Starting phenix.real_space_refine on Tue Feb 13 18:32:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p9v_13267/02_2024/7p9v_13267.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p9v_13267/02_2024/7p9v_13267.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p9v_13267/02_2024/7p9v_13267.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p9v_13267/02_2024/7p9v_13267.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p9v_13267/02_2024/7p9v_13267.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p9v_13267/02_2024/7p9v_13267.pdb" } resolution = 3.4 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= -0.002 sd= 0.046 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 27 5.16 5 C 4751 2.51 5 N 1185 2.21 5 O 1323 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 181": "NH1" <-> "NH2" Residue "A ARG 183": "NH1" <-> "NH2" Residue "A ARG 212": "NH1" <-> "NH2" Residue "A GLU 394": "OE1" <-> "OE2" Residue "A GLU 414": "OE1" <-> "OE2" Residue "A GLU 534": "OE1" <-> "OE2" Residue "A ARG 535": "NH1" <-> "NH2" Residue "A GLU 621": "OE1" <-> "OE2" Residue "A PHE 627": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 48": "NH1" <-> "NH2" Residue "B GLU 99": "OE1" <-> "OE2" Residue "B GLU 130": "OE1" <-> "OE2" Residue "B ARG 135": "NH1" <-> "NH2" Residue "B GLU 353": "OE1" <-> "OE2" Residue "B ARG 419": "NH1" <-> "NH2" Residue "B ARG 475": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 7286 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3616 Classifications: {'peptide': 464} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 441} Chain: "B" Number of atoms: 3558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 455, 3558 Classifications: {'peptide': 455} Link IDs: {'PTRANS': 23, 'TRANS': 431} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 4.40, per 1000 atoms: 0.60 Number of scatterers: 7286 At special positions: 0 Unit cell: (85.696, 79.872, 131.456, 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 27 16.00 O 1323 8.00 N 1185 7.00 C 4751 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 211 " - pdb=" SG CYS B 158 " distance=2.21 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 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG C 1 " - " ASN A 507 " " NAG D 1 " - " ASN A 366 " " NAG E 1 " - " ASN A 382 " " NAG F 1 " - " ASN A 425 " Time building additional restraints: 3.05 Conformation dependent library (CDL) restraints added in 1.3 seconds 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1696 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 5 sheets defined 57.5% alpha, 5.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'A' and resid 168 through 175 Processing helix chain 'A' and resid 179 through 208 removed outlier: 3.574A pdb=" N ARG A 183 " --> pdb=" O TRP A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 236 Processing helix chain 'A' and resid 242 through 247 Processing helix chain 'A' and resid 248 through 255 Processing helix chain 'A' and resid 283 through 286 Processing helix chain 'A' and resid 287 through 301 removed outlier: 3.704A pdb=" N SER A 293 " --> pdb=" O GLU A 289 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LYS A 300 " --> pdb=" O GLN A 296 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LYS A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 342 removed outlier: 4.336A pdb=" N LYS A 332 " --> pdb=" O ALA A 328 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LEU A 339 " --> pdb=" O LEU A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 372 removed outlier: 3.746A pdb=" N PHE A 360 " --> pdb=" O ASP A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 393 Processing helix chain 'A' and resid 405 through 407 No H-bonds generated for 'chain 'A' and resid 405 through 407' Processing helix chain 'A' and resid 414 through 427 removed outlier: 4.261A pdb=" N VAL A 420 " --> pdb=" O THR A 416 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N THR A 427 " --> pdb=" O TYR A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 449 No H-bonds generated for 'chain 'A' and resid 447 through 449' Processing helix chain 'A' and resid 450 through 461 removed outlier: 3.650A pdb=" N GLN A 455 " --> pdb=" O LEU A 451 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU A 456 " --> pdb=" O ARG A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 515 removed outlier: 3.811A pdb=" N GLU A 515 " --> pdb=" O LYS A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 534 Processing helix chain 'A' and resid 534 through 540 removed outlier: 3.624A pdb=" N LEU A 538 " --> pdb=" O GLU A 534 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N HIS A 539 " --> pdb=" O ARG A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 589 removed outlier: 4.006A pdb=" N SER A 589 " --> pdb=" O ALA A 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 58 removed outlier: 3.809A pdb=" N THR B 56 " --> pdb=" O ILE B 52 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE B 58 " --> pdb=" O ILE B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 72 Proline residue: B 66 - end of helix removed outlier: 3.602A pdb=" N ASN B 72 " --> pdb=" O GLY B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 105 removed outlier: 3.653A pdb=" N ILE B 82 " --> pdb=" O MET B 78 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR B 84 " --> pdb=" O LEU B 80 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS B 105 " --> pdb=" O GLY B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 116 removed outlier: 3.899A pdb=" N GLU B 116 " --> pdb=" O THR B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 133 removed outlier: 3.618A pdb=" N ALA B 123 " --> pdb=" O GLY B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 152 removed outlier: 3.579A pdb=" N ALA B 145 " --> pdb=" O VAL B 141 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG B 148 " --> pdb=" O LEU B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 183 removed outlier: 3.536A pdb=" N ILE B 165 " --> pdb=" O PRO B 161 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS B 166 " --> pdb=" O GLU B 162 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER B 183 " --> pdb=" O LEU B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 211 removed outlier: 3.927A pdb=" N ILE B 190 " --> pdb=" O TRP B 186 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLN B 191 " --> pdb=" O SER B 187 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE B 202 " --> pdb=" O LYS B 198 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ILE B 205 " --> pdb=" O ALA B 201 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL B 207 " --> pdb=" O LEU B 203 " (cutoff:3.500A) Proline residue: B 208 - end of helix Processing helix chain 'B' and resid 231 through 233 No H-bonds generated for 'chain 'B' and resid 231 through 233' Processing helix chain 'B' and resid 234 through 246 removed outlier: 3.739A pdb=" N ALA B 238 " --> pdb=" O ARG B 234 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N TYR B 246 " --> pdb=" O GLY B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 292 removed outlier: 4.365A pdb=" N ILE B 276 " --> pdb=" O ILE B 272 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL B 277 " --> pdb=" O SER B 273 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N THR B 291 " --> pdb=" O ALA B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 300 Processing helix chain 'B' and resid 302 through 312 removed outlier: 3.772A pdb=" N THR B 306 " --> pdb=" O ALA B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 332 removed outlier: 3.589A pdb=" N ALA B 318 " --> pdb=" O ASN B 314 " (cutoff:3.500A) Proline residue: B 320 - end of helix removed outlier: 4.944A pdb=" N ALA B 324 " --> pdb=" O PRO B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 335 No H-bonds generated for 'chain 'B' and resid 333 through 335' Processing helix chain 'B' and resid 336 through 348 removed outlier: 3.985A pdb=" N LEU B 341 " --> pdb=" O ALA B 337 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG B 347 " --> pdb=" O TYR B 343 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N GLU B 348 " --> pdb=" O VAL B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 355 Processing helix chain 'B' and resid 365 through 370 removed outlier: 3.536A pdb=" N VAL B 369 " --> pdb=" O PRO B 365 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE B 370 " --> pdb=" O LEU B 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 365 through 370' Processing helix chain 'B' and resid 371 through 382 removed outlier: 4.265A pdb=" N LEU B 375 " --> pdb=" O VAL B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 402 removed outlier: 4.271A pdb=" N ASN B 390 " --> pdb=" O ASP B 386 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA B 395 " --> pdb=" O PHE B 391 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE B 399 " --> pdb=" O ALA B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 411 removed outlier: 3.858A pdb=" N LEU B 407 " --> pdb=" O ALA B 403 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ILE B 408 " --> pdb=" O VAL B 404 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR B 409 " --> pdb=" O ALA B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 439 removed outlier: 5.537A pdb=" N PHE B 433 " --> pdb=" O ALA B 429 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N THR B 434 " --> pdb=" O LEU B 430 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N PHE B 437 " --> pdb=" O PHE B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 443 removed outlier: 3.786A pdb=" N LEU B 443 " --> pdb=" O ALA B 440 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 440 through 443' Processing helix chain 'B' and resid 450 through 460 Processing helix chain 'B' and resid 461 through 466 removed outlier: 3.582A pdb=" N TYR B 464 " --> pdb=" O VAL B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 492 Processing sheet with id=AA1, first strand: chain 'A' and resid 400 through 403 removed outlier: 7.316A pdb=" N LEU A 377 " --> pdb=" O LEU A 400 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N THR A 402 " --> pdb=" O LEU A 377 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N ALA A 379 " --> pdb=" O THR A 402 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N PHE A 346 " --> pdb=" O ILE A 378 " (cutoff:3.500A) removed outlier: 8.752A pdb=" N GLY A 380 " --> pdb=" O PHE A 346 " (cutoff:3.500A) removed outlier: 8.637A pdb=" N GLN A 347 " --> pdb=" O VAL A 305 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N LEU A 307 " --> pdb=" O GLN A 347 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASP A 308 " --> pdb=" O LEU A 262 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 266 through 268 removed outlier: 6.171A pdb=" N GLN A 280 " --> pdb=" O LYS A 267 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 541 through 545 removed outlier: 3.567A pdb=" N PHE A 545 " --> pdb=" O SER A 553 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N SER A 553 " --> pdb=" O PHE A 545 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 609 through 611 removed outlier: 7.052A pdb=" N LEU A 624 " --> pdb=" O LEU A 597 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 357 through 359 318 hydrogen bonds defined for protein. 924 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: 2.36 Time building geometry restraints manager: 3.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2252 1.34 - 1.46: 1535 1.46 - 1.58: 3631 1.58 - 1.69: 0 1.69 - 1.81: 45 Bond restraints: 7463 Sorted by residual: bond pdb=" C1 NAG C 1 " pdb=" O5 NAG C 1 " ideal model delta sigma weight residual 1.406 1.456 -0.050 2.00e-02 2.50e+03 6.38e+00 bond pdb=" CA LEU A 335 " pdb=" C LEU A 335 " ideal model delta sigma weight residual 1.522 1.492 0.030 1.43e-02 4.89e+03 4.44e+00 bond pdb=" C LEU A 335 " pdb=" N GLU A 336 " ideal model delta sigma weight residual 1.332 1.310 0.022 1.29e-02 6.01e+03 2.96e+00 bond pdb=" C1 NAG E 1 " pdb=" O5 NAG E 1 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.66e+00 bond pdb=" C1 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.52e+00 ... (remaining 7458 not shown) Histogram of bond angle deviations from ideal: 99.26 - 106.22: 195 106.22 - 113.19: 4156 113.19 - 120.15: 2738 120.15 - 127.11: 2965 127.11 - 134.08: 97 Bond angle restraints: 10151 Sorted by residual: angle pdb=" N ILE B 205 " pdb=" CA ILE B 205 " pdb=" C ILE B 205 " ideal model delta sigma weight residual 111.90 109.22 2.68 8.10e-01 1.52e+00 1.10e+01 angle pdb=" N GLY B 334 " pdb=" CA GLY B 334 " pdb=" C GLY B 334 " ideal model delta sigma weight residual 115.66 110.27 5.39 1.63e+00 3.76e-01 1.10e+01 angle pdb=" N LEU B 430 " pdb=" CA LEU B 430 " pdb=" C LEU B 430 " ideal model delta sigma weight residual 114.75 110.66 4.09 1.26e+00 6.30e-01 1.05e+01 angle pdb=" N VAL B 76 " pdb=" CA VAL B 76 " pdb=" C VAL B 76 " ideal model delta sigma weight residual 111.56 108.80 2.76 8.60e-01 1.35e+00 1.03e+01 angle pdb=" CA TRP B 476 " pdb=" CB TRP B 476 " pdb=" CG TRP B 476 " ideal model delta sigma weight residual 113.60 107.53 6.07 1.90e+00 2.77e-01 1.02e+01 ... (remaining 10146 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.89: 4167 21.89 - 43.78: 280 43.78 - 65.66: 29 65.66 - 87.55: 11 87.55 - 109.44: 9 Dihedral angle restraints: 4496 sinusoidal: 1857 harmonic: 2639 Sorted by residual: dihedral pdb=" CA PRO B 320 " pdb=" C PRO B 320 " pdb=" N ILE B 321 " pdb=" CA ILE B 321 " ideal model delta harmonic sigma weight residual 180.00 158.09 21.91 0 5.00e+00 4.00e-02 1.92e+01 dihedral pdb=" CA LYS A 270 " pdb=" C LYS A 270 " pdb=" N ASP A 271 " pdb=" CA ASP A 271 " ideal model delta harmonic sigma weight residual 180.00 158.58 21.42 0 5.00e+00 4.00e-02 1.84e+01 dihedral pdb=" CA ALA B 429 " pdb=" C ALA B 429 " pdb=" N LEU B 430 " pdb=" CA LEU B 430 " ideal model delta harmonic sigma weight residual 180.00 159.75 20.25 0 5.00e+00 4.00e-02 1.64e+01 ... (remaining 4493 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 1125 0.092 - 0.185: 67 0.185 - 0.277: 2 0.277 - 0.369: 0 0.369 - 0.461: 1 Chirality restraints: 1195 Sorted by residual: chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 366 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.94 -0.46 2.00e-01 2.50e+01 5.32e+00 chirality pdb=" C2 NAG D 1 " pdb=" C1 NAG D 1 " pdb=" C3 NAG D 1 " pdb=" N2 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.49 -2.29 -0.20 2.00e-01 2.50e+01 9.91e-01 chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN A 425 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-01 2.50e+01 9.13e-01 ... (remaining 1192 not shown) Planarity restraints: 1262 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 476 " -0.032 2.00e-02 2.50e+03 2.67e-02 1.78e+01 pdb=" CG TRP B 476 " 0.072 2.00e-02 2.50e+03 pdb=" CD1 TRP B 476 " -0.029 2.00e-02 2.50e+03 pdb=" CD2 TRP B 476 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 476 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP B 476 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 476 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 476 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 476 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP B 476 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 627 " -0.060 5.00e-02 4.00e+02 9.29e-02 1.38e+01 pdb=" N PRO A 628 " 0.161 5.00e-02 4.00e+02 pdb=" CA PRO A 628 " -0.052 5.00e-02 4.00e+02 pdb=" CD PRO A 628 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 321 " 0.010 2.00e-02 2.50e+03 2.00e-02 3.99e+00 pdb=" C ILE B 321 " -0.035 2.00e-02 2.50e+03 pdb=" O ILE B 321 " 0.013 2.00e-02 2.50e+03 pdb=" N PHE B 322 " 0.012 2.00e-02 2.50e+03 ... (remaining 1259 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 138 2.66 - 3.22: 7319 3.22 - 3.78: 11063 3.78 - 4.34: 15376 4.34 - 4.90: 25040 Nonbonded interactions: 58936 Sorted by model distance: nonbonded pdb=" OD2 ASP B 446 " pdb=" OG SER B 449 " model vdw 2.104 2.440 nonbonded pdb=" OH TYR B 111 " pdb=" OE2 GLU B 348 " model vdw 2.110 2.440 nonbonded pdb=" OH TYR A 469 " pdb=" O PRO A 488 " model vdw 2.110 2.440 nonbonded pdb=" O TRP A 492 " pdb=" NZ LYS A 511 " model vdw 2.202 2.520 nonbonded pdb=" OG SER B 75 " pdb=" O ALA B 224 " model vdw 2.203 2.440 ... (remaining 58931 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 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 1.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 7.030 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 23.310 Find NCS groups from input model: 0.250 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 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 : 0.005 0.056 7463 Z= 0.332 Angle : 0.819 10.988 10151 Z= 0.439 Chirality : 0.048 0.461 1195 Planarity : 0.005 0.093 1258 Dihedral : 15.249 109.438 2797 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 15.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.48 % Favored : 88.52 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: -2.67 (0.27), residues: 915 helix: -1.08 (0.24), residues: 461 sheet: -2.92 (0.63), residues: 63 loop : -2.34 (0.31), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.072 0.003 TRP B 476 HIS 0.011 0.001 HIS B 350 PHE 0.023 0.002 PHE A 291 TYR 0.015 0.002 TYR A 629 ARG 0.005 0.001 ARG A 563 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 160 time to evaluate : 0.807 Fit side-chains revert: symmetry clash REVERT: B 476 TRP cc_start: 0.3558 (m100) cc_final: 0.2302 (m100) outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 0.1743 time to fit residues: 38.3131 Evaluate side-chains 125 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 76 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 chunk 46 optimal weight: 0.7980 chunk 36 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 27 optimal weight: 0.3980 chunk 43 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 110 HIS ** B 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 285 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.1309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7463 Z= 0.235 Angle : 0.709 11.925 10151 Z= 0.344 Chirality : 0.045 0.320 1195 Planarity : 0.005 0.054 1258 Dihedral : 10.953 90.425 1151 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.62 % Favored : 90.38 % Rotamer: Outliers : 1.41 % Allowed : 10.15 % Favored : 88.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: -2.32 (0.27), residues: 915 helix: -0.59 (0.23), residues: 473 sheet: -2.83 (0.58), residues: 72 loop : -2.47 (0.31), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 476 HIS 0.006 0.001 HIS B 350 PHE 0.025 0.002 PHE A 524 TYR 0.028 0.002 TYR A 313 ARG 0.005 0.000 ARG B 148 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 145 time to evaluate : 0.851 Fit side-chains REVERT: A 460 THR cc_start: 0.8157 (p) cc_final: 0.7895 (p) REVERT: B 476 TRP cc_start: 0.3439 (m100) cc_final: 0.2585 (m100) outliers start: 11 outliers final: 6 residues processed: 148 average time/residue: 0.1862 time to fit residues: 38.3230 Evaluate side-chains 134 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 128 time to evaluate : 1.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 465 TYR Chi-restraints excluded: chain B residue 480 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 45 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 68 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 82 optimal weight: 0.8980 chunk 89 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7463 Z= 0.236 Angle : 0.667 11.094 10151 Z= 0.322 Chirality : 0.044 0.308 1195 Planarity : 0.004 0.049 1258 Dihedral : 9.801 76.302 1151 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.18 % Favored : 90.82 % Rotamer: Outliers : 2.83 % Allowed : 11.83 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: -2.02 (0.27), residues: 915 helix: -0.27 (0.24), residues: 476 sheet: -2.58 (0.64), residues: 64 loop : -2.51 (0.30), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 476 HIS 0.003 0.001 HIS B 418 PHE 0.024 0.002 PHE A 524 TYR 0.029 0.001 TYR A 313 ARG 0.005 0.000 ARG B 126 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 135 time to evaluate : 0.827 Fit side-chains REVERT: A 186 LEU cc_start: 0.7842 (mm) cc_final: 0.7572 (mp) REVERT: A 307 LEU cc_start: 0.7789 (OUTLIER) cc_final: 0.7521 (tt) REVERT: A 460 THR cc_start: 0.8216 (p) cc_final: 0.7948 (p) REVERT: B 357 MET cc_start: 0.8285 (mtt) cc_final: 0.7894 (mtt) REVERT: B 417 MET cc_start: 0.6005 (OUTLIER) cc_final: 0.5760 (ppp) REVERT: B 476 TRP cc_start: 0.3423 (m100) cc_final: 0.2545 (m100) outliers start: 22 outliers final: 15 residues processed: 144 average time/residue: 0.1666 time to fit residues: 34.2705 Evaluate side-chains 134 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 117 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 445 PHE Chi-restraints excluded: chain A residue 627 PHE Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 196 PHE Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 331 MET Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 417 MET Chi-restraints excluded: chain B residue 465 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 62 optimal weight: 0.0020 chunk 42 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 chunk 39 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 87 optimal weight: 0.2980 chunk 43 optimal weight: 0.0870 chunk 78 optimal weight: 0.0770 chunk 23 optimal weight: 0.0980 chunk 73 optimal weight: 0.8980 overall best weight: 0.1124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7463 Z= 0.162 Angle : 0.618 9.896 10151 Z= 0.296 Chirality : 0.042 0.282 1195 Planarity : 0.004 0.057 1258 Dihedral : 8.677 62.207 1151 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 2.70 % Allowed : 14.65 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: -1.58 (0.28), residues: 915 helix: 0.04 (0.24), residues: 479 sheet: -2.29 (0.63), residues: 74 loop : -2.24 (0.32), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 128 HIS 0.007 0.001 HIS B 350 PHE 0.027 0.001 PHE A 524 TYR 0.021 0.001 TYR A 313 ARG 0.005 0.000 ARG A 535 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 145 time to evaluate : 0.907 Fit side-chains REVERT: A 186 LEU cc_start: 0.7738 (mm) cc_final: 0.7522 (mp) REVERT: A 262 LEU cc_start: 0.7823 (tp) cc_final: 0.7531 (tp) REVERT: A 307 LEU cc_start: 0.7764 (OUTLIER) cc_final: 0.7516 (tp) REVERT: A 460 THR cc_start: 0.8153 (p) cc_final: 0.7941 (p) REVERT: A 485 MET cc_start: 0.6702 (ppp) cc_final: 0.5956 (tpt) REVERT: A 564 PHE cc_start: 0.7908 (m-80) cc_final: 0.7617 (m-80) REVERT: B 417 MET cc_start: 0.5991 (OUTLIER) cc_final: 0.5727 (ppp) REVERT: B 476 TRP cc_start: 0.3214 (m100) cc_final: 0.2634 (m100) outliers start: 21 outliers final: 11 residues processed: 155 average time/residue: 0.1495 time to fit residues: 33.5376 Evaluate side-chains 142 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 129 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 445 PHE Chi-restraints excluded: chain A residue 627 PHE Chi-restraints excluded: chain B residue 196 PHE Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 417 MET Chi-restraints excluded: chain B residue 465 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 49 optimal weight: 3.9990 chunk 1 optimal weight: 4.9990 chunk 65 optimal weight: 0.6980 chunk 36 optimal weight: 5.9990 chunk 75 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 44 optimal weight: 0.1980 chunk 78 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 29 optimal weight: 0.0670 overall best weight: 0.9922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7463 Z= 0.238 Angle : 0.655 11.454 10151 Z= 0.313 Chirality : 0.043 0.285 1195 Planarity : 0.004 0.053 1258 Dihedral : 8.007 57.099 1151 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer: Outliers : 3.21 % Allowed : 16.45 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: -1.57 (0.28), residues: 915 helix: 0.03 (0.24), residues: 478 sheet: -2.24 (0.66), residues: 74 loop : -2.20 (0.32), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 476 HIS 0.007 0.001 HIS B 350 PHE 0.026 0.002 PHE A 524 TYR 0.029 0.001 TYR A 313 ARG 0.005 0.000 ARG A 563 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 136 time to evaluate : 0.875 Fit side-chains REVERT: A 186 LEU cc_start: 0.7834 (mm) cc_final: 0.7606 (mp) REVERT: A 307 LEU cc_start: 0.7854 (OUTLIER) cc_final: 0.7640 (tt) REVERT: A 460 THR cc_start: 0.8175 (p) cc_final: 0.7905 (p) REVERT: A 485 MET cc_start: 0.6703 (ppp) cc_final: 0.5993 (tpt) REVERT: B 110 HIS cc_start: 0.7411 (t-170) cc_final: 0.7110 (t-170) REVERT: B 315 PHE cc_start: 0.7428 (p90) cc_final: 0.7202 (p90) REVERT: B 417 MET cc_start: 0.5964 (OUTLIER) cc_final: 0.5089 (ppp) REVERT: B 476 TRP cc_start: 0.3377 (m100) cc_final: 0.2355 (m100) outliers start: 25 outliers final: 16 residues processed: 145 average time/residue: 0.1549 time to fit residues: 32.2880 Evaluate side-chains 146 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 128 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 445 PHE Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 627 PHE Chi-restraints excluded: chain B residue 196 PHE Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 331 MET Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 417 MET Chi-restraints excluded: chain B residue 465 TYR Chi-restraints excluded: chain B residue 479 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 79 optimal weight: 0.7980 chunk 17 optimal weight: 0.3980 chunk 51 optimal weight: 0.6980 chunk 21 optimal weight: 3.9990 chunk 88 optimal weight: 0.5980 chunk 73 optimal weight: 0.1980 chunk 40 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 46 optimal weight: 0.0670 chunk 84 optimal weight: 0.5980 overall best weight: 0.3718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7463 Z= 0.174 Angle : 0.618 10.431 10151 Z= 0.296 Chirality : 0.042 0.270 1195 Planarity : 0.004 0.055 1258 Dihedral : 7.477 59.642 1151 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 2.96 % Allowed : 17.61 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: -1.44 (0.29), residues: 915 helix: 0.20 (0.24), residues: 479 sheet: -2.51 (0.60), residues: 80 loop : -2.16 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 128 HIS 0.007 0.001 HIS B 350 PHE 0.027 0.001 PHE A 524 TYR 0.024 0.001 TYR A 313 ARG 0.003 0.000 ARG B 126 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 140 time to evaluate : 0.818 Fit side-chains REVERT: A 186 LEU cc_start: 0.7770 (mm) cc_final: 0.7545 (mp) REVERT: A 307 LEU cc_start: 0.7727 (OUTLIER) cc_final: 0.7378 (tt) REVERT: A 460 THR cc_start: 0.8182 (p) cc_final: 0.7972 (p) REVERT: A 485 MET cc_start: 0.6727 (ppp) cc_final: 0.5974 (tpt) REVERT: B 110 HIS cc_start: 0.7318 (t-170) cc_final: 0.7096 (t-170) REVERT: B 357 MET cc_start: 0.8401 (mtt) cc_final: 0.7560 (mtt) REVERT: B 417 MET cc_start: 0.5951 (OUTLIER) cc_final: 0.5126 (ppp) REVERT: B 476 TRP cc_start: 0.3223 (m100) cc_final: 0.2398 (m100) outliers start: 23 outliers final: 18 residues processed: 150 average time/residue: 0.1484 time to fit residues: 32.2308 Evaluate side-chains 149 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 129 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 445 PHE Chi-restraints excluded: chain A residue 627 PHE Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 196 PHE Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 331 MET Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 417 MET Chi-restraints excluded: chain B residue 465 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 9 optimal weight: 5.9990 chunk 50 optimal weight: 0.8980 chunk 64 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 74 optimal weight: 0.7980 chunk 87 optimal weight: 0.9980 chunk 54 optimal weight: 0.7980 chunk 53 optimal weight: 0.0870 chunk 40 optimal weight: 4.9990 chunk 35 optimal weight: 0.8980 chunk 52 optimal weight: 0.8980 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7463 Z= 0.200 Angle : 0.628 10.942 10151 Z= 0.300 Chirality : 0.043 0.269 1195 Planarity : 0.004 0.053 1258 Dihedral : 7.120 58.105 1151 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.42 % Favored : 91.58 % Rotamer: Outliers : 3.21 % Allowed : 17.74 % Favored : 79.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: -1.36 (0.29), residues: 915 helix: 0.21 (0.25), residues: 478 sheet: -2.12 (0.63), residues: 74 loop : -2.12 (0.32), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 128 HIS 0.007 0.001 HIS B 350 PHE 0.028 0.001 PHE A 524 TYR 0.032 0.001 TYR A 313 ARG 0.004 0.000 ARG A 563 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 135 time to evaluate : 0.754 Fit side-chains REVERT: A 307 LEU cc_start: 0.7823 (OUTLIER) cc_final: 0.7471 (tt) REVERT: A 460 THR cc_start: 0.8194 (p) cc_final: 0.7917 (p) REVERT: A 485 MET cc_start: 0.6724 (ppp) cc_final: 0.5936 (tpt) REVERT: B 110 HIS cc_start: 0.7404 (t-170) cc_final: 0.7177 (t-170) REVERT: B 357 MET cc_start: 0.8413 (mtt) cc_final: 0.7691 (mtt) REVERT: B 417 MET cc_start: 0.5896 (OUTLIER) cc_final: 0.5097 (ppp) REVERT: B 476 TRP cc_start: 0.3243 (m100) cc_final: 0.2275 (m100) outliers start: 25 outliers final: 20 residues processed: 148 average time/residue: 0.1474 time to fit residues: 31.4609 Evaluate side-chains 148 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 126 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 445 PHE Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 627 PHE Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 196 PHE Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 331 MET Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 348 GLU Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 417 MET Chi-restraints excluded: chain B residue 465 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 26 optimal weight: 0.0670 chunk 17 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 chunk 55 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 chunk 8 optimal weight: 0.5980 chunk 68 optimal weight: 2.9990 chunk 79 optimal weight: 0.6980 chunk 84 optimal weight: 0.9980 chunk 76 optimal weight: 5.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.2646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7463 Z= 0.190 Angle : 0.637 10.587 10151 Z= 0.307 Chirality : 0.043 0.307 1195 Planarity : 0.004 0.053 1258 Dihedral : 6.957 56.885 1151 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer: Outliers : 3.21 % Allowed : 18.51 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: -1.27 (0.29), residues: 915 helix: 0.27 (0.25), residues: 477 sheet: -2.01 (0.64), residues: 74 loop : -2.07 (0.33), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 128 HIS 0.006 0.001 HIS B 350 PHE 0.029 0.001 PHE A 524 TYR 0.025 0.001 TYR A 313 ARG 0.003 0.000 ARG A 535 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 131 time to evaluate : 0.810 Fit side-chains REVERT: A 307 LEU cc_start: 0.7793 (OUTLIER) cc_final: 0.7435 (tt) REVERT: A 460 THR cc_start: 0.8192 (p) cc_final: 0.7972 (p) REVERT: A 485 MET cc_start: 0.6718 (ppp) cc_final: 0.5942 (tpt) REVERT: B 357 MET cc_start: 0.8407 (mtt) cc_final: 0.7703 (mtt) REVERT: B 417 MET cc_start: 0.5852 (OUTLIER) cc_final: 0.5059 (ppp) REVERT: B 476 TRP cc_start: 0.3178 (m100) cc_final: 0.2275 (m100) outliers start: 25 outliers final: 22 residues processed: 144 average time/residue: 0.1585 time to fit residues: 33.3230 Evaluate side-chains 151 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 127 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 445 PHE Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 627 PHE Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 196 PHE Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 331 MET Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 348 GLU Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 417 MET Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain B residue 465 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 81 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 64 optimal weight: 0.5980 chunk 25 optimal weight: 0.6980 chunk 73 optimal weight: 0.1980 chunk 77 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 396 ASN ** B 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7463 Z= 0.197 Angle : 0.634 10.812 10151 Z= 0.302 Chirality : 0.043 0.261 1195 Planarity : 0.004 0.051 1258 Dihedral : 6.771 55.394 1151 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.09 % Favored : 91.91 % Rotamer: Outliers : 3.47 % Allowed : 17.87 % Favored : 78.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: -1.20 (0.29), residues: 915 helix: 0.32 (0.25), residues: 477 sheet: -1.82 (0.70), residues: 64 loop : -2.09 (0.32), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 128 HIS 0.011 0.001 HIS B 110 PHE 0.028 0.001 PHE A 524 TYR 0.034 0.002 TYR A 313 ARG 0.003 0.000 ARG A 430 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 127 time to evaluate : 0.791 Fit side-chains REVERT: A 307 LEU cc_start: 0.7784 (OUTLIER) cc_final: 0.7441 (tt) REVERT: A 460 THR cc_start: 0.8197 (p) cc_final: 0.7920 (p) REVERT: A 485 MET cc_start: 0.6707 (ppp) cc_final: 0.5954 (tpt) REVERT: B 110 HIS cc_start: 0.7187 (t-170) cc_final: 0.6857 (t70) REVERT: B 357 MET cc_start: 0.8398 (mtt) cc_final: 0.7736 (mtt) REVERT: B 476 TRP cc_start: 0.3208 (m100) cc_final: 0.2268 (m100) outliers start: 27 outliers final: 22 residues processed: 141 average time/residue: 0.1380 time to fit residues: 28.8619 Evaluate side-chains 147 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 124 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 445 PHE Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 595 ASP Chi-restraints excluded: chain A residue 627 PHE Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 196 PHE Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 331 MET Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain B residue 465 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 41 optimal weight: 0.3980 chunk 60 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 7 optimal weight: 7.9990 chunk 55 optimal weight: 0.6980 chunk 44 optimal weight: 0.7980 chunk 57 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 275 GLN ** B 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.2769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7463 Z= 0.203 Angle : 0.647 11.063 10151 Z= 0.306 Chirality : 0.043 0.254 1195 Planarity : 0.004 0.051 1258 Dihedral : 6.588 55.590 1151 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.98 % Favored : 92.02 % Rotamer: Outliers : 3.21 % Allowed : 18.38 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: -1.17 (0.29), residues: 915 helix: 0.35 (0.25), residues: 476 sheet: -1.83 (0.71), residues: 64 loop : -2.06 (0.32), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 128 HIS 0.009 0.001 HIS B 110 PHE 0.026 0.001 PHE A 524 TYR 0.034 0.002 TYR A 313 ARG 0.003 0.000 ARG A 430 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 130 time to evaluate : 0.871 Fit side-chains REVERT: A 307 LEU cc_start: 0.7707 (OUTLIER) cc_final: 0.7364 (tt) REVERT: A 460 THR cc_start: 0.8185 (p) cc_final: 0.7910 (p) REVERT: A 485 MET cc_start: 0.6724 (ppp) cc_final: 0.6005 (tpt) REVERT: B 110 HIS cc_start: 0.7132 (t-170) cc_final: 0.6888 (t70) REVERT: B 357 MET cc_start: 0.8392 (mtt) cc_final: 0.7651 (mtt) REVERT: B 476 TRP cc_start: 0.3351 (m100) cc_final: 0.2365 (m100) outliers start: 25 outliers final: 21 residues processed: 144 average time/residue: 0.1481 time to fit residues: 30.9508 Evaluate side-chains 144 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 122 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 445 PHE Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 595 ASP Chi-restraints excluded: chain A residue 627 PHE Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 196 PHE Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 331 MET Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain B residue 465 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 66 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 72 optimal weight: 0.7980 chunk 30 optimal weight: 0.0070 chunk 74 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 219 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 = 0.3933 r_free = 0.3933 target = 0.156822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.141047 restraints weight = 11787.118| |-----------------------------------------------------------------------------| r_work (start): 0.3742 rms_B_bonded: 2.12 r_work: 0.3662 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3544 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.2805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7463 Z= 0.204 Angle : 0.655 10.967 10151 Z= 0.308 Chirality : 0.044 0.255 1195 Planarity : 0.004 0.051 1258 Dihedral : 6.451 55.618 1151 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.42 % Favored : 91.58 % Rotamer: Outliers : 3.08 % Allowed : 18.89 % Favored : 78.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: -1.12 (0.29), residues: 915 helix: 0.38 (0.25), residues: 477 sheet: -1.84 (0.70), residues: 64 loop : -2.03 (0.32), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 128 HIS 0.008 0.001 HIS B 110 PHE 0.029 0.001 PHE A 524 TYR 0.032 0.002 TYR A 313 ARG 0.003 0.000 ARG A 430 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1927.20 seconds wall clock time: 35 minutes 29.57 seconds (2129.57 seconds total)