 14 " --> pdb=" O LEU C 10 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N MET C 15 " --> pdb=" O GLU C 11 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N MET C 16 " --> pdb=" O ARG C 12 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N PHE C 17 " --> pdb=" O ASN C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 32 removed outlier: 4.378A pdb=" N GLU C 28 " --> pdb=" O ASP C 24 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N VAL C 29 " --> pdb=" O GLU C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 45 Processing helix chain 'C' and resid 50 through 63 Processing helix chain 'C' and resid 71 through 77 removed outlier: 4.973A pdb=" N ALA C 75 " --> pdb=" O PHE C 72 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU C 76 " --> pdb=" O TYR C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 91 removed outlier: 3.837A pdb=" N GLU C 86 " --> pdb=" O GLU C 82 " (cutoff:3.500A) Proline residue: C 90 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 285 through 290 removed outlier: 6.481A pdb=" N PHE A 154 " --> pdb=" O GLU A 286 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N ILE A 288 " --> pdb=" O PHE A 154 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N PHE A 156 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N VAL A 290 " --> pdb=" O PHE A 156 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N HIS A 158 " --> pdb=" O VAL A 290 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N THR A 272 " --> pdb=" O LEU A 157 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N THR A 245 " --> pdb=" O ARG A 267 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N LEU A 269 " --> pdb=" O THR A 245 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N PHE A 247 " --> pdb=" O LEU A 269 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N THR A 271 " --> pdb=" O PHE A 247 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N PHE A 249 " --> pdb=" O THR A 271 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N SER A 186 " --> pdb=" O LEU A 246 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N VAL A 248 " --> pdb=" O SER A 186 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N VAL A 188 " --> pdb=" O VAL A 248 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N ASP A 250 " --> pdb=" O VAL A 188 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N LEU A 190 " --> pdb=" O ASP A 250 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N VAL A 252 " --> pdb=" O LEU A 190 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 445 through 447 Processing sheet with id= C, first strand: chain 'B' and resid 286 through 290 removed outlier: 3.635A pdb=" N THR B 272 " --> pdb=" O LEU B 157 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY B 159 " --> pdb=" O THR B 272 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N THR B 245 " --> pdb=" O ARG B 267 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N LEU B 269 " --> pdb=" O THR B 245 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N PHE B 247 " --> pdb=" O LEU B 269 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N THR B 271 " --> pdb=" O PHE B 247 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N PHE B 249 " --> pdb=" O THR B 271 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N SER B 186 " --> pdb=" O LEU B 246 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N VAL B 248 " --> pdb=" O SER B 186 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N VAL B 188 " --> pdb=" O VAL B 248 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N ASP B 250 " --> pdb=" O VAL B 188 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N LEU B 190 " --> pdb=" O ASP B 250 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N VAL B 252 " --> pdb=" O LEU B 190 " (cutoff:3.500A) 326 hydrogen bonds defined for protein. 912 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: 2.10 Time building geometry restraints manager: 3.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2514 1.33 - 1.46: 1796 1.46 - 1.59: 4252 1.59 - 1.72: 6 1.72 - 1.85: 92 Bond restraints: 8660 Sorted by residual: bond pdb=" C4 ATP A 602 " pdb=" C5 ATP A 602 " ideal model delta sigma weight residual 1.388 1.483 -0.095 1.00e-02 1.00e+04 8.95e+01 bond pdb=" C4 ATP B 602 " pdb=" C5 ATP B 602 " ideal model delta sigma weight residual 1.388 1.480 -0.092 1.00e-02 1.00e+04 8.53e+01 bond pdb=" C5 ATP A 602 " pdb=" C6 ATP A 602 " ideal model delta sigma weight residual 1.409 1.492 -0.083 1.00e-02 1.00e+04 6.84e+01 bond pdb=" C5 ATP B 602 " pdb=" N7 ATP B 602 " ideal model delta sigma weight residual 1.387 1.332 0.055 1.00e-02 1.00e+04 3.01e+01 bond pdb=" C8 ATP A 602 " pdb=" N7 ATP A 602 " ideal model delta sigma weight residual 1.310 1.356 -0.046 1.00e-02 1.00e+04 2.09e+01 ... (remaining 8655 not shown) Histogram of bond angle deviations from ideal: 96.59 - 104.55: 161 104.55 - 112.51: 4239 112.51 - 120.47: 3971 120.47 - 128.43: 3308 128.43 - 136.39: 52 Bond angle restraints: 11731 Sorted by residual: angle pdb=" PB ATP A 602 " pdb=" O3B ATP A 602 " pdb=" PG ATP A 602 " ideal model delta sigma weight residual 139.87 114.14 25.73 1.00e+00 1.00e+00 6.62e+02 angle pdb=" PA ATP B 602 " pdb=" O3A ATP B 602 " pdb=" PB ATP B 602 " ideal model delta sigma weight residual 136.83 119.12 17.71 1.00e+00 1.00e+00 3.14e+02 angle pdb=" PB ATP B 602 " pdb=" O3B ATP B 602 " pdb=" PG ATP B 602 " ideal model delta sigma weight residual 139.87 122.83 17.04 1.00e+00 1.00e+00 2.90e+02 angle pdb=" PA ATP A 602 " pdb=" O3A ATP A 602 " pdb=" PB ATP A 602 " ideal model delta sigma weight residual 136.83 121.64 15.19 1.00e+00 1.00e+00 2.31e+02 angle pdb=" N3 ATP B 602 " pdb=" C4 ATP B 602 " pdb=" N9 ATP B 602 " ideal model delta sigma weight residual 127.04 136.39 -9.35 1.15e+00 7.59e-01 6.64e+01 ... (remaining 11726 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.39: 4606 17.39 - 34.79: 480 34.79 - 52.18: 162 52.18 - 69.58: 78 69.58 - 86.97: 13 Dihedral angle restraints: 5339 sinusoidal: 2140 harmonic: 3199 Sorted by residual: dihedral pdb=" CA ASP B 216 " pdb=" C ASP B 216 " pdb=" N LEU B 217 " pdb=" CA LEU B 217 " ideal model delta harmonic sigma weight residual 180.00 153.89 26.11 0 5.00e+00 4.00e-02 2.73e+01 dihedral pdb=" CA ASP A 216 " pdb=" C ASP A 216 " pdb=" N LEU A 217 " pdb=" CA LEU A 217 " ideal model delta harmonic sigma weight residual 180.00 154.86 25.14 0 5.00e+00 4.00e-02 2.53e+01 dihedral pdb=" CA CYS A 268 " pdb=" C CYS A 268 " pdb=" N LEU A 269 " pdb=" CA LEU A 269 " ideal model delta harmonic sigma weight residual 180.00 158.55 21.45 0 5.00e+00 4.00e-02 1.84e+01 ... (remaining 5336 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 960 0.070 - 0.140: 301 0.140 - 0.210: 76 0.210 - 0.279: 19 0.279 - 0.349: 4 Chirality restraints: 1360 Sorted by residual: chirality pdb=" CA PHE A 532 " pdb=" N PHE A 532 " pdb=" C PHE A 532 " pdb=" CB PHE A 532 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.05e+00 chirality pdb=" CA LYS A 212 " pdb=" N LYS A 212 " pdb=" C LYS A 212 " pdb=" CB LYS A 212 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 2.99e+00 chirality pdb=" CA PHE B 532 " pdb=" N PHE B 532 " pdb=" C PHE B 532 " pdb=" CB PHE B 532 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.69e+00 ... (remaining 1357 not shown) Planarity restraints: 1502 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL C 87 " 0.015 2.00e-02 2.50e+03 3.04e-02 9.22e+00 pdb=" C VAL C 87 " -0.053 2.00e-02 2.50e+03 pdb=" O VAL C 87 " 0.020 2.00e-02 2.50e+03 pdb=" N LEU C 88 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 253 " 0.015 2.00e-02 2.50e+03 2.95e-02 8.71e+00 pdb=" C VAL A 253 " -0.051 2.00e-02 2.50e+03 pdb=" O VAL A 253 " 0.019 2.00e-02 2.50e+03 pdb=" N GLN A 254 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 220 " -0.039 5.00e-02 4.00e+02 5.97e-02 5.71e+00 pdb=" N PRO B 221 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO B 221 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 221 " -0.032 5.00e-02 4.00e+02 ... (remaining 1499 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1350 2.75 - 3.29: 9150 3.29 - 3.83: 14134 3.83 - 4.36: 18355 4.36 - 4.90: 27803 Nonbonded interactions: 70792 Sorted by model distance: nonbonded pdb=" O1B ATP A 602 " pdb=" O2G ATP A 602 " model vdw 2.214 3.040 nonbonded pdb=" O ARG A 259 " pdb=" N GLN A 262 " model vdw 2.275 2.520 nonbonded pdb=" O4' ATP A 602 " pdb=" O5' ATP A 602 " model vdw 2.319 2.432 nonbonded pdb=" OG SER B 166 " pdb="MG MG B 601 " model vdw 2.341 2.170 nonbonded pdb=" O LEU B 120 " pdb=" N ASN B 123 " model vdw 2.349 2.520 ... (remaining 70787 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 98 or resid 106 through 416 or resid 426 through \ 543 or resid 601 through 602)) selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.930 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 26.560 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.040 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:10.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7047 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 : 0.009 0.095 8660 Z= 0.591 Angle : 1.462 25.735 11731 Z= 1.023 Chirality : 0.074 0.349 1360 Planarity : 0.005 0.060 1502 Dihedral : 18.200 86.969 3243 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 35.79 Ramachandran Plot: Outliers : 0.84 % Allowed : 12.32 % Favored : 86.83 % Rotamer: Outliers : 16.43 % Allowed : 15.21 % Favored : 68.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -4.77 (0.21), residues: 1071 helix: -3.29 (0.15), residues: 632 sheet: -2.60 (0.61), residues: 60 loop : -2.63 (0.29), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.005 TRP B 189 HIS 0.003 0.001 HIS B 225 PHE 0.018 0.003 PHE A 156 TYR 0.022 0.004 TYR B 184 ARG 0.003 0.001 ARG B 265 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 215 time to evaluate : 1.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 149 outliers final: 10 residues processed: 317 average time/residue: 0.9065 time to fit residues: 310.4388 Evaluate side-chains 135 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 125 time to evaluate : 0.963 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 7 residues processed: 4 average time/residue: 0.7880 time to fit residues: 4.7688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.8980 chunk 81 optimal weight: 0.9980 chunk 45 optimal weight: 6.9990 chunk 27 optimal weight: 0.9980 chunk 55 optimal weight: 0.6980 chunk 43 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 51 optimal weight: 9.9990 chunk 63 optimal weight: 4.9990 chunk 98 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN A 40 HIS A 123 ASN A 219 ASN A 329 ASN A 461 HIS A 471 GLN A 482 GLN A 534 GLN B 34 ASN B 64 GLN B 76 ASN B 113 GLN B 244 ASN ** B 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 482 GLN B 534 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.4934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8660 Z= 0.224 Angle : 0.770 11.468 11731 Z= 0.377 Chirality : 0.042 0.184 1360 Planarity : 0.006 0.054 1502 Dihedral : 10.200 81.923 1228 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 6.50 % Allowed : 27.12 % Favored : 66.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -2.26 (0.24), residues: 1071 helix: -1.24 (0.19), residues: 640 sheet: -2.33 (0.54), residues: 58 loop : -1.52 (0.31), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 260 HIS 0.003 0.001 HIS A 40 PHE 0.019 0.002 PHE B 220 TYR 0.016 0.002 TYR A 77 ARG 0.010 0.001 ARG A 483 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 119 time to evaluate : 1.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 59 outliers final: 17 residues processed: 163 average time/residue: 0.9500 time to fit residues: 167.2060 Evaluate side-chains 111 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 94 time to evaluate : 0.940 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 13 residues processed: 4 average time/residue: 0.1717 time to fit residues: 2.2325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 0.0270 chunk 30 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 chunk 27 optimal weight: 9.9990 chunk 98 optimal weight: 3.9990 chunk 106 optimal weight: 20.0000 chunk 87 optimal weight: 5.9990 chunk 97 optimal weight: 4.9990 chunk 33 optimal weight: 0.8980 chunk 78 optimal weight: 8.9990 overall best weight: 2.5844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 HIS A 123 ASN A 244 ASN ** B 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 262 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.8743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 8660 Z= 0.312 Angle : 0.817 11.541 11731 Z= 0.400 Chirality : 0.044 0.145 1360 Planarity : 0.006 0.054 1502 Dihedral : 10.071 82.344 1228 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.42 % Favored : 94.49 % Rotamer: Outliers : 6.39 % Allowed : 24.70 % Favored : 68.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -1.14 (0.25), residues: 1071 helix: -0.41 (0.20), residues: 660 sheet: -1.77 (0.60), residues: 56 loop : -0.95 (0.34), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 410 HIS 0.006 0.001 HIS A 458 PHE 0.028 0.002 PHE B 395 TYR 0.017 0.002 TYR B 369 ARG 0.007 0.001 ARG A 390 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 84 time to evaluate : 1.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 58 outliers final: 12 residues processed: 130 average time/residue: 1.0894 time to fit residues: 152.3545 Evaluate side-chains 78 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 66 time to evaluate : 1.086 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 11 residues processed: 1 average time/residue: 0.2338 time to fit residues: 1.7199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 7.9990 chunk 73 optimal weight: 8.9990 chunk 50 optimal weight: 6.9990 chunk 10 optimal weight: 10.0000 chunk 46 optimal weight: 0.6980 chunk 65 optimal weight: 6.9990 chunk 98 optimal weight: 7.9990 chunk 104 optimal weight: 30.0000 chunk 51 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 chunk 28 optimal weight: 5.9990 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 262 GLN ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 64 GLN B 158 HIS ** B 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 1.0985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 8660 Z= 0.415 Angle : 0.775 9.772 11731 Z= 0.385 Chirality : 0.045 0.159 1360 Planarity : 0.006 0.058 1502 Dihedral : 9.657 88.518 1228 Min Nonbonded Distance : 1.719 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 6.84 % Allowed : 25.36 % Favored : 67.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.25), residues: 1071 helix: 0.13 (0.20), residues: 657 sheet: -2.08 (0.65), residues: 44 loop : -0.92 (0.32), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 410 HIS 0.006 0.001 HIS A 19 PHE 0.024 0.002 PHE B 337 TYR 0.033 0.002 TYR B 369 ARG 0.009 0.001 ARG A 8 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 67 time to evaluate : 1.021 Fit side-chains outliers start: 62 outliers final: 11 residues processed: 121 average time/residue: 1.0803 time to fit residues: 141.6562 Evaluate side-chains 70 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 59 time to evaluate : 1.059 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 10 residues processed: 1 average time/residue: 0.2443 time to fit residues: 1.7404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 1 optimal weight: 4.9990 chunk 77 optimal weight: 8.9990 chunk 43 optimal weight: 0.5980 chunk 89 optimal weight: 0.2980 chunk 72 optimal weight: 0.4980 chunk 0 optimal weight: 7.9990 chunk 53 optimal weight: 8.9990 chunk 93 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 262 GLN A 425 GLN ** B 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 1.1166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8660 Z= 0.187 Angle : 0.661 10.419 11731 Z= 0.317 Chirality : 0.040 0.192 1360 Planarity : 0.005 0.054 1502 Dihedral : 8.661 82.512 1228 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.76 % Allowed : 27.56 % Favored : 69.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.26), residues: 1071 helix: 0.71 (0.21), residues: 659 sheet: -1.44 (0.65), residues: 46 loop : -0.81 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 410 HIS 0.003 0.000 HIS B 82 PHE 0.014 0.001 PHE A 204 TYR 0.012 0.001 TYR B 135 ARG 0.007 0.000 ARG A 8 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 60 time to evaluate : 1.066 Fit side-chains revert: symmetry clash outliers start: 25 outliers final: 11 residues processed: 84 average time/residue: 1.1877 time to fit residues: 107.1533 Evaluate side-chains 65 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 54 time to evaluate : 1.064 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 11 residues processed: 0 time to fit residues: 1.4635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 1.9990 chunk 94 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 61 optimal weight: 0.5980 chunk 25 optimal weight: 6.9990 chunk 104 optimal weight: 50.0000 chunk 86 optimal weight: 2.9990 chunk 48 optimal weight: 9.9990 chunk 8 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 54 optimal weight: 0.0010 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 262 GLN A 283 GLN ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 475 ASN B 254 GLN B 379 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 1.1390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8660 Z= 0.175 Angle : 0.654 13.820 11731 Z= 0.309 Chirality : 0.040 0.174 1360 Planarity : 0.005 0.054 1502 Dihedral : 8.422 88.527 1228 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.43 % Allowed : 27.56 % Favored : 70.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.26), residues: 1071 helix: 0.90 (0.21), residues: 662 sheet: -0.81 (0.69), residues: 46 loop : -0.71 (0.31), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 410 HIS 0.003 0.000 HIS B 82 PHE 0.016 0.001 PHE A 204 TYR 0.018 0.001 TYR B 77 ARG 0.007 0.000 ARG A 8 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 60 time to evaluate : 0.956 Fit side-chains revert: symmetry clash outliers start: 22 outliers final: 11 residues processed: 81 average time/residue: 1.0174 time to fit residues: 89.6125 Evaluate side-chains 66 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 55 time to evaluate : 1.150 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 11 residues processed: 1 average time/residue: 0.2442 time to fit residues: 1.6715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 0.0870 chunk 11 optimal weight: 3.9990 chunk 59 optimal weight: 6.9990 chunk 76 optimal weight: 10.0000 chunk 87 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 104 optimal weight: 9.9990 chunk 65 optimal weight: 6.9990 chunk 63 optimal weight: 1.9990 chunk 48 optimal weight: 10.0000 chunk 64 optimal weight: 1.9990 overall best weight: 2.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 262 GLN ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 1.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 8660 Z= 0.238 Angle : 0.682 14.350 11731 Z= 0.324 Chirality : 0.041 0.176 1360 Planarity : 0.005 0.056 1502 Dihedral : 8.490 89.232 1228 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.65 % Allowed : 28.45 % Favored : 68.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.26), residues: 1071 helix: 0.87 (0.21), residues: 668 sheet: -0.31 (0.72), residues: 46 loop : -0.59 (0.32), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 410 HIS 0.004 0.001 HIS B 82 PHE 0.018 0.001 PHE A 204 TYR 0.016 0.001 TYR B 77 ARG 0.005 0.000 ARG A 8 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 53 time to evaluate : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 11 residues processed: 75 average time/residue: 0.9643 time to fit residues: 79.3584 Evaluate side-chains 65 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 54 time to evaluate : 1.055 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 11 residues processed: 0 time to fit residues: 1.4167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 0.9990 chunk 62 optimal weight: 10.0000 chunk 31 optimal weight: 4.9990 chunk 20 optimal weight: 0.9980 chunk 66 optimal weight: 7.9990 chunk 70 optimal weight: 3.9990 chunk 51 optimal weight: 7.9990 chunk 9 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 chunk 99 optimal weight: 9.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 ASN A 262 GLN ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 1.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 8660 Z= 0.223 Angle : 0.688 15.685 11731 Z= 0.323 Chirality : 0.041 0.172 1360 Planarity : 0.004 0.055 1502 Dihedral : 8.457 88.345 1228 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.21 % Allowed : 28.45 % Favored : 69.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.26), residues: 1071 helix: 0.85 (0.21), residues: 670 sheet: -0.04 (0.74), residues: 46 loop : -0.57 (0.32), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 189 HIS 0.006 0.001 HIS A 19 PHE 0.018 0.001 PHE A 204 TYR 0.016 0.001 TYR B 77 ARG 0.005 0.000 ARG A 8 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 54 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 13 residues processed: 72 average time/residue: 0.9461 time to fit residues: 74.6067 Evaluate side-chains 65 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 52 time to evaluate : 1.036 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 12 residues processed: 1 average time/residue: 1.0650 time to fit residues: 2.5321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 0.9990 chunk 97 optimal weight: 4.9990 chunk 99 optimal weight: 7.9990 chunk 58 optimal weight: 3.9990 chunk 42 optimal weight: 10.0000 chunk 76 optimal weight: 9.9990 chunk 29 optimal weight: 6.9990 chunk 87 optimal weight: 0.9980 chunk 91 optimal weight: 5.9990 chunk 96 optimal weight: 0.9980 chunk 63 optimal weight: 0.3980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 GLN ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 1.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 8660 Z= 0.206 Angle : 0.693 13.747 11731 Z= 0.322 Chirality : 0.041 0.171 1360 Planarity : 0.004 0.055 1502 Dihedral : 8.338 85.485 1228 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.76 % Allowed : 28.56 % Favored : 69.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.26), residues: 1071 helix: 0.89 (0.21), residues: 669 sheet: 0.22 (0.76), residues: 46 loop : -0.51 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 410 HIS 0.004 0.001 HIS B 82 PHE 0.018 0.001 PHE A 204 TYR 0.015 0.001 TYR B 77 ARG 0.006 0.000 ARG A 8 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 57 time to evaluate : 1.113 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 13 residues processed: 72 average time/residue: 1.0538 time to fit residues: 82.6594 Evaluate side-chains 67 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 54 time to evaluate : 1.048 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 13 residues processed: 1 average time/residue: 0.2173 time to fit residues: 1.7066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 7.9990 chunk 62 optimal weight: 8.9990 chunk 48 optimal weight: 3.9990 chunk 71 optimal weight: 6.9990 chunk 107 optimal weight: 0.7980 chunk 99 optimal weight: 8.9990 chunk 85 optimal weight: 0.1980 chunk 8 optimal weight: 1.9990 chunk 66 optimal weight: 0.0270 chunk 52 optimal weight: 0.0570 chunk 68 optimal weight: 0.0000 overall best weight: 0.2160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 1.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8660 Z= 0.178 Angle : 0.708 16.675 11731 Z= 0.323 Chirality : 0.040 0.166 1360 Planarity : 0.004 0.057 1502 Dihedral : 7.999 74.119 1228 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.54 % Allowed : 28.89 % Favored : 69.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.26), residues: 1071 helix: 1.04 (0.22), residues: 645 sheet: 0.47 (0.76), residues: 46 loop : -0.30 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 410 HIS 0.004 0.001 HIS B 82 PHE 0.015 0.001 PHE A 204 TYR 0.015 0.001 TYR B 77 ARG 0.005 0.000 ARG A 8 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 61 time to evaluate : 1.084 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 10 residues processed: 74 average time/residue: 0.9974 time to fit residues: 80.3220 Evaluate side-chains 64 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 54 time to evaluate : 1.017 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 9 residues processed: 1 average time/residue: 0.1339 time to fit residues: 1.6403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.5980 chunk 26 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 12 optimal weight: 0.0370 chunk 23 optimal weight: 0.7980 chunk 85 optimal weight: 0.0980 chunk 35 optimal weight: 5.9990 chunk 88 optimal weight: 5.9990 chunk 10 optimal weight: 0.4980 chunk 15 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 overall best weight: 0.4058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 262 GLN ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.061153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.046209 restraints weight = 35579.572| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 4.41 r_work: 0.2750 rms_B_bonded: 4.89 restraints_weight: 0.5000 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 moved from start: 1.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8660 Z= 0.180 Angle : 0.718 15.888 11731 Z= 0.326 Chirality : 0.040 0.165 1360 Planarity : 0.004 0.058 1502 Dihedral : 7.762 71.314 1228 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.65 % Allowed : 29.33 % Favored : 69.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.26), residues: 1071 helix: 1.07 (0.22), residues: 644 sheet: 0.57 (0.75), residues: 46 loop : -0.23 (0.31), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 410 HIS 0.004 0.001 HIS B 82 PHE 0.017 0.001 PHE A 204 TYR 0.015 0.001 TYR B 77 ARG 0.005 0.000 ARG A 8 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2885.59 seconds wall clock time: 52 minutes 14.92 seconds (3134.92 seconds total)