Starting phenix.real_space_refine (version: 1.21rc1) on Thu Aug 10 18:36:01 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jol_36459/08_2023/8jol_36459_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jol_36459/08_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_36459/08_2023/8jol_36459.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jol_36459/08_2023/8jol_36459.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jol_36459/08_2023/8jol_36459_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jol_36459/08_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-1.21rc1-5044/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: 4.70, per 1000 atoms: 0.55 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: 3.38 Conformation dependent library (CDL) restraints added in 1.4 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: 1.45 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: 2.20 Time building geometry restraints manager: 3.68 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: 4597 17.39 - 34.79: 463 34.79 - 52.18: 149 52.18 - 69.58: 61 69.58 - 86.97: 7 Dihedral angle restraints: 5277 sinusoidal: 2078 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 5274 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: 1.020 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: 4.290 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 24.990 Find NCS groups from input model: 0.490 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:11.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.920 ------------------------------------------------------------------------------- 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 : 17.244 86.969 3181 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 % 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 *********************** 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 : 1.064 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: 0.9047 time to fit residues: 310.0651 Evaluate side-chains 135 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 125 time to evaluate : 0.919 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 7 residues processed: 4 average time/residue: 0.7067 time to fit residues: 4.3936 ------------------------------------------------------------------------------- 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: 0.7481 moved from start: 0.4941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 8660 Z= 0.232 Angle : 0.765 10.744 11731 Z= 0.377 Chirality : 0.042 0.185 1360 Planarity : 0.005 0.055 1502 Dihedral : 6.229 88.247 1166 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 15.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer Outliers : 6.50 % 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: -2.28 (0.24), residues: 1071 helix: -1.26 (0.19), residues: 641 sheet: -2.32 (0.54), residues: 58 loop : -1.51 (0.31), residues: 372 *********************** 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 176 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 117 time to evaluate : 1.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 59 outliers final: 18 residues processed: 162 average time/residue: 0.9757 time to fit residues: 171.0838 Evaluate side-chains 109 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 91 time to evaluate : 1.021 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 14 residues processed: 5 average time/residue: 0.2063 time to fit residues: 2.7719 ------------------------------------------------------------------------------- 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: 3.9990 chunk 30 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 27 optimal weight: 10.0000 chunk 98 optimal weight: 4.9990 chunk 106 optimal weight: 40.0000 chunk 87 optimal weight: 5.9990 chunk 97 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 78 optimal weight: 7.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 ASN A 536 HIS ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.9323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.046 8660 Z= 0.354 Angle : 0.831 9.123 11731 Z= 0.414 Chirality : 0.045 0.174 1360 Planarity : 0.006 0.081 1502 Dihedral : 6.527 89.907 1166 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer Outliers : 7.06 % 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: -1.24 (0.25), residues: 1071 helix: -0.49 (0.19), residues: 653 sheet: -1.75 (0.59), residues: 56 loop : -0.99 (0.33), residues: 362 *********************** 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 146 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 82 time to evaluate : 1.040 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 64 outliers final: 17 residues processed: 132 average time/residue: 1.0981 time to fit residues: 155.6786 Evaluate side-chains 85 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 68 time to evaluate : 0.968 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 15 residues processed: 2 average time/residue: 0.2027 time to fit residues: 1.9274 ------------------------------------------------------------------------------- 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: 0.9980 chunk 73 optimal weight: 9.9990 chunk 50 optimal weight: 9.9990 chunk 10 optimal weight: 0.0870 chunk 46 optimal weight: 0.8980 chunk 65 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 chunk 104 optimal weight: 7.9990 chunk 51 optimal weight: 0.8980 chunk 93 optimal weight: 5.9990 chunk 28 optimal weight: 6.9990 overall best weight: 1.1760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 HIS A 96 ASN A 425 GLN B 40 HIS B 64 GLN B 158 HIS ** B 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.9868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 8660 Z= 0.195 Angle : 0.664 9.287 11731 Z= 0.323 Chirality : 0.041 0.193 1360 Planarity : 0.005 0.062 1502 Dihedral : 5.965 89.932 1166 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer Outliers : 3.75 % 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: -0.34 (0.26), residues: 1071 helix: 0.34 (0.21), residues: 661 sheet: -1.51 (0.60), residues: 56 loop : -0.89 (0.32), residues: 354 *********************** 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 107 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 73 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 17 residues processed: 100 average time/residue: 0.9219 time to fit residues: 100.5804 Evaluate side-chains 84 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 67 time to evaluate : 0.998 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 15 residues processed: 3 average time/residue: 0.4784 time to fit residues: 2.9906 ------------------------------------------------------------------------------- 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: 0.5980 chunk 59 optimal weight: 10.0000 chunk 1 optimal weight: 0.7980 chunk 77 optimal weight: 9.9990 chunk 43 optimal weight: 0.0870 chunk 89 optimal weight: 8.9990 chunk 72 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 53 optimal weight: 9.9990 chunk 93 optimal weight: 6.9990 chunk 26 optimal weight: 7.9990 overall best weight: 2.2962 ------------------------------------------------------------------------------- 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** ** B 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 1.0724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 8660 Z= 0.258 Angle : 0.691 14.207 11731 Z= 0.334 Chirality : 0.042 0.189 1360 Planarity : 0.005 0.059 1502 Dihedral : 5.945 84.292 1166 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer Outliers : 4.30 % 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: -0.03 (0.26), residues: 1071 helix: 0.58 (0.21), residues: 672 sheet: -1.04 (0.66), residues: 46 loop : -0.89 (0.33), residues: 353 *********************** 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 102 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 63 time to evaluate : 1.102 Fit side-chains outliers start: 39 outliers final: 10 residues processed: 96 average time/residue: 0.9970 time to fit residues: 103.8925 Evaluate side-chains 70 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 60 time to evaluate : 0.963 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 10 residues processed: 0 time to fit residues: 1.3497 ------------------------------------------------------------------------------- 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: 4.9990 chunk 94 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 61 optimal weight: 0.0030 chunk 25 optimal weight: 4.9990 chunk 104 optimal weight: 9.9990 chunk 86 optimal weight: 0.4980 chunk 48 optimal weight: 0.0020 chunk 8 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 54 optimal weight: 8.9990 overall best weight: 0.5000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 GLN B 254 GLN B 379 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 1.0887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 8660 Z= 0.171 Angle : 0.645 12.201 11731 Z= 0.307 Chirality : 0.040 0.184 1360 Planarity : 0.004 0.055 1502 Dihedral : 5.674 81.215 1166 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer Outliers : 2.54 % 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: 0.27 (0.26), residues: 1071 helix: 0.88 (0.21), residues: 661 sheet: -0.69 (0.69), residues: 46 loop : -0.89 (0.31), residues: 364 *********************** 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 87 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 64 time to evaluate : 0.986 Fit side-chains outliers start: 23 outliers final: 10 residues processed: 84 average time/residue: 1.0653 time to fit residues: 96.9399 Evaluate side-chains 71 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 61 time to evaluate : 0.977 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 9 residues processed: 1 average time/residue: 0.1299 time to fit residues: 1.6701 ------------------------------------------------------------------------------- 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: 50.0000 chunk 11 optimal weight: 0.9980 chunk 59 optimal weight: 9.9990 chunk 76 optimal weight: 4.9990 chunk 87 optimal weight: 8.9990 chunk 58 optimal weight: 7.9990 chunk 104 optimal weight: 5.9990 chunk 65 optimal weight: 6.9990 chunk 63 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- 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** A 475 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 1.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.066 8660 Z= 0.329 Angle : 0.735 12.717 11731 Z= 0.352 Chirality : 0.043 0.178 1360 Planarity : 0.005 0.056 1502 Dihedral : 5.738 74.516 1166 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer Outliers : 3.86 % 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: 0.14 (0.26), residues: 1071 helix: 0.62 (0.21), residues: 677 sheet: -0.24 (0.72), residues: 46 loop : -0.74 (0.33), residues: 348 *********************** 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 94 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 59 time to evaluate : 1.062 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 14 residues processed: 90 average time/residue: 0.9742 time to fit residues: 95.4858 Evaluate side-chains 69 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 55 time to evaluate : 1.022 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 13 residues processed: 1 average time/residue: 1.0094 time to fit residues: 2.3564 ------------------------------------------------------------------------------- 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: 9.9990 chunk 62 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 70 optimal weight: 0.5980 chunk 51 optimal weight: 5.9990 chunk 9 optimal weight: 7.9990 chunk 81 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 99 optimal weight: 8.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 1.1858 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= 0.204 Angle : 0.694 13.048 11731 Z= 0.325 Chirality : 0.041 0.183 1360 Planarity : 0.004 0.054 1502 Dihedral : 5.476 71.036 1166 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer Outliers : 2.54 % 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: 0.32 (0.26), residues: 1071 helix: 0.80 (0.21), residues: 669 sheet: 0.00 (0.73), residues: 46 loop : -0.77 (0.32), residues: 356 *********************** 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 78 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 55 time to evaluate : 1.043 Fit side-chains revert: symmetry clash outliers start: 23 outliers final: 15 residues processed: 76 average time/residue: 1.0553 time to fit residues: 87.1853 Evaluate side-chains 68 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 53 time to evaluate : 1.031 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 14 residues processed: 2 average time/residue: 0.2008 time to fit residues: 1.9322 ------------------------------------------------------------------------------- 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: 0.0570 chunk 97 optimal weight: 7.9990 chunk 99 optimal weight: 0.1980 chunk 58 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 chunk 76 optimal weight: 9.9990 chunk 29 optimal weight: 0.0000 chunk 87 optimal weight: 6.9990 chunk 91 optimal weight: 1.9990 chunk 96 optimal weight: 5.9990 chunk 63 optimal weight: 2.9990 overall best weight: 0.6504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 1.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 8660 Z= 0.187 Angle : 0.712 12.274 11731 Z= 0.330 Chirality : 0.041 0.210 1360 Planarity : 0.004 0.053 1502 Dihedral : 5.358 67.054 1166 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer Outliers : 1.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 0.38 (0.26), residues: 1071 helix: 0.84 (0.21), residues: 668 sheet: 0.31 (0.75), residues: 46 loop : -0.75 (0.32), residues: 357 *********************** 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 72 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 54 time to evaluate : 1.033 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 14 residues processed: 69 average time/residue: 1.0216 time to fit residues: 76.9193 Evaluate side-chains 68 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 54 time to evaluate : 1.010 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 13 residues processed: 2 average time/residue: 0.1814 time to fit residues: 1.9691 ------------------------------------------------------------------------------- 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: 10.0000 chunk 62 optimal weight: 7.9990 chunk 48 optimal weight: 7.9990 chunk 71 optimal weight: 2.9990 chunk 107 optimal weight: 20.0000 chunk 99 optimal weight: 20.0000 chunk 85 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 chunk 66 optimal weight: 0.3980 chunk 52 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 1.2199 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= 0.257 Angle : 0.744 16.029 11731 Z= 0.347 Chirality : 0.042 0.234 1360 Planarity : 0.004 0.053 1502 Dihedral : 5.434 72.533 1166 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer Outliers : 1.98 % 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: 0.78 (0.21), residues: 664 sheet: 0.48 (0.75), residues: 46 loop : -0.67 (0.32), residues: 361 ********************** 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 71 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 53 time to evaluate : 1.042 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 12 residues processed: 67 average time/residue: 0.9982 time to fit residues: 73.1946 Evaluate side-chains 65 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 53 time to evaluate : 0.985 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 12 residues processed: 2 average time/residue: 0.2292 time to fit residues: 1.9495 ------------------------------------------------------------------------------- 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: 0.9990 chunk 26 optimal weight: 0.8980 chunk 79 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 85 optimal weight: 0.0570 chunk 35 optimal weight: 6.9990 chunk 88 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 15 optimal weight: 0.7980 chunk 75 optimal weight: 0.9980 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.060160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.043863 restraints weight = 35749.477| |-----------------------------------------------------------------------------| r_work (start): 0.2888 rms_B_bonded: 3.92 r_work: 0.2735 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8796 moved from start: 1.2294 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= 0.186 Angle : 0.719 15.454 11731 Z= 0.330 Chirality : 0.041 0.186 1360 Planarity : 0.004 0.052 1502 Dihedral : 5.265 69.384 1166 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer Outliers : 1.43 % 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 (0.27), residues: 1071 helix: 0.85 (0.22), residues: 664 sheet: 0.48 (0.74), residues: 46 loop : -0.62 (0.32), residues: 361 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2812.84 seconds wall clock time: 50 minutes 57.63 seconds (3057.63 seconds total)