Starting phenix.real_space_refine on Tue Nov 14 03:32:32 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p9v_13267/11_2023/7p9v_13267.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p9v_13267/11_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_13267/11_2023/7p9v_13267.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p9v_13267/11_2023/7p9v_13267.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p9v_13267/11_2023/7p9v_13267.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p9v_13267/11_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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/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 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 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 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 chiralities: 2 Time building chain proxies: 4.38, 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: 2.87 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: 0.76 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: 3.16 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 - 17.85: 3899 17.85 - 35.69: 367 35.69 - 53.54: 53 53.54 - 71.38: 2 71.38 - 89.23: 7 Dihedral angle restraints: 4328 sinusoidal: 1689 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 4325 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: 3.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 7.220 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 23.810 Find NCS groups from input model: 0.230 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:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.600 ------------------------------------------------------------------------------- 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 : 13.768 89.228 2629 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 *********************** 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 : 0.829 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 0.1740 time to fit residues: 38.6270 Evaluate side-chains 125 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 0.749 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0136 ------------------------------------------------------------------------------- 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: 0.7631 moved from start: 0.1306 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= 0.235 Angle : 0.703 11.919 10151 Z= 0.342 Chirality : 0.045 0.306 1195 Planarity : 0.005 0.054 1258 Dihedral : 5.435 22.189 983 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.73 % Favored : 90.27 % Rotamer: Outliers : 1.29 % Allowed : 10.28 % 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: -2.33 (0.27), residues: 915 helix: -0.61 (0.23), residues: 474 sheet: -2.83 (0.58), residues: 72 loop : -2.45 (0.31), residues: 369 *********************** 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 : 0.865 Fit side-chains outliers start: 10 outliers final: 6 residues processed: 147 average time/residue: 0.1765 time to fit residues: 35.7618 Evaluate side-chains 134 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 128 time to evaluate : 0.755 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0750 time to fit residues: 1.8402 ------------------------------------------------------------------------------- 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: 3.9990 chunk 25 optimal weight: 0.6980 chunk 68 optimal weight: 0.4980 chunk 56 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 73 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 81 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 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: 0.7621 moved from start: 0.1612 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= 0.218 Angle : 0.650 10.671 10151 Z= 0.315 Chirality : 0.043 0.287 1195 Planarity : 0.004 0.049 1258 Dihedral : 5.156 21.365 983 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.07 % Favored : 90.93 % Rotamer: Outliers : 1.80 % Allowed : 12.98 % Favored : 85.22 % 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: -1.99 (0.27), residues: 915 helix: -0.26 (0.24), residues: 477 sheet: -2.56 (0.64), residues: 64 loop : -2.49 (0.31), residues: 374 *********************** 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 156 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 142 time to evaluate : 0.737 Fit side-chains outliers start: 14 outliers final: 7 residues processed: 147 average time/residue: 0.1693 time to fit residues: 35.9946 Evaluate side-chains 126 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 119 time to evaluate : 0.798 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0800 time to fit residues: 2.1431 ------------------------------------------------------------------------------- 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: 0.0470 chunk 42 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 78 optimal weight: 0.0070 chunk 23 optimal weight: 0.3980 chunk 73 optimal weight: 1.9990 overall best weight: 0.4898 ------------------------------------------------------------------------------- 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: 0.7585 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7463 Z= 0.186 Angle : 0.620 10.240 10151 Z= 0.301 Chirality : 0.043 0.268 1195 Planarity : 0.004 0.054 1258 Dihedral : 4.948 22.461 983 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer: Outliers : 1.93 % Allowed : 15.55 % Favored : 82.52 % 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: -1.71 (0.28), residues: 915 helix: -0.07 (0.24), residues: 480 sheet: -2.34 (0.63), residues: 74 loop : -2.30 (0.32), residues: 361 *********************** 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 155 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 140 time to evaluate : 0.880 Fit side-chains outliers start: 15 outliers final: 8 residues processed: 148 average time/residue: 0.1491 time to fit residues: 31.9074 Evaluate side-chains 134 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 126 time to evaluate : 0.840 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0704 time to fit residues: 2.1508 ------------------------------------------------------------------------------- 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: 0.9990 chunk 65 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 0 optimal weight: 0.6980 chunk 44 optimal weight: 5.9990 chunk 78 optimal weight: 8.9990 chunk 22 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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: 0.7615 moved from start: 0.2091 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= 0.224 Angle : 0.644 10.842 10151 Z= 0.309 Chirality : 0.043 0.264 1195 Planarity : 0.004 0.054 1258 Dihedral : 4.897 21.419 983 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer: Outliers : 1.03 % Allowed : 16.97 % Favored : 82.01 % 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: -1.65 (0.28), residues: 915 helix: -0.05 (0.24), residues: 480 sheet: -2.31 (0.65), residues: 74 loop : -2.23 (0.32), residues: 361 *********************** 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: 8 poor density : 135 time to evaluate : 0.902 Fit side-chains outliers start: 8 outliers final: 3 residues processed: 140 average time/residue: 0.1519 time to fit residues: 31.4110 Evaluate side-chains 130 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 127 time to evaluate : 0.876 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0819 time to fit residues: 1.4616 ------------------------------------------------------------------------------- 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: 0.9980 chunk 17 optimal weight: 0.7980 chunk 51 optimal weight: 0.6980 chunk 21 optimal weight: 3.9990 chunk 88 optimal weight: 0.8980 chunk 73 optimal weight: 0.9990 chunk 40 optimal weight: 5.9990 chunk 7 optimal weight: 0.0970 chunk 29 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 84 optimal weight: 0.7980 overall best weight: 0.6178 ------------------------------------------------------------------------------- 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: 0.7585 moved from start: 0.2298 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= 0.190 Angle : 0.624 10.690 10151 Z= 0.300 Chirality : 0.043 0.259 1195 Planarity : 0.004 0.054 1258 Dihedral : 4.782 22.730 983 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.31 % Favored : 91.69 % Rotamer: Outliers : 1.29 % Allowed : 18.51 % Favored : 80.21 % 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: -1.50 (0.28), residues: 915 helix: 0.07 (0.24), residues: 481 sheet: -2.25 (0.68), residues: 64 loop : -2.18 (0.32), residues: 370 *********************** 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 156 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 146 time to evaluate : 0.862 Fit side-chains outliers start: 10 outliers final: 8 residues processed: 150 average time/residue: 0.1547 time to fit residues: 33.4494 Evaluate side-chains 144 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 136 time to evaluate : 0.847 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0734 time to fit residues: 2.2097 ------------------------------------------------------------------------------- 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: 5.9990 chunk 50 optimal weight: 0.9980 chunk 64 optimal weight: 0.1980 chunk 49 optimal weight: 3.9990 chunk 74 optimal weight: 0.4980 chunk 87 optimal weight: 0.0370 chunk 54 optimal weight: 0.9980 chunk 53 optimal weight: 0.6980 chunk 40 optimal weight: 4.9990 chunk 35 optimal weight: 0.3980 chunk 52 optimal weight: 0.9990 overall best weight: 0.3658 ------------------------------------------------------------------------------- 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: 0.2527 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= 0.171 Angle : 0.618 9.979 10151 Z= 0.296 Chirality : 0.042 0.253 1195 Planarity : 0.004 0.055 1258 Dihedral : 4.664 22.058 983 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.98 % Favored : 92.02 % Rotamer: Outliers : 0.77 % Allowed : 19.67 % Favored : 79.56 % 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 (0.29), residues: 915 helix: 0.23 (0.24), residues: 479 sheet: -2.55 (0.61), residues: 80 loop : -2.15 (0.33), residues: 356 *********************** 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 151 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 145 time to evaluate : 0.834 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 149 average time/residue: 0.1597 time to fit residues: 34.1592 Evaluate side-chains 136 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 134 time to evaluate : 0.714 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0765 time to fit residues: 1.2914 ------------------------------------------------------------------------------- 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: 0.0970 chunk 17 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 55 optimal weight: 0.5980 chunk 59 optimal weight: 0.6980 chunk 43 optimal weight: 5.9990 chunk 8 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 84 optimal weight: 0.0980 chunk 76 optimal weight: 0.9990 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 235 GLN 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.2664 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= 0.182 Angle : 0.626 10.132 10151 Z= 0.301 Chirality : 0.043 0.254 1195 Planarity : 0.004 0.053 1258 Dihedral : 4.630 23.031 983 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer: Outliers : 0.51 % Allowed : 21.34 % 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: -1.24 (0.29), residues: 915 helix: 0.32 (0.25), residues: 477 sheet: -2.09 (0.64), residues: 74 loop : -2.07 (0.33), residues: 364 *********************** 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 146 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 142 time to evaluate : 0.904 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 145 average time/residue: 0.1570 time to fit residues: 32.7176 Evaluate side-chains 134 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 132 time to evaluate : 0.757 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0673 time to fit residues: 1.2890 ------------------------------------------------------------------------------- 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: 0.9980 chunk 84 optimal weight: 0.5980 chunk 49 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 73 optimal weight: 0.9980 chunk 77 optimal weight: 0.8980 chunk 53 optimal weight: 0.5980 chunk 86 optimal weight: 0.7980 chunk 52 optimal weight: 0.2980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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: 0.7555 moved from start: 0.2771 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= 0.195 Angle : 0.641 10.334 10151 Z= 0.306 Chirality : 0.043 0.256 1195 Planarity : 0.004 0.052 1258 Dihedral : 4.586 23.381 983 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.76 % Favored : 92.24 % Rotamer: Outliers : 0.13 % Allowed : 21.34 % Favored : 78.53 % 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: -1.19 (0.29), residues: 915 helix: 0.34 (0.25), residues: 474 sheet: -1.89 (0.70), residues: 64 loop : -2.06 (0.32), residues: 377 *********************** 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 139 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 138 time to evaluate : 0.756 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 139 average time/residue: 0.1558 time to fit residues: 31.2359 Evaluate side-chains 131 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 130 time to evaluate : 0.897 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0884 time to fit residues: 1.3060 ------------------------------------------------------------------------------- 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: 0.3980 chunk 60 optimal weight: 0.7980 chunk 90 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 72 optimal weight: 0.8980 chunk 7 optimal weight: 0.0870 chunk 55 optimal weight: 0.5980 chunk 44 optimal weight: 0.2980 chunk 57 optimal weight: 0.6980 chunk 76 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 overall best weight: 0.4158 ------------------------------------------------------------------------------- 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: 0.7536 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7463 Z= 0.182 Angle : 0.652 12.384 10151 Z= 0.306 Chirality : 0.043 0.253 1195 Planarity : 0.004 0.053 1258 Dihedral : 4.561 25.559 983 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 0.26 % Allowed : 21.21 % Favored : 78.53 % 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: 0.46 (0.25), residues: 476 sheet: -1.69 (0.71), residues: 63 loop : -2.05 (0.32), residues: 376 ********************** 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 141 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 139 time to evaluate : 0.775 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 140 average time/residue: 0.1419 time to fit residues: 29.2598 Evaluate side-chains 135 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 134 time to evaluate : 0.797 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0762 time to fit residues: 1.2564 ------------------------------------------------------------------------------- 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: 0.0570 chunk 10 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 72 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 74 optimal weight: 0.5980 chunk 9 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 52 optimal weight: 0.7980 overall best weight: 0.8902 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.155499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.139857 restraints weight = 11799.277| |-----------------------------------------------------------------------------| r_work (start): 0.3737 rms_B_bonded: 2.12 r_work: 0.3658 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3541 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.2849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 7463 Z= 0.231 Angle : 0.682 11.773 10151 Z= 0.322 Chirality : 0.044 0.265 1195 Planarity : 0.004 0.032 1258 Dihedral : 4.631 23.778 983 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.85 % Favored : 91.15 % Rotamer: Outliers : 0.26 % Allowed : 21.08 % 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: -1.10 (0.29), residues: 915 helix: 0.40 (0.25), residues: 479 sheet: -1.89 (0.70), residues: 64 loop : -2.01 (0.32), residues: 372 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1893.63 seconds wall clock time: 34 minutes 42.14 seconds (2082.14 seconds total)