Starting phenix.real_space_refine on Tue Feb 13 19:20:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8avx_15686/02_2024/8avx_15686_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8avx_15686/02_2024/8avx_15686.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8avx_15686/02_2024/8avx_15686.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8avx_15686/02_2024/8avx_15686.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8avx_15686/02_2024/8avx_15686_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8avx_15686/02_2024/8avx_15686_updated.pdb" } resolution = 3.5 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= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 22 5.16 5 C 4715 2.51 5 N 1327 2.21 5 O 1363 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 22": "OE1" <-> "OE2" Residue "A GLU 25": "OE1" <-> "OE2" Residue "A GLU 50": "OE1" <-> "OE2" Residue "A GLU 120": "OE1" <-> "OE2" Residue "A GLU 127": "OE1" <-> "OE2" Residue "A GLU 158": "OE1" <-> "OE2" Residue "A GLU 185": "OE1" <-> "OE2" Residue "A ARG 192": "NH1" <-> "NH2" Residue "A ARG 202": "NH1" <-> "NH2" Residue "A ARG 228": "NH1" <-> "NH2" Residue "A ARG 254": "NH1" <-> "NH2" Residue "A ARG 265": "NH1" <-> "NH2" Residue "A ARG 310": "NH1" <-> "NH2" Residue "A ARG 337": "NH1" <-> "NH2" Residue "A GLU 373": "OE1" <-> "OE2" Residue "A ARG 375": "NH1" <-> "NH2" Residue "A GLU 381": "OE1" <-> "OE2" Residue "A GLU 432": "OE1" <-> "OE2" Residue "A ARG 442": "NH1" <-> "NH2" Residue "A GLU 474": "OE1" <-> "OE2" Residue "A ARG 495": "NH1" <-> "NH2" Residue "B GLU 22": "OE1" <-> "OE2" Residue "B GLU 25": "OE1" <-> "OE2" Residue "B GLU 50": "OE1" <-> "OE2" Residue "B GLU 120": "OE1" <-> "OE2" Residue "B GLU 127": "OE1" <-> "OE2" Residue "B GLU 158": "OE1" <-> "OE2" Residue "B GLU 185": "OE1" <-> "OE2" Residue "B ARG 192": "NH1" <-> "NH2" Residue "B ARG 202": "NH1" <-> "NH2" Residue "B ARG 228": "NH1" <-> "NH2" Residue "B ARG 254": "NH1" <-> "NH2" Residue "B ARG 265": "NH1" <-> "NH2" Residue "B ARG 310": "NH1" <-> "NH2" Residue "B ARG 337": "NH1" <-> "NH2" Residue "B GLU 373": "OE1" <-> "OE2" Residue "B ARG 375": "NH1" <-> "NH2" Residue "B GLU 381": "OE1" <-> "OE2" Residue "B GLU 432": "OE1" <-> "OE2" Residue "B ARG 442": "NH1" <-> "NH2" Residue "B GLU 474": "OE1" <-> "OE2" Residue "B ARG 477": "NH1" <-> "NH2" Residue "B ARG 495": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 7427 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3668 Classifications: {'peptide': 480} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 443} Chain breaks: 3 Chain: "B" Number of atoms: 3673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 3673 Classifications: {'peptide': 481} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 444} Chain breaks: 2 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'BLA': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'BLA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.49, per 1000 atoms: 0.60 Number of scatterers: 7427 At special positions: 0 Unit cell: (81.8615, 95.6487, 121.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 22 16.00 O 1363 8.00 N 1327 7.00 C 4715 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: 2.81 Conformation dependent library (CDL) restraints added in 1.4 seconds 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1774 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 32 helices and 6 sheets defined 34.5% alpha, 18.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.72 Creating SS restraints... Processing helix chain 'A' and resid 56 through 62 removed outlier: 3.973A pdb=" N ALA A 59 " --> pdb=" O LEU A 56 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE A 61 " --> pdb=" O ALA A 58 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N LEU A 62 " --> pdb=" O ALA A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 69 No H-bonds generated for 'chain 'A' and resid 66 through 69' Processing helix chain 'A' and resid 74 through 77 No H-bonds generated for 'chain 'A' and resid 74 through 77' Processing helix chain 'A' and resid 82 through 88 removed outlier: 4.440A pdb=" N ALA A 87 " --> pdb=" O PRO A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 148 removed outlier: 3.524A pdb=" N PHE A 145 " --> pdb=" O ARG A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 167 Processing helix chain 'A' and resid 210 through 218 removed outlier: 3.578A pdb=" N LEU A 215 " --> pdb=" O GLN A 211 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG A 218 " --> pdb=" O ALA A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 267 removed outlier: 3.749A pdb=" N MET A 267 " --> pdb=" O TYR A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 330 removed outlier: 3.916A pdb=" N THR A 303 " --> pdb=" O PRO A 299 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N THR A 304 " --> pdb=" O ASP A 300 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL A 316 " --> pdb=" O LEU A 312 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N GLN A 317 " --> pdb=" O SER A 313 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL A 318 " --> pdb=" O LEU A 314 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA A 321 " --> pdb=" O GLN A 317 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N VAL A 324 " --> pdb=" O GLU A 320 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA A 325 " --> pdb=" O ALA A 321 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N PHE A 327 " --> pdb=" O ASP A 323 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLN A 329 " --> pdb=" O ALA A 325 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N SER A 330 " --> pdb=" O ALA A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 341 removed outlier: 4.152A pdb=" N ARG A 337 " --> pdb=" O GLU A 333 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL A 338 " --> pdb=" O HIS A 334 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA A 341 " --> pdb=" O ARG A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 363 No H-bonds generated for 'chain 'A' and resid 360 through 363' Processing helix chain 'A' and resid 385 through 397 removed outlier: 3.511A pdb=" N ALA A 390 " --> pdb=" O PRO A 386 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA A 393 " --> pdb=" O ASP A 389 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLU A 396 " --> pdb=" O LEU A 392 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N THR A 397 " --> pdb=" O ALA A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 411 No H-bonds generated for 'chain 'A' and resid 408 through 411' Processing helix chain 'A' and resid 466 through 473 removed outlier: 3.901A pdb=" N THR A 471 " --> pdb=" O HIS A 467 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N TYR A 472 " --> pdb=" O SER A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 498 removed outlier: 3.625A pdb=" N GLU A 490 " --> pdb=" O GLY A 486 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASP A 493 " --> pdb=" O GLU A 489 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ARG A 495 " --> pdb=" O ALA A 491 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASP A 496 " --> pdb=" O GLN A 492 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N THR A 497 " --> pdb=" O ASP A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 520 removed outlier: 4.050A pdb=" N VAL A 508 " --> pdb=" O GLU A 504 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE A 509 " --> pdb=" O ARG A 505 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG A 510 " --> pdb=" O LEU A 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 62 removed outlier: 3.974A pdb=" N ALA B 59 " --> pdb=" O LEU B 56 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE B 61 " --> pdb=" O ALA B 58 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N LEU B 62 " --> pdb=" O ALA B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 69 No H-bonds generated for 'chain 'B' and resid 66 through 69' Processing helix chain 'B' and resid 74 through 77 No H-bonds generated for 'chain 'B' and resid 74 through 77' Processing helix chain 'B' and resid 82 through 88 removed outlier: 4.418A pdb=" N ALA B 87 " --> pdb=" O PRO B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 148 removed outlier: 3.522A pdb=" N PHE B 145 " --> pdb=" O ARG B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 167 Processing helix chain 'B' and resid 210 through 218 removed outlier: 3.581A pdb=" N LEU B 215 " --> pdb=" O GLN B 211 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG B 218 " --> pdb=" O ALA B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 267 removed outlier: 3.751A pdb=" N MET B 267 " --> pdb=" O TYR B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 330 removed outlier: 3.933A pdb=" N THR B 303 " --> pdb=" O PRO B 299 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N THR B 304 " --> pdb=" O ASP B 300 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL B 316 " --> pdb=" O LEU B 312 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLN B 317 " --> pdb=" O SER B 313 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL B 318 " --> pdb=" O LEU B 314 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ALA B 321 " --> pdb=" O GLN B 317 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL B 324 " --> pdb=" O GLU B 320 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA B 325 " --> pdb=" O ALA B 321 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N PHE B 327 " --> pdb=" O ASP B 323 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN B 329 " --> pdb=" O ALA B 325 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER B 330 " --> pdb=" O ALA B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 341 removed outlier: 4.150A pdb=" N ARG B 337 " --> pdb=" O GLU B 333 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL B 338 " --> pdb=" O HIS B 334 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA B 341 " --> pdb=" O ARG B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 360 through 363 No H-bonds generated for 'chain 'B' and resid 360 through 363' Processing helix chain 'B' and resid 385 through 397 removed outlier: 3.512A pdb=" N ALA B 390 " --> pdb=" O PRO B 386 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA B 393 " --> pdb=" O ASP B 389 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU B 396 " --> pdb=" O LEU B 392 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N THR B 397 " --> pdb=" O ALA B 393 " (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 466 through 473 removed outlier: 3.894A pdb=" N THR B 471 " --> pdb=" O HIS B 467 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N TYR B 472 " --> pdb=" O SER B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 485 through 498 removed outlier: 3.624A pdb=" N GLU B 490 " --> pdb=" O GLY B 486 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASP B 493 " --> pdb=" O GLU B 489 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG B 495 " --> pdb=" O ALA B 491 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASP B 496 " --> pdb=" O GLN B 492 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N THR B 497 " --> pdb=" O ASP B 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 520 removed outlier: 4.041A pdb=" N VAL B 508 " --> pdb=" O GLU B 504 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE B 509 " --> pdb=" O ARG B 505 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG B 510 " --> pdb=" O LEU B 506 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 99 through 104 removed outlier: 3.531A pdb=" N LEU A 103 " --> pdb=" O LEU A 111 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ASP A 45 " --> pdb=" O VAL A 51 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N VAL A 51 " --> pdb=" O ASP A 45 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 183 through 190 removed outlier: 3.689A pdb=" N THR A 183 " --> pdb=" O ALA A 179 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N LEU A 175 " --> pdb=" O ILE A 187 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N GLU A 189 " --> pdb=" O VAL A 173 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N VAL A 173 " --> pdb=" O GLU A 189 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA A 288 " --> pdb=" O MET A 174 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N TRP A 284 " --> pdb=" O PHE A 178 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N VAL A 277 " --> pdb=" O TRP A 284 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N LEU A 286 " --> pdb=" O VAL A 275 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N VAL A 275 " --> pdb=" O LEU A 286 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ALA A 288 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N LEU A 273 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N HIS A 290 " --> pdb=" O SER A 271 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N SER A 271 " --> pdb=" O HIS A 290 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 375 through 380 removed outlier: 4.585A pdb=" N GLU A 436 " --> pdb=" O VAL A 430 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY A 424 " --> pdb=" O ARG A 442 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 99 through 105 removed outlier: 3.521A pdb=" N LEU B 103 " --> pdb=" O LEU B 111 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ASP B 45 " --> pdb=" O VAL B 51 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N VAL B 51 " --> pdb=" O ASP B 45 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 183 through 190 removed outlier: 3.689A pdb=" N THR B 183 " --> pdb=" O ALA B 179 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N LEU B 175 " --> pdb=" O ILE B 187 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N GLU B 189 " --> pdb=" O VAL B 173 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N VAL B 173 " --> pdb=" O GLU B 189 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA B 288 " --> pdb=" O MET B 174 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N TRP B 284 " --> pdb=" O PHE B 178 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N VAL B 277 " --> pdb=" O TRP B 284 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N LEU B 286 " --> pdb=" O VAL B 275 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N VAL B 275 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ALA B 288 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N LEU B 273 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N HIS B 290 " --> pdb=" O SER B 271 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N SER B 271 " --> pdb=" O HIS B 290 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 375 through 380 removed outlier: 4.568A pdb=" N GLU B 436 " --> pdb=" O VAL B 430 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY B 424 " --> pdb=" O ARG B 442 " (cutoff:3.500A) 256 hydrogen bonds defined for protein. 717 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: 2.17 Time building geometry restraints manager: 3.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1481 1.33 - 1.45: 1744 1.45 - 1.57: 4349 1.57 - 1.70: 0 1.70 - 1.82: 36 Bond restraints: 7610 Sorted by residual: bond pdb=" C2B BLA B1000 " pdb=" C3B BLA B1000 " ideal model delta sigma weight residual 1.357 1.432 -0.075 2.00e-02 2.50e+03 1.39e+01 bond pdb=" C2B BLA A1000 " pdb=" C3B BLA A1000 " ideal model delta sigma weight residual 1.357 1.429 -0.072 2.00e-02 2.50e+03 1.29e+01 bond pdb=" C1D BLA A1000 " pdb=" CHD BLA A1000 " ideal model delta sigma weight residual 1.440 1.373 0.067 2.00e-02 2.50e+03 1.12e+01 bond pdb=" C2C BLA A1000 " pdb=" C3C BLA A1000 " ideal model delta sigma weight residual 1.351 1.415 -0.064 2.00e-02 2.50e+03 1.03e+01 bond pdb=" C1D BLA B1000 " pdb=" CHD BLA B1000 " ideal model delta sigma weight residual 1.440 1.377 0.063 2.00e-02 2.50e+03 1.00e+01 ... (remaining 7605 not shown) Histogram of bond angle deviations from ideal: 100.08 - 107.43: 419 107.43 - 114.78: 4270 114.78 - 122.13: 3391 122.13 - 129.48: 2249 129.48 - 136.83: 81 Bond angle restraints: 10410 Sorted by residual: angle pdb=" C PHE B 203 " pdb=" CA PHE B 203 " pdb=" CB PHE B 203 " ideal model delta sigma weight residual 108.87 115.23 -6.36 1.55e+00 4.16e-01 1.68e+01 angle pdb=" C PHE A 203 " pdb=" CA PHE A 203 " pdb=" CB PHE A 203 " ideal model delta sigma weight residual 108.87 115.05 -6.18 1.55e+00 4.16e-01 1.59e+01 angle pdb=" CB ARG A 375 " pdb=" CG ARG A 375 " pdb=" CD ARG A 375 " ideal model delta sigma weight residual 111.30 120.43 -9.13 2.30e+00 1.89e-01 1.58e+01 angle pdb=" C PRO B 384 " pdb=" N ALA B 385 " pdb=" CA ALA B 385 " ideal model delta sigma weight residual 120.09 124.82 -4.73 1.25e+00 6.40e-01 1.43e+01 angle pdb=" C PRO A 384 " pdb=" N ALA A 385 " pdb=" CA ALA A 385 " ideal model delta sigma weight residual 120.09 124.79 -4.70 1.25e+00 6.40e-01 1.41e+01 ... (remaining 10405 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.27: 3915 17.27 - 34.54: 440 34.54 - 51.80: 120 51.80 - 69.07: 71 69.07 - 86.34: 6 Dihedral angle restraints: 4552 sinusoidal: 1808 harmonic: 2744 Sorted by residual: dihedral pdb=" CA HIS B 219 " pdb=" C HIS B 219 " pdb=" N LEU B 220 " pdb=" CA LEU B 220 " ideal model delta harmonic sigma weight residual -180.00 -160.72 -19.28 0 5.00e+00 4.00e-02 1.49e+01 dihedral pdb=" CA HIS A 219 " pdb=" C HIS A 219 " pdb=" N LEU A 220 " pdb=" CA LEU A 220 " ideal model delta harmonic sigma weight residual -180.00 -160.76 -19.24 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CG ARG B 514 " pdb=" CD ARG B 514 " pdb=" NE ARG B 514 " pdb=" CZ ARG B 514 " ideal model delta sinusoidal sigma weight residual 180.00 135.38 44.62 2 1.50e+01 4.44e-03 1.05e+01 ... (remaining 4549 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 627 0.050 - 0.100: 285 0.100 - 0.151: 190 0.151 - 0.201: 54 0.201 - 0.251: 17 Chirality restraints: 1173 Sorted by residual: chirality pdb=" CB VAL A 237 " pdb=" CA VAL A 237 " pdb=" CG1 VAL A 237 " pdb=" CG2 VAL A 237 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" CB VAL A 449 " pdb=" CA VAL A 449 " pdb=" CG1 VAL A 449 " pdb=" CG2 VAL A 449 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CA ASN B 243 " pdb=" N ASN B 243 " pdb=" C ASN B 243 " pdb=" CB ASN B 243 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.44e+00 ... (remaining 1170 not shown) Planarity restraints: 1364 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1C BLA B1000 " -0.001 2.00e-02 2.50e+03 2.84e-01 2.01e+03 pdb=" C1D BLA B1000 " 0.520 2.00e-02 2.50e+03 pdb=" C2C BLA B1000 " -0.007 2.00e-02 2.50e+03 pdb=" C3C BLA B1000 " -0.040 2.00e-02 2.50e+03 pdb=" C4C BLA B1000 " -0.264 2.00e-02 2.50e+03 pdb=" CAC BLA B1000 " 0.147 2.00e-02 2.50e+03 pdb=" CHD BLA B1000 " -0.254 2.00e-02 2.50e+03 pdb=" CMC BLA B1000 " 0.055 2.00e-02 2.50e+03 pdb=" NC BLA B1000 " -0.503 2.00e-02 2.50e+03 pdb=" OC BLA B1000 " 0.347 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" NB BLA B1000 " -0.384 2.00e-02 2.50e+03 2.82e-01 1.98e+03 pdb=" OB BLA B1000 " 0.184 2.00e-02 2.50e+03 pdb=" C1B BLA B1000 " -0.180 2.00e-02 2.50e+03 pdb=" C2B BLA B1000 " -0.174 2.00e-02 2.50e+03 pdb=" C3B BLA B1000 " 0.071 2.00e-02 2.50e+03 pdb=" C4A BLA B1000 " 0.543 2.00e-02 2.50e+03 pdb=" C4B BLA B1000 " -0.019 2.00e-02 2.50e+03 pdb=" CAB BLA B1000 " 0.348 2.00e-02 2.50e+03 pdb=" CHB BLA B1000 " -0.032 2.00e-02 2.50e+03 pdb=" CMB BLA B1000 " -0.357 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1C BLA A1000 " -0.034 2.00e-02 2.50e+03 2.78e-01 1.93e+03 pdb=" C1D BLA A1000 " 0.551 2.00e-02 2.50e+03 pdb=" C2C BLA A1000 " 0.033 2.00e-02 2.50e+03 pdb=" C3C BLA A1000 " -0.075 2.00e-02 2.50e+03 pdb=" C4C BLA A1000 " -0.247 2.00e-02 2.50e+03 pdb=" CAC BLA A1000 " 0.008 2.00e-02 2.50e+03 pdb=" CHD BLA A1000 " -0.175 2.00e-02 2.50e+03 pdb=" CMC BLA A1000 " 0.210 2.00e-02 2.50e+03 pdb=" NC BLA A1000 " -0.515 2.00e-02 2.50e+03 pdb=" OC BLA A1000 " 0.243 2.00e-02 2.50e+03 ... (remaining 1361 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 1581 2.83 - 3.35: 6142 3.35 - 3.87: 12015 3.87 - 4.38: 13388 4.38 - 4.90: 23364 Nonbonded interactions: 56490 Sorted by model distance: nonbonded pdb=" O ALA A 107 " pdb=" N GLY A 109 " model vdw 2.316 2.520 nonbonded pdb=" O LEU B 516 " pdb=" OG SER B 519 " model vdw 2.584 2.440 nonbonded pdb=" O LEU A 516 " pdb=" OG SER A 519 " model vdw 2.585 2.440 nonbonded pdb=" O GLY A 39 " pdb=" ND2 ASN A 57 " model vdw 2.600 2.520 nonbonded pdb=" O GLY B 39 " pdb=" ND2 ASN B 57 " model vdw 2.601 2.520 ... (remaining 56485 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' selection = (chain 'B' and (resid 22 through 107 or resid 109 through 521 or resid 1000)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.210 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: 18.380 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 23.720 Find NCS groups from input model: 0.460 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: 0.010 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.010 Internal consistency checks: 0.000 Total: 50.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6525 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 : 0.008 0.075 7610 Z= 0.528 Angle : 1.384 9.131 10410 Z= 0.921 Chirality : 0.079 0.251 1173 Planarity : 0.015 0.284 1364 Dihedral : 17.707 86.341 2778 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 1.69 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.54 % Favored : 95.25 % Rotamer: Outliers : 4.23 % Allowed : 11.64 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -4.05 (0.22), residues: 947 helix: -3.67 (0.16), residues: 369 sheet: -1.34 (0.36), residues: 180 loop : -2.13 (0.26), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 451 HIS 0.006 0.002 HIS A 349 PHE 0.011 0.002 PHE B 170 TYR 0.030 0.003 TYR B 307 ARG 0.014 0.001 ARG A 100 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 146 time to evaluate : 0.817 Fit side-chains revert: symmetry clash REVERT: A 26 ARG cc_start: 0.6840 (mtp180) cc_final: 0.5248 (tpt170) REVERT: A 466 ARG cc_start: 0.4224 (OUTLIER) cc_final: 0.1647 (mmp80) REVERT: B 227 THR cc_start: 0.7630 (p) cc_final: 0.7188 (p) REVERT: B 381 GLU cc_start: 0.7836 (pm20) cc_final: 0.7243 (pp20) REVERT: B 493 ASP cc_start: 0.7568 (OUTLIER) cc_final: 0.7326 (t0) outliers start: 32 outliers final: 4 residues processed: 174 average time/residue: 0.2347 time to fit residues: 52.1826 Evaluate side-chains 94 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 88 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 466 ARG Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 493 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 49 optimal weight: 7.9990 chunk 38 optimal weight: 5.9990 chunk 75 optimal weight: 0.6980 chunk 29 optimal weight: 0.7980 chunk 45 optimal weight: 0.6980 chunk 56 optimal weight: 0.0010 chunk 87 optimal weight: 0.6980 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 GLN A 110 HIS A 239 ASN ** A 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 513 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 290 HIS B 334 HIS B 335 HIS B 410 GLN ** B 513 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6609 moved from start: 0.2881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7610 Z= 0.186 Angle : 0.632 9.106 10410 Z= 0.291 Chirality : 0.041 0.147 1173 Planarity : 0.004 0.029 1364 Dihedral : 7.139 76.717 1103 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 4.37 % Allowed : 17.06 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -2.48 (0.25), residues: 947 helix: -2.23 (0.23), residues: 362 sheet: -0.79 (0.37), residues: 188 loop : -1.26 (0.30), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 284 HIS 0.010 0.001 HIS B 335 PHE 0.018 0.002 PHE B 126 TYR 0.016 0.002 TYR A 479 ARG 0.004 0.000 ARG B 466 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 98 time to evaluate : 0.763 Fit side-chains REVERT: A 26 ARG cc_start: 0.6679 (mtp180) cc_final: 0.5194 (tpt170) REVERT: A 363 MET cc_start: 0.6060 (tpp) cc_final: 0.5827 (tpp) REVERT: A 466 ARG cc_start: 0.4300 (OUTLIER) cc_final: 0.1609 (mmt180) REVERT: B 45 ASP cc_start: 0.6008 (t70) cc_final: 0.5429 (m-30) REVERT: B 72 GLN cc_start: 0.5378 (tt0) cc_final: 0.5171 (tm-30) REVERT: B 313 SER cc_start: 0.7831 (m) cc_final: 0.7579 (p) REVERT: B 381 GLU cc_start: 0.7997 (pm20) cc_final: 0.7522 (pp20) outliers start: 33 outliers final: 6 residues processed: 125 average time/residue: 0.2123 time to fit residues: 34.8166 Evaluate side-chains 84 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 77 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 466 ARG Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 103 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 48 optimal weight: 7.9990 chunk 27 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 59 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 chunk 87 optimal weight: 0.0980 chunk 94 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 GLN A 266 ASN ** A 513 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 57 ASN B 110 HIS B 329 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6712 moved from start: 0.3706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7610 Z= 0.202 Angle : 0.610 9.519 10410 Z= 0.282 Chirality : 0.041 0.141 1173 Planarity : 0.004 0.036 1364 Dihedral : 6.640 78.022 1096 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.17 % Allowed : 19.44 % Favored : 77.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -1.85 (0.26), residues: 947 helix: -1.40 (0.25), residues: 363 sheet: -0.59 (0.36), residues: 185 loop : -1.18 (0.29), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 284 HIS 0.005 0.001 HIS B 467 PHE 0.019 0.002 PHE B 327 TYR 0.014 0.002 TYR B 295 ARG 0.004 0.000 ARG A 172 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 87 time to evaluate : 0.834 Fit side-chains revert: symmetry clash REVERT: A 363 MET cc_start: 0.6651 (tpp) cc_final: 0.6362 (tpp) REVERT: A 466 ARG cc_start: 0.4229 (OUTLIER) cc_final: 0.1387 (mmt180) REVERT: B 45 ASP cc_start: 0.6063 (t70) cc_final: 0.5397 (m-30) REVERT: B 72 GLN cc_start: 0.5859 (tt0) cc_final: 0.5649 (tt0) REVERT: B 125 GLU cc_start: 0.7583 (OUTLIER) cc_final: 0.6438 (mm-30) REVERT: B 355 PRO cc_start: 0.6292 (Cg_exo) cc_final: 0.6084 (Cg_endo) REVERT: B 381 GLU cc_start: 0.8021 (pm20) cc_final: 0.7655 (pp20) REVERT: B 432 GLU cc_start: 0.7205 (tp30) cc_final: 0.6984 (tp30) outliers start: 24 outliers final: 11 residues processed: 108 average time/residue: 0.1954 time to fit residues: 28.7759 Evaluate side-chains 84 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 71 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 466 ARG Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 50 GLU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 273 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 7.9990 chunk 65 optimal weight: 0.0000 chunk 45 optimal weight: 0.7980 chunk 9 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 92 optimal weight: 0.0970 chunk 83 optimal weight: 0.0980 chunk 25 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 overall best weight: 0.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 513 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 72 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6661 moved from start: 0.4056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7610 Z= 0.138 Angle : 0.564 9.094 10410 Z= 0.255 Chirality : 0.040 0.187 1173 Planarity : 0.004 0.037 1364 Dihedral : 6.289 85.573 1096 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 2.51 % Allowed : 21.30 % Favored : 76.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -1.28 (0.26), residues: 947 helix: -0.77 (0.27), residues: 359 sheet: -0.51 (0.36), residues: 185 loop : -0.91 (0.30), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 284 HIS 0.009 0.001 HIS A 484 PHE 0.019 0.001 PHE B 327 TYR 0.012 0.001 TYR A 307 ARG 0.002 0.000 ARG A 310 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 83 time to evaluate : 0.802 Fit side-chains revert: symmetry clash REVERT: A 26 ARG cc_start: 0.6886 (mtp180) cc_final: 0.5250 (tpt170) REVERT: A 238 LEU cc_start: 0.7720 (OUTLIER) cc_final: 0.7226 (mm) REVERT: A 363 MET cc_start: 0.6883 (tpp) cc_final: 0.6507 (tpp) REVERT: A 466 ARG cc_start: 0.4298 (OUTLIER) cc_final: 0.1313 (mmt180) REVERT: B 45 ASP cc_start: 0.5922 (t70) cc_final: 0.5397 (m-30) REVERT: B 105 TRP cc_start: 0.6455 (m-10) cc_final: 0.6210 (m-10) REVERT: B 259 MET cc_start: 0.7903 (tpp) cc_final: 0.7675 (ptp) REVERT: B 381 GLU cc_start: 0.8038 (pm20) cc_final: 0.7631 (pp20) outliers start: 19 outliers final: 12 residues processed: 98 average time/residue: 0.2081 time to fit residues: 27.4416 Evaluate side-chains 87 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 73 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 174 MET Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 466 ARG Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 50 GLU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 103 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 52 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 38 optimal weight: 0.0570 chunk 79 optimal weight: 0.6980 chunk 64 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 47 optimal weight: 0.0050 chunk 83 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 31 optimal weight: 6.9990 overall best weight: 1.1516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 HIS ** A 513 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 57 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6814 moved from start: 0.4786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7610 Z= 0.267 Angle : 0.679 10.556 10410 Z= 0.315 Chirality : 0.044 0.182 1173 Planarity : 0.005 0.037 1364 Dihedral : 6.542 59.276 1096 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 4.89 % Allowed : 20.11 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -1.35 (0.26), residues: 947 helix: -0.78 (0.27), residues: 362 sheet: -0.47 (0.37), residues: 186 loop : -1.04 (0.30), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 284 HIS 0.007 0.002 HIS B 335 PHE 0.023 0.002 PHE B 327 TYR 0.027 0.003 TYR A 307 ARG 0.004 0.001 ARG A 172 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 77 time to evaluate : 0.801 Fit side-chains revert: symmetry clash REVERT: A 26 ARG cc_start: 0.6889 (mtp180) cc_final: 0.5270 (tpt170) REVERT: A 238 LEU cc_start: 0.7750 (OUTLIER) cc_final: 0.7272 (mm) REVERT: A 363 MET cc_start: 0.6512 (tpp) cc_final: 0.6293 (tpp) REVERT: A 376 TRP cc_start: 0.6662 (p-90) cc_final: 0.6446 (p90) REVERT: A 466 ARG cc_start: 0.4693 (OUTLIER) cc_final: 0.1688 (mmt180) REVERT: B 45 ASP cc_start: 0.6048 (t70) cc_final: 0.5657 (m-30) REVERT: B 241 GLN cc_start: 0.7244 (OUTLIER) cc_final: 0.6968 (mt0) REVERT: B 357 LEU cc_start: 0.5669 (mp) cc_final: 0.5404 (mp) REVERT: B 381 GLU cc_start: 0.8076 (pm20) cc_final: 0.7651 (pp20) outliers start: 37 outliers final: 26 residues processed: 104 average time/residue: 0.2046 time to fit residues: 28.6431 Evaluate side-chains 100 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 71 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 72 GLN Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 138 HIS Chi-restraints excluded: chain A residue 174 MET Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 466 ARG Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 57 ASN Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 241 GLN Chi-restraints excluded: chain B residue 508 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 83 optimal weight: 2.9990 chunk 18 optimal weight: 0.0970 chunk 54 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 30 optimal weight: 0.5980 chunk 48 optimal weight: 6.9990 chunk 89 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 513 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 57 ASN B 398 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6775 moved from start: 0.5026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7610 Z= 0.187 Angle : 0.611 9.829 10410 Z= 0.278 Chirality : 0.041 0.199 1173 Planarity : 0.004 0.037 1364 Dihedral : 6.074 55.233 1096 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 4.23 % Allowed : 21.69 % Favored : 74.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -1.01 (0.27), residues: 947 helix: -0.45 (0.28), residues: 360 sheet: -0.46 (0.36), residues: 194 loop : -0.80 (0.31), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 284 HIS 0.005 0.001 HIS B 467 PHE 0.024 0.001 PHE B 327 TYR 0.027 0.002 TYR A 263 ARG 0.004 0.000 ARG A 477 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 73 time to evaluate : 0.831 Fit side-chains revert: symmetry clash REVERT: A 26 ARG cc_start: 0.7010 (mtp180) cc_final: 0.5467 (tpt170) REVERT: A 238 LEU cc_start: 0.7721 (OUTLIER) cc_final: 0.7229 (mm) REVERT: A 363 MET cc_start: 0.6676 (tpp) cc_final: 0.6421 (tpp) REVERT: A 466 ARG cc_start: 0.4788 (OUTLIER) cc_final: 0.1791 (mmt180) REVERT: B 45 ASP cc_start: 0.6046 (OUTLIER) cc_final: 0.5649 (m-30) REVERT: B 202 ARG cc_start: 0.7206 (mtp85) cc_final: 0.6612 (mtp85) REVERT: B 241 GLN cc_start: 0.7109 (OUTLIER) cc_final: 0.6812 (mt0) REVERT: B 357 LEU cc_start: 0.5848 (mp) cc_final: 0.5604 (mp) REVERT: B 381 GLU cc_start: 0.8059 (pm20) cc_final: 0.7653 (pp20) outliers start: 32 outliers final: 26 residues processed: 100 average time/residue: 0.2108 time to fit residues: 28.2047 Evaluate side-chains 98 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 68 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 138 HIS Chi-restraints excluded: chain A residue 174 MET Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 466 ARG Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 45 ASP Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 50 GLU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 241 GLN Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 398 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 10 optimal weight: 0.5980 chunk 52 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 92 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 42 optimal weight: 0.1980 chunk 36 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 513 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 57 ASN B 398 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6780 moved from start: 0.5317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7610 Z= 0.184 Angle : 0.597 9.811 10410 Z= 0.275 Chirality : 0.041 0.182 1173 Planarity : 0.004 0.037 1364 Dihedral : 5.769 50.185 1096 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 4.63 % Allowed : 21.56 % Favored : 73.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -0.86 (0.27), residues: 947 helix: -0.26 (0.28), residues: 358 sheet: -0.43 (0.36), residues: 195 loop : -0.77 (0.31), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 284 HIS 0.006 0.001 HIS B 467 PHE 0.021 0.001 PHE B 327 TYR 0.029 0.002 TYR A 263 ARG 0.004 0.000 ARG A 202 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 73 time to evaluate : 0.845 Fit side-chains revert: symmetry clash REVERT: A 26 ARG cc_start: 0.7103 (mtp180) cc_final: 0.5627 (tpt170) REVERT: A 138 HIS cc_start: 0.6980 (OUTLIER) cc_final: 0.6128 (t-90) REVERT: A 238 LEU cc_start: 0.7758 (OUTLIER) cc_final: 0.7275 (mm) REVERT: A 261 MET cc_start: 0.6253 (mtm) cc_final: 0.6051 (mtm) REVERT: A 363 MET cc_start: 0.6702 (tpp) cc_final: 0.6460 (tpp) REVERT: B 45 ASP cc_start: 0.6047 (OUTLIER) cc_final: 0.5515 (m-30) REVERT: B 105 TRP cc_start: 0.6476 (m-10) cc_final: 0.6193 (m-10) REVERT: B 202 ARG cc_start: 0.7201 (mtp85) cc_final: 0.6628 (mtp85) REVERT: B 241 GLN cc_start: 0.7090 (OUTLIER) cc_final: 0.6778 (mt0) REVERT: B 357 LEU cc_start: 0.5849 (mp) cc_final: 0.5618 (mp) REVERT: B 381 GLU cc_start: 0.7996 (pm20) cc_final: 0.7630 (pp20) outliers start: 35 outliers final: 25 residues processed: 101 average time/residue: 0.2180 time to fit residues: 29.4429 Evaluate side-chains 99 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 70 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 138 HIS Chi-restraints excluded: chain A residue 174 MET Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 466 ARG Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 45 ASP Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 50 GLU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 144 MET Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 241 GLN Chi-restraints excluded: chain B residue 273 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 27 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 72 optimal weight: 0.9990 chunk 84 optimal weight: 5.9990 chunk 88 optimal weight: 0.9980 chunk 80 optimal weight: 0.0030 overall best weight: 0.7590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 513 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 57 ASN B 398 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6795 moved from start: 0.5627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7610 Z= 0.196 Angle : 0.615 9.882 10410 Z= 0.282 Chirality : 0.041 0.173 1173 Planarity : 0.004 0.039 1364 Dihedral : 5.788 51.072 1096 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 4.76 % Allowed : 22.22 % Favored : 73.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -0.83 (0.27), residues: 947 helix: -0.30 (0.28), residues: 356 sheet: -0.21 (0.37), residues: 190 loop : -0.78 (0.31), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 284 HIS 0.006 0.001 HIS B 467 PHE 0.020 0.002 PHE B 327 TYR 0.020 0.002 TYR A 307 ARG 0.003 0.000 ARG A 202 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 73 time to evaluate : 0.755 Fit side-chains revert: symmetry clash REVERT: A 26 ARG cc_start: 0.7125 (mtp180) cc_final: 0.5542 (tpt90) REVERT: A 138 HIS cc_start: 0.6936 (OUTLIER) cc_final: 0.5848 (t-90) REVERT: A 238 LEU cc_start: 0.7761 (OUTLIER) cc_final: 0.7285 (mm) REVERT: A 363 MET cc_start: 0.6730 (tpp) cc_final: 0.6512 (tpp) REVERT: B 45 ASP cc_start: 0.6049 (OUTLIER) cc_final: 0.5507 (m-30) REVERT: B 105 TRP cc_start: 0.6345 (m-10) cc_final: 0.6119 (m-10) REVERT: B 202 ARG cc_start: 0.7242 (mtp85) cc_final: 0.6675 (mtp85) REVERT: B 241 GLN cc_start: 0.6987 (OUTLIER) cc_final: 0.6703 (mt0) REVERT: B 357 LEU cc_start: 0.5719 (mp) cc_final: 0.5431 (mp) REVERT: B 363 MET cc_start: 0.6774 (tpp) cc_final: 0.6220 (tpp) REVERT: B 381 GLU cc_start: 0.8034 (pm20) cc_final: 0.7639 (pp20) outliers start: 36 outliers final: 27 residues processed: 102 average time/residue: 0.1963 time to fit residues: 26.8283 Evaluate side-chains 99 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 68 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 138 HIS Chi-restraints excluded: chain A residue 174 MET Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 466 ARG Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 45 ASP Chi-restraints excluded: chain B residue 50 GLU Chi-restraints excluded: chain B residue 57 ASN Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 144 MET Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 241 GLN Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 376 TRP Chi-restraints excluded: chain B residue 398 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 5.9990 chunk 88 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 37 optimal weight: 6.9990 chunk 67 optimal weight: 0.1980 chunk 26 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 81 optimal weight: 5.9990 chunk 85 optimal weight: 2.9990 chunk 56 optimal weight: 0.2980 chunk 91 optimal weight: 0.0970 overall best weight: 0.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 513 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 57 ASN ** B 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 398 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6763 moved from start: 0.5716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7610 Z= 0.159 Angle : 0.579 9.155 10410 Z= 0.267 Chirality : 0.040 0.174 1173 Planarity : 0.004 0.037 1364 Dihedral : 5.604 56.199 1096 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 4.23 % Allowed : 22.75 % Favored : 73.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -0.58 (0.27), residues: 947 helix: -0.02 (0.29), residues: 347 sheet: -0.30 (0.37), residues: 193 loop : -0.58 (0.31), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 284 HIS 0.006 0.001 HIS B 467 PHE 0.019 0.001 PHE B 327 TYR 0.022 0.002 TYR A 307 ARG 0.004 0.000 ARG A 202 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 71 time to evaluate : 0.829 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 ARG cc_start: 0.7118 (mtp180) cc_final: 0.5574 (tpt90) REVERT: A 138 HIS cc_start: 0.6966 (OUTLIER) cc_final: 0.5889 (t-90) REVERT: A 238 LEU cc_start: 0.7798 (OUTLIER) cc_final: 0.7338 (mm) REVERT: A 363 MET cc_start: 0.6766 (tpp) cc_final: 0.6515 (tpp) REVERT: B 45 ASP cc_start: 0.6054 (t70) cc_final: 0.5509 (m-30) REVERT: B 105 TRP cc_start: 0.6261 (m-10) cc_final: 0.6060 (m-10) REVERT: B 202 ARG cc_start: 0.7238 (mtp85) cc_final: 0.6686 (mtp85) REVERT: B 241 GLN cc_start: 0.6981 (OUTLIER) cc_final: 0.6719 (mt0) REVERT: B 357 LEU cc_start: 0.5750 (mp) cc_final: 0.5478 (mp) REVERT: B 363 MET cc_start: 0.6731 (tpp) cc_final: 0.6193 (tpp) REVERT: B 381 GLU cc_start: 0.8060 (pm20) cc_final: 0.7649 (pp20) outliers start: 32 outliers final: 24 residues processed: 97 average time/residue: 0.2445 time to fit residues: 30.8483 Evaluate side-chains 93 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 66 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 138 HIS Chi-restraints excluded: chain A residue 174 MET Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 201 HIS Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 466 ARG Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 50 GLU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 241 GLN Chi-restraints excluded: chain B residue 376 TRP Chi-restraints excluded: chain B residue 398 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 55 optimal weight: 0.9980 chunk 43 optimal weight: 0.0870 chunk 63 optimal weight: 0.9990 chunk 95 optimal weight: 0.8980 chunk 88 optimal weight: 3.9990 chunk 76 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 58 optimal weight: 0.5980 chunk 46 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 81 optimal weight: 5.9990 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 513 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 57 ASN ** B 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6786 moved from start: 0.5853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7610 Z= 0.182 Angle : 0.595 9.411 10410 Z= 0.276 Chirality : 0.041 0.178 1173 Planarity : 0.004 0.038 1364 Dihedral : 5.697 55.477 1096 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.70 % Allowed : 23.02 % Favored : 73.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -0.58 (0.27), residues: 947 helix: -0.08 (0.28), residues: 347 sheet: -0.18 (0.37), residues: 189 loop : -0.60 (0.31), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 284 HIS 0.006 0.001 HIS B 467 PHE 0.019 0.001 PHE B 327 TYR 0.015 0.002 TYR B 307 ARG 0.003 0.000 ARG A 202 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 65 time to evaluate : 0.826 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 ARG cc_start: 0.7126 (mtp180) cc_final: 0.5530 (tpt90) REVERT: A 238 LEU cc_start: 0.7808 (OUTLIER) cc_final: 0.7331 (mm) REVERT: A 363 MET cc_start: 0.6783 (tpp) cc_final: 0.6530 (tpp) REVERT: B 45 ASP cc_start: 0.6071 (OUTLIER) cc_final: 0.5547 (m-30) REVERT: B 202 ARG cc_start: 0.7324 (mtp85) cc_final: 0.6765 (mtp85) REVERT: B 241 GLN cc_start: 0.6989 (OUTLIER) cc_final: 0.6721 (mt0) REVERT: B 357 LEU cc_start: 0.5747 (mp) cc_final: 0.5488 (mp) REVERT: B 363 MET cc_start: 0.6766 (tpp) cc_final: 0.6179 (tpp) REVERT: B 381 GLU cc_start: 0.8068 (pm20) cc_final: 0.7654 (pp20) outliers start: 28 outliers final: 25 residues processed: 88 average time/residue: 0.2168 time to fit residues: 26.0369 Evaluate side-chains 91 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 63 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 138 HIS Chi-restraints excluded: chain A residue 174 MET Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 466 ARG Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 45 ASP Chi-restraints excluded: chain B residue 50 GLU Chi-restraints excluded: chain B residue 57 ASN Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 241 GLN Chi-restraints excluded: chain B residue 273 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 23 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 11 optimal weight: 0.9980 chunk 21 optimal weight: 0.0020 chunk 76 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 78 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 overall best weight: 0.9190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 513 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.181806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.159471 restraints weight = 13415.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.161553 restraints weight = 8860.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.162964 restraints weight = 6134.145| |-----------------------------------------------------------------------------| r_work (final): 0.4203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6592 moved from start: 0.5864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.123 7610 Z= 0.285 Angle : 0.993 59.199 10410 Z= 0.565 Chirality : 0.045 0.618 1173 Planarity : 0.005 0.038 1364 Dihedral : 5.707 55.440 1096 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.17 % Favored : 96.73 % Rotamer: Outliers : 3.97 % Allowed : 22.75 % Favored : 73.28 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 2.78 % 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 (0.27), residues: 947 helix: -0.11 (0.28), residues: 347 sheet: -0.18 (0.37), residues: 189 loop : -0.59 (0.31), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 284 HIS 0.005 0.001 HIS B 467 PHE 0.018 0.001 PHE B 327 TYR 0.013 0.001 TYR B 307 ARG 0.004 0.000 ARG A 202 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1832.58 seconds wall clock time: 34 minutes 0.36 seconds (2040.36 seconds total)