Starting phenix.real_space_refine on Fri Dec 8 05:40:05 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p9v_13267/12_2023/7p9v_13267.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p9v_13267/12_2023/7p9v_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_13267/12_2023/7p9v_13267.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p9v_13267/12_2023/7p9v_13267.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p9v_13267/12_2023/7p9v_13267.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p9v_13267/12_2023/7p9v_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-1.21rc1-5172/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: 4.37, 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: 3.28 Conformation dependent library (CDL) restraints added in 1.4 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: 0.83 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: 2.19 Time building geometry restraints manager: 3.26 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: 1.610 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: 7.180 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 23.610 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.050 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.760 ------------------------------------------------------------------------------- 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 : 0.828 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 0.1760 time to fit residues: 38.7624 Evaluate side-chains 125 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 0.840 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1829 ------------------------------------------------------------------------------- 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: 0.7630 moved from start: 0.1311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7463 Z= 0.233 Angle : 0.708 11.841 10151 Z= 0.343 Chirality : 0.045 0.327 1195 Planarity : 0.005 0.054 1258 Dihedral : 10.984 90.941 1151 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.73 % Favored : 90.27 % Rotamer: Outliers : 1.29 % Allowed : 10.41 % Favored : 88.30 % 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: -0.60 (0.23), residues: 474 sheet: -2.83 (0.58), residues: 72 loop : -2.46 (0.31), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 476 HIS 0.006 0.001 HIS B 350 PHE 0.025 0.002 PHE A 524 TYR 0.029 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 155 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 145 time to evaluate : 0.901 Fit side-chains outliers start: 10 outliers final: 6 residues processed: 147 average time/residue: 0.1783 time to fit residues: 36.3732 Evaluate side-chains 135 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 129 time to evaluate : 0.863 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0755 time to fit residues: 1.9725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 45 optimal weight: 0.0770 chunk 25 optimal weight: 0.8980 chunk 68 optimal weight: 0.0570 chunk 56 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 chunk 89 optimal weight: 0.0000 chunk 73 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 66 optimal weight: 0.4980 chunk 81 optimal weight: 0.6980 overall best weight: 0.2660 ------------------------------------------------------------------------------- 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: 0.7569 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7463 Z= 0.175 Angle : 0.638 9.845 10151 Z= 0.307 Chirality : 0.043 0.303 1195 Planarity : 0.004 0.053 1258 Dihedral : 9.760 76.517 1151 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.98 % Favored : 92.02 % Rotamer: Outliers : 1.67 % Allowed : 12.47 % Favored : 85.86 % 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: -1.85 (0.28), residues: 915 helix: -0.13 (0.24), residues: 476 sheet: -2.46 (0.65), residues: 64 loop : -2.43 (0.31), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 476 HIS 0.004 0.001 HIS B 418 PHE 0.024 0.001 PHE A 524 TYR 0.028 0.001 TYR A 313 ARG 0.003 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 161 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 148 time to evaluate : 0.839 Fit side-chains outliers start: 13 outliers final: 6 residues processed: 152 average time/residue: 0.1646 time to fit residues: 36.1163 Evaluate side-chains 131 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 125 time to evaluate : 0.779 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0810 time to fit residues: 1.9519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 62 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 9 optimal weight: 6.9990 chunk 39 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 83 optimal weight: 0.4980 chunk 87 optimal weight: 0.0370 chunk 43 optimal weight: 1.9990 chunk 78 optimal weight: 0.0570 chunk 23 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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: 0.7612 moved from start: 0.1935 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= 0.228 Angle : 0.650 10.792 10151 Z= 0.313 Chirality : 0.044 0.298 1195 Planarity : 0.004 0.054 1258 Dihedral : 8.953 65.148 1151 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer: Outliers : 1.93 % Allowed : 15.17 % Favored : 82.90 % 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: -1.74 (0.28), residues: 915 helix: -0.08 (0.24), residues: 480 sheet: -2.38 (0.62), residues: 74 loop : -2.33 (0.32), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 128 HIS 0.003 0.001 HIS B 359 PHE 0.024 0.001 PHE A 524 TYR 0.027 0.001 TYR A 313 ARG 0.006 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 151 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 136 time to evaluate : 0.825 Fit side-chains outliers start: 15 outliers final: 9 residues processed: 145 average time/residue: 0.1513 time to fit residues: 31.7398 Evaluate side-chains 132 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 123 time to evaluate : 0.825 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0733 time to fit residues: 2.2989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.5980 chunk 36 optimal weight: 2.9990 chunk 75 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 chunk 0 optimal weight: 0.6980 chunk 44 optimal weight: 4.9990 chunk 78 optimal weight: 0.7980 chunk 22 optimal weight: 0.0770 chunk 29 optimal weight: 0.7980 overall best weight: 0.5938 ------------------------------------------------------------------------------- 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: 0.7587 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7463 Z= 0.190 Angle : 0.622 10.196 10151 Z= 0.299 Chirality : 0.043 0.283 1195 Planarity : 0.004 0.055 1258 Dihedral : 8.237 56.837 1151 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.98 % Favored : 92.02 % Rotamer: Outliers : 1.29 % Allowed : 16.07 % 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: -1.55 (0.28), residues: 915 helix: 0.03 (0.24), residues: 480 sheet: -2.13 (0.67), residues: 74 loop : -2.22 (0.32), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 128 HIS 0.002 0.001 HIS B 359 PHE 0.027 0.001 PHE A 524 TYR 0.027 0.001 TYR A 313 ARG 0.003 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 143 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 133 time to evaluate : 0.879 Fit side-chains outliers start: 10 outliers final: 5 residues processed: 139 average time/residue: 0.1551 time to fit residues: 31.3314 Evaluate side-chains 132 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 127 time to evaluate : 0.819 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0771 time to fit residues: 1.7956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 79 optimal weight: 0.5980 chunk 17 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 chunk 21 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 73 optimal weight: 0.8980 chunk 40 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 46 optimal weight: 0.0000 chunk 84 optimal weight: 0.2980 overall best weight: 0.4584 ------------------------------------------------------------------------------- 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: 0.7560 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7463 Z= 0.177 Angle : 0.628 10.117 10151 Z= 0.303 Chirality : 0.043 0.274 1195 Planarity : 0.004 0.055 1258 Dihedral : 7.552 59.345 1151 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer: Outliers : 0.77 % Allowed : 18.25 % Favored : 80.98 % 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: -1.42 (0.28), residues: 915 helix: 0.13 (0.24), residues: 481 sheet: -2.15 (0.63), residues: 74 loop : -2.11 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 128 HIS 0.003 0.001 HIS B 359 PHE 0.032 0.001 PHE A 564 TYR 0.023 0.001 TYR A 313 ARG 0.003 0.000 ARG A 535 *********************** 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 160 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 154 time to evaluate : 0.828 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 155 average time/residue: 0.1544 time to fit residues: 34.5699 Evaluate side-chains 135 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 133 time to evaluate : 0.759 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0752 time to fit residues: 1.4908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 9 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 64 optimal weight: 0.4980 chunk 49 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 chunk 87 optimal weight: 0.8980 chunk 54 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 chunk 40 optimal weight: 4.9990 chunk 35 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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** A 266 HIS A 268 ASN A 275 GLN ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7463 Z= 0.210 Angle : 0.640 10.426 10151 Z= 0.307 Chirality : 0.043 0.271 1195 Planarity : 0.004 0.052 1258 Dihedral : 7.225 58.259 1151 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.42 % Favored : 91.58 % Rotamer: Outliers : 1.54 % Allowed : 19.54 % Favored : 78.92 % 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: -1.37 (0.28), residues: 915 helix: 0.17 (0.24), residues: 479 sheet: -2.14 (0.63), residues: 74 loop : -2.09 (0.32), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 128 HIS 0.002 0.001 HIS B 359 PHE 0.027 0.001 PHE A 524 TYR 0.030 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 145 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 133 time to evaluate : 0.837 Fit side-chains outliers start: 12 outliers final: 8 residues processed: 140 average time/residue: 0.1511 time to fit residues: 30.9615 Evaluate side-chains 133 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 125 time to evaluate : 0.845 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0725 time to fit residues: 2.2080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 26 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 55 optimal weight: 0.5980 chunk 59 optimal weight: 2.9990 chunk 43 optimal weight: 0.0060 chunk 8 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 79 optimal weight: 0.7980 chunk 84 optimal weight: 0.8980 chunk 76 optimal weight: 0.7980 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 235 GLN A 266 HIS ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.2658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7463 Z= 0.193 Angle : 0.632 10.253 10151 Z= 0.303 Chirality : 0.043 0.265 1195 Planarity : 0.004 0.052 1258 Dihedral : 6.964 56.860 1151 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer: Outliers : 0.26 % Allowed : 20.44 % Favored : 79.31 % 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: -1.24 (0.29), residues: 915 helix: 0.25 (0.25), residues: 478 sheet: -1.95 (0.70), residues: 64 loop : -2.02 (0.32), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 128 HIS 0.003 0.001 HIS B 373 PHE 0.029 0.001 PHE A 524 TYR 0.028 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 137 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 135 time to evaluate : 0.782 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 136 average time/residue: 0.1595 time to fit residues: 30.7726 Evaluate side-chains 123 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 122 time to evaluate : 0.853 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0718 time to fit residues: 1.3219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 81 optimal weight: 3.9990 chunk 84 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 64 optimal weight: 0.8980 chunk 25 optimal weight: 0.5980 chunk 73 optimal weight: 0.6980 chunk 77 optimal weight: 0.0470 chunk 53 optimal weight: 0.8980 chunk 86 optimal weight: 0.5980 chunk 52 optimal weight: 0.9980 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 HIS ** 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: 0.7561 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7463 Z= 0.192 Angle : 0.632 10.248 10151 Z= 0.302 Chirality : 0.043 0.261 1195 Planarity : 0.004 0.051 1258 Dihedral : 6.763 55.133 1151 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer: Outliers : 0.39 % Allowed : 21.47 % Favored : 78.15 % 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: -1.16 (0.29), residues: 915 helix: 0.32 (0.25), residues: 478 sheet: -1.87 (0.71), residues: 64 loop : -2.00 (0.32), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 128 HIS 0.003 0.001 HIS B 373 PHE 0.028 0.001 PHE A 524 TYR 0.029 0.001 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 134 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 131 time to evaluate : 0.847 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 133 average time/residue: 0.1460 time to fit residues: 28.7441 Evaluate side-chains 128 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 127 time to evaluate : 0.881 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0917 time to fit residues: 1.3507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 41 optimal weight: 0.0050 chunk 60 optimal weight: 0.8980 chunk 90 optimal weight: 0.8980 chunk 83 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 7 optimal weight: 7.9990 chunk 55 optimal weight: 0.9980 chunk 44 optimal weight: 0.0030 chunk 57 optimal weight: 0.3980 chunk 76 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 overall best weight: 0.4404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 HIS 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.2929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 7463 Z= 0.185 Angle : 0.642 10.141 10151 Z= 0.303 Chirality : 0.043 0.257 1195 Planarity : 0.004 0.052 1258 Dihedral : 6.558 54.669 1151 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.76 % Favored : 92.24 % Rotamer: Outliers : 0.26 % Allowed : 21.34 % 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: -1.06 (0.29), residues: 915 helix: 0.42 (0.25), residues: 476 sheet: -1.75 (0.72), residues: 64 loop : -1.99 (0.32), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 397 HIS 0.003 0.001 HIS B 110 PHE 0.029 0.001 PHE A 524 TYR 0.026 0.001 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 139 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 137 time to evaluate : 0.861 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 138 average time/residue: 0.1568 time to fit residues: 31.6767 Evaluate side-chains 133 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 132 time to evaluate : 0.876 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1023 time to fit residues: 1.3043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 66 optimal weight: 0.0070 chunk 10 optimal weight: 7.9990 chunk 20 optimal weight: 3.9990 chunk 72 optimal weight: 0.4980 chunk 30 optimal weight: 4.9990 chunk 74 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 52 optimal weight: 0.1980 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 HIS ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.158122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.142555 restraints weight = 11809.868| |-----------------------------------------------------------------------------| r_work (start): 0.3770 rms_B_bonded: 2.13 r_work: 0.3691 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3573 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.3023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 7463 Z= 0.188 Angle : 0.647 10.159 10151 Z= 0.304 Chirality : 0.043 0.253 1195 Planarity : 0.004 0.034 1258 Dihedral : 6.377 54.786 1151 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 0.39 % Allowed : 21.59 % 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: -0.97 (0.29), residues: 915 helix: 0.46 (0.25), residues: 479 sheet: -1.73 (0.72), residues: 64 loop : -1.90 (0.33), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 128 HIS 0.004 0.001 HIS B 373 PHE 0.028 0.001 PHE A 524 TYR 0.023 0.001 TYR A 313 ARG 0.003 0.000 ARG A 535 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1951.54 seconds wall clock time: 35 minutes 57.85 seconds (2157.85 seconds total)