Starting phenix.real_space_refine on Thu Jul 2 17:57:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7zay_14582/07_2026/7zay_14582.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zay_14582/07_2026/7zay_14582.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7zay_14582/07_2026/7zay_14582.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7zay_14582/07_2026/7zay_14582.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7zay_14582/07_2026/7zay_14582.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zay_14582/07_2026/7zay_14582.map" model { file = "/net/cci-nas-00/data/ceres_data/7zay_14582/07_2026/7zay_14582.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zay_14582/07_2026/7zay_14582.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 46 5.16 5 C 6010 2.51 5 N 1571 2.21 5 O 1710 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9339 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 566, 4573 Classifications: {'peptide': 566} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 539} Chain breaks: 4 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 21 Chain: "B" Number of atoms: 4688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 580, 4688 Classifications: {'peptide': 580} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 2, 'PTRANS': 33, 'TRANS': 544} Chain breaks: 4 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'NAG': 1, 'UDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.99, per 1000 atoms: 0.21 Number of scatterers: 9339 At special positions: 0 Unit cell: (97.44, 102.48, 102.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 46 16.00 P 2 15.00 O 1710 8.00 N 1571 7.00 C 6010 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 98 " - pdb=" SG CYS A 103 " distance=2.03 Simple disulfide: pdb=" SG CYS A 109 " - pdb=" SG CYS A 152 " distance=2.04 Simple disulfide: pdb=" SG CYS A 298 " - pdb=" SG CYS A 312 " distance=2.03 Simple disulfide: pdb=" SG CYS A 334 " - pdb=" SG CYS A 355 " distance=2.03 Simple disulfide: pdb=" SG CYS A 652 " - pdb=" SG CYS A 704 " distance=2.03 Simple disulfide: pdb=" SG CYS B 85 " - pdb=" SG CYS B 90 " distance=2.03 Simple disulfide: pdb=" SG CYS B 96 " - pdb=" SG CYS B 151 " distance=2.03 Simple disulfide: pdb=" SG CYS B 286 " - pdb=" SG CYS B 300 " distance=2.03 Simple disulfide: pdb=" SG CYS B 318 " - pdb=" SG CYS B 339 " distance=2.04 Simple disulfide: pdb=" SG CYS B 626 " - pdb=" SG CYS B 676 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 C 2 " - " BMA C 3 " NAG-ASN " NAG A 800 " - " ASN A 330 " " NAG C 1 " - " ASN B 637 " Time building additional restraints: 0.96 Conformation dependent library (CDL) restraints added in 322.7 milliseconds 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2188 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 11 sheets defined 37.2% alpha, 12.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 94 through 98 removed outlier: 4.026A pdb=" N LYS A 97 " --> pdb=" O LYS A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 140 Processing helix chain 'A' and resid 173 through 180 Processing helix chain 'A' and resid 184 through 188 Processing helix chain 'A' and resid 279 through 283 Processing helix chain 'A' and resid 312 through 320 Processing helix chain 'A' and resid 323 through 330 Processing helix chain 'A' and resid 345 through 353 Processing helix chain 'A' and resid 382 through 387 removed outlier: 3.765A pdb=" N LEU A 386 " --> pdb=" O GLU A 383 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N LEU A 387 " --> pdb=" O ARG A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 396 Processing helix chain 'A' and resid 397 through 416 Processing helix chain 'A' and resid 418 through 433 Processing helix chain 'A' and resid 441 through 447 removed outlier: 3.885A pdb=" N TRP A 445 " --> pdb=" O ASN A 441 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASN A 446 " --> pdb=" O SER A 442 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS A 447 " --> pdb=" O LEU A 443 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 441 through 447' Processing helix chain 'A' and resid 461 through 465 Processing helix chain 'A' and resid 498 through 506 Processing helix chain 'A' and resid 546 through 551 removed outlier: 3.969A pdb=" N ARG A 549 " --> pdb=" O MET A 546 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU A 551 " --> pdb=" O SER A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 585 Processing helix chain 'A' and resid 628 through 637 removed outlier: 3.606A pdb=" N TYR A 632 " --> pdb=" O LYS A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 650 removed outlier: 3.550A pdb=" N LYS A 643 " --> pdb=" O PRO A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 666 Processing helix chain 'A' and resid 699 through 713 Processing helix chain 'B' and resid 127 through 140 Processing helix chain 'B' and resid 146 through 150 removed outlier: 3.704A pdb=" N ALA B 150 " --> pdb=" O ILE B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 165 removed outlier: 3.548A pdb=" N THR B 164 " --> pdb=" O ASN B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 177 Processing helix chain 'B' and resid 235 through 240 Processing helix chain 'B' and resid 263 through 276 removed outlier: 3.994A pdb=" N LYS B 275 " --> pdb=" O ALA B 271 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N HIS B 276 " --> pdb=" O LEU B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 314 removed outlier: 4.206A pdb=" N GLN B 313 " --> pdb=" O PRO B 309 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU B 314 " --> pdb=" O GLN B 310 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 309 through 314' Processing helix chain 'B' and resid 329 through 337 removed outlier: 3.971A pdb=" N ASP B 333 " --> pdb=" O ALA B 329 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA B 337 " --> pdb=" O ASP B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 361 Processing helix chain 'B' and resid 369 through 371 No H-bonds generated for 'chain 'B' and resid 369 through 371' Processing helix chain 'B' and resid 372 through 380 removed outlier: 3.686A pdb=" N ILE B 380 " --> pdb=" O ILE B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 400 Processing helix chain 'B' and resid 402 through 419 Processing helix chain 'B' and resid 425 through 431 Processing helix chain 'B' and resid 432 through 439 removed outlier: 3.826A pdb=" N GLY B 438 " --> pdb=" O ALA B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 477 Processing helix chain 'B' and resid 518 through 524 removed outlier: 3.581A pdb=" N ASN B 521 " --> pdb=" O LYS B 518 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N PHE B 524 " --> pdb=" O ASN B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 545 through 559 removed outlier: 3.589A pdb=" N GLU B 558 " --> pdb=" O GLU B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 609 removed outlier: 3.721A pdb=" N TYR B 606 " --> pdb=" O LYS B 602 " (cutoff:3.500A) Processing helix chain 'B' and resid 615 through 623 Processing helix chain 'B' and resid 626 through 640 removed outlier: 3.853A pdb=" N ALA B 630 " --> pdb=" O CYS B 626 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N MET B 631 " --> pdb=" O GLU B 627 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N ASN B 632 " --> pdb=" O ASP B 628 " (cutoff:3.500A) Processing helix chain 'B' and resid 672 through 685 removed outlier: 3.705A pdb=" N CYS B 676 " --> pdb=" O GLU B 672 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 116 through 118 removed outlier: 6.341A pdb=" N TYR A 117 " --> pdb=" O VAL A 155 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N PHE A 154 " --> pdb=" O LEU A 191 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N PHE A 193 " --> pdb=" O PHE A 154 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N HIS A 190 " --> pdb=" O MET A 215 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N ALA A 217 " --> pdb=" O HIS A 190 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ILE A 192 " --> pdb=" O ALA A 217 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N ALA A 219 " --> pdb=" O ILE A 192 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N ASN A 194 " --> pdb=" O ALA A 219 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N LEU A 216 " --> pdb=" O VAL A 232 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N ILE A 234 " --> pdb=" O LEU A 216 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N LYS A 218 " --> pdb=" O ILE A 234 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 292 through 295 removed outlier: 4.039A pdb=" N LEU A 335 " --> pdb=" O VAL A 265 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N LYS A 267 " --> pdb=" O LEU A 335 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU A 360 " --> pdb=" O VAL A 336 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 510 through 514 removed outlier: 6.696A pdb=" N PHE A 480 " --> pdb=" O GLN A 512 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N ILE A 514 " --> pdb=" O PHE A 480 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N ALA A 482 " --> pdb=" O ILE A 514 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA A 624 " --> pdb=" O SER A 563 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 605 through 609 Processing sheet with id=AA5, first strand: chain 'A' and resid 722 through 726 removed outlier: 6.991A pdb=" N VAL B 643 " --> pdb=" O HIS B 694 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ALA B 696 " --> pdb=" O VAL B 643 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N LYS B 645 " --> pdb=" O ALA B 696 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N LEU B 563 " --> pdb=" O ILE B 644 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N VAL B 646 " --> pdb=" O LEU B 563 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N GLY B 565 " --> pdb=" O VAL B 646 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N THR B 457 " --> pdb=" O LEU B 535 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N ILE B 537 " --> pdb=" O THR B 457 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ILE B 459 " --> pdb=" O ILE B 537 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N PHE B 456 " --> pdb=" O LYS B 484 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N LEU B 486 " --> pdb=" O PHE B 456 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N ALA B 458 " --> pdb=" O LEU B 486 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N VAL B 488 " --> pdb=" O ALA B 458 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N VAL B 460 " --> pdb=" O VAL B 488 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL B 512 " --> pdb=" O VAL B 487 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N TRP B 489 " --> pdb=" O VAL B 512 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 106 through 108 Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 190 Processing sheet with id=AA8, first strand: chain 'B' and resid 217 through 218 removed outlier: 4.680A pdb=" N PHE B 217 " --> pdb=" O ILE B 349 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 281 through 283 removed outlier: 6.153A pdb=" N PHE B 253 " --> pdb=" O PHE B 317 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N VAL B 319 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N LEU B 255 " --> pdb=" O VAL B 319 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N THR B 316 " --> pdb=" O VAL B 340 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N VAL B 342 " --> pdb=" O THR B 316 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N CYS B 318 " --> pdb=" O VAL B 342 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 298 through 300 Processing sheet with id=AB2, first strand: chain 'B' and resid 579 through 583 removed outlier: 3.589A pdb=" N LEU B 572 " --> pdb=" O LYS B 581 " (cutoff:3.500A) 294 hydrogen bonds defined for protein. 813 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: 1.81 Time building geometry restraints manager: 1.22 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: 2958 1.34 - 1.46: 2340 1.46 - 1.58: 4214 1.58 - 1.70: 2 1.70 - 1.82: 71 Bond restraints: 9585 Sorted by residual: bond pdb=" O1A UDP A 801 " pdb=" PA UDP A 801 " ideal model delta sigma weight residual 1.482 1.526 -0.044 1.00e-02 1.00e+04 1.96e+01 bond pdb=" O2A UDP A 801 " pdb=" PA UDP A 801 " ideal model delta sigma weight residual 1.527 1.482 0.045 1.80e-02 3.09e+03 6.21e+00 bond pdb=" C1 NAG A 800 " pdb=" O5 NAG A 800 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.56e+00 bond pdb=" C1 BMA C 3 " pdb=" C2 BMA C 3 " ideal model delta sigma weight residual 1.519 1.548 -0.029 2.00e-02 2.50e+03 2.10e+00 bond pdb=" C1 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.79e+00 ... (remaining 9580 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.89: 12930 2.89 - 5.77: 87 5.77 - 8.66: 9 8.66 - 11.54: 2 11.54 - 14.43: 1 Bond angle restraints: 13029 Sorted by residual: angle pdb=" C GLY B 260 " pdb=" N LEU B 261 " pdb=" CA LEU B 261 " ideal model delta sigma weight residual 121.54 132.03 -10.49 1.91e+00 2.74e-01 3.02e+01 angle pdb=" O5' UDP A 801 " pdb=" PA UDP A 801 " pdb=" O1A UDP A 801 " ideal model delta sigma weight residual 106.70 111.08 -4.38 1.00e+00 1.00e+00 1.92e+01 angle pdb=" O2A UDP A 801 " pdb=" PA UDP A 801 " pdb=" O3A UDP A 801 " ideal model delta sigma weight residual 105.97 110.23 -4.26 1.00e+00 1.00e+00 1.81e+01 angle pdb=" N LEU B 261 " pdb=" CA LEU B 261 " pdb=" CB LEU B 261 " ideal model delta sigma weight residual 110.49 117.47 -6.98 1.69e+00 3.50e-01 1.70e+01 angle pdb=" CA LEU B 261 " pdb=" CB LEU B 261 " pdb=" CG LEU B 261 " ideal model delta sigma weight residual 116.30 130.73 -14.43 3.50e+00 8.16e-02 1.70e+01 ... (remaining 13024 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.74: 5302 17.74 - 35.48: 302 35.48 - 53.22: 64 53.22 - 70.96: 9 70.96 - 88.70: 6 Dihedral angle restraints: 5683 sinusoidal: 2296 harmonic: 3387 Sorted by residual: dihedral pdb=" CD ARG A 723 " pdb=" NE ARG A 723 " pdb=" CZ ARG A 723 " pdb=" NH1 ARG A 723 " ideal model delta sinusoidal sigma weight residual 0.00 71.37 -71.37 1 1.00e+01 1.00e-02 6.53e+01 dihedral pdb=" CA ALA B 202 " pdb=" C ALA B 202 " pdb=" N LEU B 203 " pdb=" CA LEU B 203 " ideal model delta harmonic sigma weight residual 180.00 159.10 20.90 0 5.00e+00 4.00e-02 1.75e+01 dihedral pdb=" CA TRP A 445 " pdb=" C TRP A 445 " pdb=" N ASN A 446 " pdb=" CA ASN A 446 " ideal model delta harmonic sigma weight residual 180.00 -163.73 -16.27 0 5.00e+00 4.00e-02 1.06e+01 ... (remaining 5680 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1178 0.054 - 0.108: 217 0.108 - 0.161: 34 0.161 - 0.215: 3 0.215 - 0.269: 1 Chirality restraints: 1433 Sorted by residual: chirality pdb=" C5 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" C6 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CA PRO B 263 " pdb=" N PRO B 263 " pdb=" C PRO B 263 " pdb=" CB PRO B 263 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 7.67e-01 chirality pdb=" CB ILE B 344 " pdb=" CA ILE B 344 " pdb=" CG1 ILE B 344 " pdb=" CG2 ILE B 344 " both_signs ideal model delta sigma weight residual False 2.64 2.81 -0.17 2.00e-01 2.50e+01 7.17e-01 ... (remaining 1430 not shown) Planarity restraints: 1652 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 723 " 0.882 9.50e-02 1.11e+02 3.97e-01 1.07e+02 pdb=" NE ARG A 723 " -0.075 2.00e-02 2.50e+03 pdb=" CZ ARG A 723 " 0.050 2.00e-02 2.50e+03 pdb=" NH1 ARG A 723 " -0.016 2.00e-02 2.50e+03 pdb=" NH2 ARG A 723 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 562 " -0.225 9.50e-02 1.11e+02 1.02e-01 8.22e+00 pdb=" NE ARG B 562 " 0.022 2.00e-02 2.50e+03 pdb=" CZ ARG B 562 " -0.022 2.00e-02 2.50e+03 pdb=" NH1 ARG B 562 " 0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG B 562 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO B 196 " 0.032 5.00e-02 4.00e+02 4.89e-02 3.82e+00 pdb=" N PRO B 197 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO B 197 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 197 " 0.025 5.00e-02 4.00e+02 ... (remaining 1649 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 865 2.74 - 3.28: 9521 3.28 - 3.82: 15843 3.82 - 4.36: 19801 4.36 - 4.90: 32647 Nonbonded interactions: 78677 Sorted by model distance: nonbonded pdb=" O ILE B 376 " pdb=" OG SER B 379 " model vdw 2.203 3.040 nonbonded pdb=" OH TYR A 271 " pdb=" O3B UDP A 801 " model vdw 2.232 3.040 nonbonded pdb=" OG1 THR A 223 " pdb=" NE2 HIS B 88 " model vdw 2.238 3.120 nonbonded pdb=" O PRO B 560 " pdb=" ND1 HIS B 601 " model vdw 2.253 3.120 nonbonded pdb=" OH TYR A 626 " pdb=" NE2 HIS A 631 " model vdw 2.261 3.120 ... (remaining 78672 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 2.270 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: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.340 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 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:9.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 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 : 0.003 0.045 9599 Z= 0.127 Angle : 0.613 14.426 13061 Z= 0.310 Chirality : 0.044 0.269 1433 Planarity : 0.011 0.397 1650 Dihedral : 11.887 88.704 3465 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.82 % Favored : 92.01 % Rotamer: Outliers : 1.09 % Allowed : 7.42 % Favored : 91.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.25), residues: 1126 helix: 0.29 (0.29), residues: 354 sheet: -2.14 (0.49), residues: 105 loop : -1.33 (0.24), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.060 0.001 ARG A 723 TYR 0.009 0.001 TYR A 608 PHE 0.009 0.001 PHE B 400 TRP 0.014 0.001 TRP A 711 HIS 0.010 0.001 HIS B 694 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.13 ( 9585) covalent geometry : angle 0.61072 / 0.31 (13029) SS BOND : bond 0.00288 / 0.16 ( 10) SS BOND : angle 0.79467 / 0.56 ( 20) hydrogen bonds : bond 0.14889 / 8.94 ( 294) hydrogen bonds : angle 7.04437 / 4.98 ( 813) link_BETA1-4 : bond 0.00450 / 0.23 ( 2) link_BETA1-4 : angle 1.34593 / 0.93 ( 6) link_NAG-ASN : bond 0.00196 / 0.10 ( 2) link_NAG-ASN : angle 2.14764 / 1.24 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 258 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 TYR cc_start: 0.7245 (m-80) cc_final: 0.7040 (m-80) REVERT: A 420 GLU cc_start: 0.7671 (tm-30) cc_final: 0.7468 (tm-30) REVERT: A 478 SER cc_start: 0.7735 (p) cc_final: 0.7275 (t) REVERT: A 670 ILE cc_start: 0.8002 (mm) cc_final: 0.7766 (mm) REVERT: B 388 MET cc_start: 0.7140 (mtp) cc_final: 0.6859 (mtp) REVERT: B 484 LYS cc_start: 0.4508 (OUTLIER) cc_final: 0.4284 (ttmm) REVERT: B 695 ARG cc_start: 0.7137 (ptt-90) cc_final: 0.6737 (ptt-90) outliers start: 11 outliers final: 1 residues processed: 264 average time/residue: 0.4220 time to fit residues: 119.9553 Evaluate side-chains 195 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 193 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 217 PHE Chi-restraints excluded: chain B residue 484 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 108 optimal weight: 4.9990 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 0.7980 chunk 113 optimal weight: 3.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.2980 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 0.0070 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 254 ASN A 471 ASN B 162 GLN B 200 ASN B 262 HIS B 389 GLN B 412 GLN B 454 GLN B 550 GLN ** B 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 694 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4925 r_free = 0.4925 target = 0.238070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4601 r_free = 0.4601 target = 0.206611 restraints weight = 11324.289| |-----------------------------------------------------------------------------| r_work (start): 0.4604 rms_B_bonded: 2.68 r_work: 0.4473 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.4473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9599 Z= 0.138 Angle : 0.671 12.435 13061 Z= 0.334 Chirality : 0.045 0.228 1433 Planarity : 0.005 0.061 1650 Dihedral : 4.779 47.434 1265 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.10 % Favored : 92.81 % Rotamer: Outliers : 3.36 % Allowed : 14.64 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.25), residues: 1126 helix: 0.32 (0.28), residues: 365 sheet: -1.96 (0.50), residues: 101 loop : -1.14 (0.25), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 595 TYR 0.012 0.001 TYR A 592 PHE 0.015 0.001 PHE B 680 TRP 0.017 0.001 TRP A 711 HIS 0.006 0.001 HIS B 694 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 ( 9585) covalent geometry : angle 0.66734 / 0.33 (13029) SS BOND : bond 0.00426 / 0.27 ( 10) SS BOND : angle 1.34528 / 1.04 ( 20) hydrogen bonds : bond 0.04311 / 2.58 ( 294) hydrogen bonds : angle 5.54668 / 3.96 ( 813) link_BETA1-4 : bond 0.00439 / 0.21 ( 2) link_BETA1-4 : angle 1.70284 / 1.29 ( 6) link_NAG-ASN : bond 0.00238 / 0.12 ( 2) link_NAG-ASN : angle 2.14442 / 1.28 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 202 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 TYR cc_start: 0.7645 (m-80) cc_final: 0.7274 (m-80) REVERT: A 420 GLU cc_start: 0.7665 (tm-30) cc_final: 0.7313 (tm-30) REVERT: A 478 SER cc_start: 0.7845 (p) cc_final: 0.7323 (t) REVERT: B 388 MET cc_start: 0.7102 (mtp) cc_final: 0.6759 (mtp) REVERT: B 441 SER cc_start: 0.8097 (p) cc_final: 0.7795 (t) REVERT: B 624 MET cc_start: 0.7423 (mmm) cc_final: 0.7169 (mmt) REVERT: B 695 ARG cc_start: 0.7529 (ptt-90) cc_final: 0.7312 (ptt-90) outliers start: 34 outliers final: 14 residues processed: 225 average time/residue: 0.3654 time to fit residues: 89.9291 Evaluate side-chains 186 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 172 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 CYS Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 721 GLN Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 217 PHE Chi-restraints excluded: chain B residue 276 HIS Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 643 VAL Chi-restraints excluded: chain B residue 700 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 25 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 18 optimal weight: 7.9990 chunk 29 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 78 optimal weight: 2.9990 chunk 52 optimal weight: 0.1980 chunk 38 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 254 ASN A 397 HIS A 431 GLN ** B 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 200 ASN B 313 GLN ** B 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4873 r_free = 0.4873 target = 0.232279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.199544 restraints weight = 11391.153| |-----------------------------------------------------------------------------| r_work (start): 0.4530 rms_B_bonded: 2.72 r_work: 0.4397 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.4397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 9599 Z= 0.203 Angle : 0.693 10.438 13061 Z= 0.349 Chirality : 0.047 0.260 1433 Planarity : 0.005 0.051 1650 Dihedral : 4.788 44.075 1261 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.28 % Favored : 92.63 % Rotamer: Outliers : 3.86 % Allowed : 16.91 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.25), residues: 1126 helix: 0.09 (0.27), residues: 369 sheet: -1.63 (0.55), residues: 87 loop : -1.14 (0.24), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 394 TYR 0.023 0.002 TYR B 107 PHE 0.020 0.002 PHE B 604 TRP 0.021 0.002 TRP A 711 HIS 0.003 0.001 HIS A 597 Details of bonding type rmsd/Z covalent geometry : bond 0.00480 / 0.20 ( 9585) covalent geometry : angle 0.68919 / 0.35 (13029) SS BOND : bond 0.00521 / 0.30 ( 10) SS BOND : angle 1.39237 / 1.07 ( 20) hydrogen bonds : bond 0.04710 / 2.81 ( 294) hydrogen bonds : angle 5.48643 / 3.91 ( 813) link_BETA1-4 : bond 0.00251 / 0.12 ( 2) link_BETA1-4 : angle 1.95654 / 1.70 ( 6) link_NAG-ASN : bond 0.00088 / 0.04 ( 2) link_NAG-ASN : angle 2.24499 / 1.43 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 183 time to evaluate : 0.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 TYR cc_start: 0.7726 (m-80) cc_final: 0.7392 (m-80) REVERT: A 420 GLU cc_start: 0.7766 (tm-30) cc_final: 0.7430 (tm-30) REVERT: A 478 SER cc_start: 0.7879 (p) cc_final: 0.7369 (t) REVERT: A 673 THR cc_start: 0.8665 (m) cc_final: 0.8407 (t) REVERT: B 314 GLU cc_start: 0.7892 (mp0) cc_final: 0.7312 (mp0) REVERT: B 388 MET cc_start: 0.7110 (mtp) cc_final: 0.6789 (mtp) REVERT: B 441 SER cc_start: 0.8152 (p) cc_final: 0.7839 (t) REVERT: B 452 GLN cc_start: 0.7204 (mt0) cc_final: 0.6915 (mp10) REVERT: B 485 LEU cc_start: 0.5713 (OUTLIER) cc_final: 0.5510 (tp) REVERT: B 624 MET cc_start: 0.7564 (mmm) cc_final: 0.7288 (mmm) outliers start: 39 outliers final: 21 residues processed: 212 average time/residue: 0.3891 time to fit residues: 89.8655 Evaluate side-chains 193 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 171 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 CYS Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 464 ASP Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 721 GLN Chi-restraints excluded: chain B residue 85 CYS Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 217 PHE Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 276 HIS Chi-restraints excluded: chain B residue 339 CYS Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 587 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 111 optimal weight: 4.9990 chunk 98 optimal weight: 0.0570 chunk 104 optimal weight: 3.9990 chunk 35 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 chunk 75 optimal weight: 5.9990 chunk 72 optimal weight: 0.7980 chunk 89 optimal weight: 0.0050 chunk 20 optimal weight: 7.9990 chunk 13 optimal weight: 3.9990 overall best weight: 0.7114 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 254 ASN A 287 HIS A 431 GLN ** B 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 389 GLN ** B 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4893 r_free = 0.4893 target = 0.234290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4557 r_free = 0.4557 target = 0.202109 restraints weight = 11430.648| |-----------------------------------------------------------------------------| r_work (start): 0.4560 rms_B_bonded: 2.71 r_work: 0.4428 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.4428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9599 Z= 0.147 Angle : 0.663 10.478 13061 Z= 0.329 Chirality : 0.046 0.321 1433 Planarity : 0.004 0.044 1650 Dihedral : 4.673 45.261 1261 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.75 % Favored : 93.07 % Rotamer: Outliers : 3.36 % Allowed : 18.99 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.25), residues: 1126 helix: 0.17 (0.27), residues: 369 sheet: -1.85 (0.50), residues: 109 loop : -1.03 (0.25), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 394 TYR 0.015 0.001 TYR A 467 PHE 0.018 0.002 PHE B 98 TRP 0.020 0.002 TRP B 394 HIS 0.004 0.001 HIS A 285 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 ( 9585) covalent geometry : angle 0.65926 / 0.33 (13029) SS BOND : bond 0.00350 / 0.21 ( 10) SS BOND : angle 1.16460 / 0.85 ( 20) hydrogen bonds : bond 0.04069 / 2.43 ( 294) hydrogen bonds : angle 5.27684 / 3.79 ( 813) link_BETA1-4 : bond 0.00343 / 0.17 ( 2) link_BETA1-4 : angle 1.70519 / 1.41 ( 6) link_NAG-ASN : bond 0.00128 / 0.06 ( 2) link_NAG-ASN : angle 2.12935 / 1.31 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 183 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 TYR cc_start: 0.7683 (m-80) cc_final: 0.7359 (m-80) REVERT: A 420 GLU cc_start: 0.7689 (tm-30) cc_final: 0.7359 (tm-30) REVERT: A 478 SER cc_start: 0.7864 (p) cc_final: 0.7353 (t) REVERT: A 722 MET cc_start: 0.7782 (tmm) cc_final: 0.7530 (tmm) REVERT: B 310 GLN cc_start: 0.7863 (tm-30) cc_final: 0.7477 (tm-30) REVERT: B 388 MET cc_start: 0.7115 (mtp) cc_final: 0.6755 (mtp) REVERT: B 441 SER cc_start: 0.8146 (p) cc_final: 0.7845 (t) REVERT: B 452 GLN cc_start: 0.7061 (mt0) cc_final: 0.6809 (mp-120) REVERT: B 592 MET cc_start: 0.7718 (mtp) cc_final: 0.7413 (mtm) outliers start: 34 outliers final: 18 residues processed: 209 average time/residue: 0.3794 time to fit residues: 86.5112 Evaluate side-chains 187 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 169 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 CYS Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 657 MET Chi-restraints excluded: chain B residue 85 CYS Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 217 PHE Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 276 HIS Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 339 CYS Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 587 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 35 optimal weight: 0.0770 chunk 83 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 73 optimal weight: 10.0000 chunk 81 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 overall best weight: 0.8942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 254 ASN A 431 GLN ** B 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4883 r_free = 0.4883 target = 0.233178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4547 r_free = 0.4547 target = 0.200911 restraints weight = 11396.957| |-----------------------------------------------------------------------------| r_work (start): 0.4551 rms_B_bonded: 2.70 r_work: 0.4418 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.4418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9599 Z= 0.164 Angle : 0.671 9.865 13061 Z= 0.333 Chirality : 0.046 0.290 1433 Planarity : 0.004 0.044 1650 Dihedral : 4.722 45.436 1261 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.84 % Favored : 92.90 % Rotamer: Outliers : 3.66 % Allowed : 18.89 % Favored : 77.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.25), residues: 1126 helix: 0.11 (0.27), residues: 373 sheet: -1.85 (0.50), residues: 114 loop : -1.07 (0.25), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 394 TYR 0.027 0.002 TYR B 107 PHE 0.021 0.002 PHE A 577 TRP 0.024 0.002 TRP A 711 HIS 0.003 0.001 HIS A 285 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.16 ( 9585) covalent geometry : angle 0.66799 / 0.33 (13029) SS BOND : bond 0.00357 / 0.21 ( 10) SS BOND : angle 1.16866 / 0.86 ( 20) hydrogen bonds : bond 0.04179 / 2.50 ( 294) hydrogen bonds : angle 5.23226 / 3.75 ( 813) link_BETA1-4 : bond 0.00281 / 0.14 ( 2) link_BETA1-4 : angle 1.76087 / 1.49 ( 6) link_NAG-ASN : bond 0.00098 / 0.05 ( 2) link_NAG-ASN : angle 2.16929 / 1.36 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 182 time to evaluate : 0.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 TYR cc_start: 0.7695 (m-80) cc_final: 0.7352 (m-80) REVERT: A 420 GLU cc_start: 0.7732 (tm-30) cc_final: 0.7404 (tm-30) REVERT: A 478 SER cc_start: 0.7879 (p) cc_final: 0.7371 (t) REVERT: A 714 TYR cc_start: 0.7072 (p90) cc_final: 0.6865 (p90) REVERT: B 80 ARG cc_start: 0.7203 (ttm110) cc_final: 0.6846 (tpp-160) REVERT: B 192 LEU cc_start: 0.8135 (mt) cc_final: 0.7896 (mt) REVERT: B 310 GLN cc_start: 0.7957 (tm-30) cc_final: 0.7534 (tm-30) REVERT: B 388 MET cc_start: 0.7142 (mtp) cc_final: 0.6816 (mtp) REVERT: B 452 GLN cc_start: 0.7126 (mt0) cc_final: 0.6866 (mp-120) REVERT: B 592 MET cc_start: 0.7730 (mtp) cc_final: 0.7522 (mtm) REVERT: B 624 MET cc_start: 0.7545 (mmm) cc_final: 0.7244 (mmm) outliers start: 37 outliers final: 26 residues processed: 207 average time/residue: 0.3855 time to fit residues: 86.6774 Evaluate side-chains 198 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 172 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 CYS Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 657 MET Chi-restraints excluded: chain A residue 721 GLN Chi-restraints excluded: chain B residue 85 CYS Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 217 PHE Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 276 HIS Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 339 CYS Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 587 THR Chi-restraints excluded: chain B residue 611 LYS Chi-restraints excluded: chain B residue 620 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 30 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 32 optimal weight: 0.9990 chunk 93 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 102 optimal weight: 0.9980 chunk 56 optimal weight: 5.9990 chunk 82 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 254 ASN A 431 GLN ** B 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 389 GLN ** B 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4865 r_free = 0.4865 target = 0.231598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4528 r_free = 0.4528 target = 0.198858 restraints weight = 11572.917| |-----------------------------------------------------------------------------| r_work (start): 0.4526 rms_B_bonded: 2.74 r_work: 0.4399 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.4399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 9599 Z= 0.183 Angle : 0.694 11.886 13061 Z= 0.345 Chirality : 0.047 0.359 1433 Planarity : 0.004 0.041 1650 Dihedral : 4.810 45.580 1261 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.66 % Favored : 93.07 % Rotamer: Outliers : 3.96 % Allowed : 19.19 % Favored : 76.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.25), residues: 1126 helix: 0.09 (0.27), residues: 372 sheet: -1.65 (0.54), residues: 102 loop : -1.08 (0.25), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 394 TYR 0.024 0.002 TYR A 467 PHE 0.017 0.002 PHE B 98 TRP 0.024 0.002 TRP A 200 HIS 0.003 0.001 HIS A 285 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.18 ( 9585) covalent geometry : angle 0.69007 / 0.34 (13029) SS BOND : bond 0.00401 / 0.24 ( 10) SS BOND : angle 1.17099 / 0.85 ( 20) hydrogen bonds : bond 0.04343 / 2.59 ( 294) hydrogen bonds : angle 5.23475 / 3.76 ( 813) link_BETA1-4 : bond 0.00271 / 0.13 ( 2) link_BETA1-4 : angle 1.86145 / 1.61 ( 6) link_NAG-ASN : bond 0.00117 / 0.06 ( 2) link_NAG-ASN : angle 2.20554 / 1.39 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 175 time to evaluate : 0.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 TYR cc_start: 0.7676 (m-80) cc_final: 0.7374 (m-80) REVERT: A 420 GLU cc_start: 0.7788 (tm-30) cc_final: 0.7517 (tm-30) REVERT: A 478 SER cc_start: 0.7910 (p) cc_final: 0.7400 (t) REVERT: A 673 THR cc_start: 0.8677 (m) cc_final: 0.8238 (t) REVERT: A 674 GLN cc_start: 0.7631 (pm20) cc_final: 0.7273 (pt0) REVERT: B 80 ARG cc_start: 0.7250 (ttm110) cc_final: 0.6897 (tpp-160) REVERT: B 192 LEU cc_start: 0.8182 (mt) cc_final: 0.7979 (mt) REVERT: B 310 GLN cc_start: 0.8008 (tm-30) cc_final: 0.7616 (tm-30) REVERT: B 388 MET cc_start: 0.7092 (mtp) cc_final: 0.6751 (mtp) REVERT: B 592 MET cc_start: 0.7747 (mtp) cc_final: 0.7543 (mtm) REVERT: B 624 MET cc_start: 0.7624 (mmm) cc_final: 0.7358 (mmm) outliers start: 40 outliers final: 24 residues processed: 202 average time/residue: 0.4028 time to fit residues: 88.2289 Evaluate side-chains 191 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 167 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 CYS Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 721 GLN Chi-restraints excluded: chain B residue 85 CYS Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 217 PHE Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 276 HIS Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 339 CYS Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 587 THR Chi-restraints excluded: chain B residue 620 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 0 optimal weight: 6.9990 chunk 105 optimal weight: 3.9990 chunk 73 optimal weight: 0.8980 chunk 58 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 87 optimal weight: 0.8980 chunk 88 optimal weight: 0.8980 chunk 84 optimal weight: 0.5980 chunk 26 optimal weight: 0.6980 chunk 42 optimal weight: 5.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 254 ASN A 431 GLN B 161 ASN B 176 GLN ** B 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4878 r_free = 0.4878 target = 0.233058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4543 r_free = 0.4543 target = 0.200465 restraints weight = 11604.651| |-----------------------------------------------------------------------------| r_work (start): 0.4545 rms_B_bonded: 2.74 r_work: 0.4420 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.4420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.2646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9599 Z= 0.153 Angle : 0.680 10.148 13061 Z= 0.336 Chirality : 0.046 0.337 1433 Planarity : 0.004 0.041 1650 Dihedral : 4.818 45.908 1261 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.48 % Favored : 93.25 % Rotamer: Outliers : 3.36 % Allowed : 20.18 % Favored : 76.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.25), residues: 1126 helix: 0.15 (0.27), residues: 373 sheet: -1.64 (0.54), residues: 102 loop : -1.04 (0.25), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 394 TYR 0.023 0.002 TYR A 467 PHE 0.012 0.001 PHE B 633 TRP 0.027 0.002 TRP A 200 HIS 0.004 0.001 HIS A 285 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.15 ( 9585) covalent geometry : angle 0.67630 / 0.34 (13029) SS BOND : bond 0.00354 / 0.21 ( 10) SS BOND : angle 1.29910 / 0.93 ( 20) hydrogen bonds : bond 0.04106 / 2.46 ( 294) hydrogen bonds : angle 5.15379 / 3.70 ( 813) link_BETA1-4 : bond 0.00275 / 0.13 ( 2) link_BETA1-4 : angle 1.70524 / 1.44 ( 6) link_NAG-ASN : bond 0.00107 / 0.05 ( 2) link_NAG-ASN : angle 2.14527 / 1.33 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 185 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 TYR cc_start: 0.7668 (m-80) cc_final: 0.7340 (m-80) REVERT: A 420 GLU cc_start: 0.7752 (tm-30) cc_final: 0.7436 (tm-30) REVERT: A 478 SER cc_start: 0.7894 (p) cc_final: 0.7376 (t) REVERT: B 80 ARG cc_start: 0.7234 (ttm110) cc_final: 0.6880 (tpp-160) REVERT: B 310 GLN cc_start: 0.8055 (tm-30) cc_final: 0.7744 (tm-30) REVERT: B 388 MET cc_start: 0.7105 (mtp) cc_final: 0.6760 (mtp) REVERT: B 592 MET cc_start: 0.7682 (mtp) cc_final: 0.7462 (mtm) REVERT: B 624 MET cc_start: 0.7615 (mmm) cc_final: 0.7365 (mmm) outliers start: 34 outliers final: 24 residues processed: 207 average time/residue: 0.4157 time to fit residues: 93.5954 Evaluate side-chains 188 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 164 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 CYS Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain B residue 85 CYS Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 217 PHE Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 276 HIS Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 339 CYS Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 587 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 700 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 86 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 82 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 13 optimal weight: 0.4980 chunk 56 optimal weight: 0.0870 chunk 19 optimal weight: 3.9990 overall best weight: 0.6762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 254 ASN A 431 GLN A 721 GLN B 176 GLN ** B 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 389 GLN ** B 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4891 r_free = 0.4891 target = 0.234054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4556 r_free = 0.4556 target = 0.201647 restraints weight = 11392.546| |-----------------------------------------------------------------------------| r_work (start): 0.4562 rms_B_bonded: 2.71 r_work: 0.4428 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.4428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.2736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9599 Z= 0.144 Angle : 0.677 9.438 13061 Z= 0.336 Chirality : 0.046 0.327 1433 Planarity : 0.004 0.041 1650 Dihedral : 4.759 45.884 1261 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.22 % Favored : 93.52 % Rotamer: Outliers : 3.36 % Allowed : 20.87 % Favored : 75.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.25), residues: 1126 helix: 0.22 (0.27), residues: 373 sheet: -1.81 (0.50), residues: 114 loop : -0.94 (0.25), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 394 TYR 0.027 0.002 TYR B 107 PHE 0.013 0.001 PHE B 98 TRP 0.029 0.002 TRP A 200 HIS 0.004 0.001 HIS A 285 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.14 ( 9585) covalent geometry : angle 0.67433 / 0.34 (13029) SS BOND : bond 0.00330 / 0.20 ( 10) SS BOND : angle 1.19578 / 0.87 ( 20) hydrogen bonds : bond 0.03978 / 2.38 ( 294) hydrogen bonds : angle 5.07487 / 3.64 ( 813) link_BETA1-4 : bond 0.00279 / 0.14 ( 2) link_BETA1-4 : angle 1.60189 / 1.32 ( 6) link_NAG-ASN : bond 0.00130 / 0.06 ( 2) link_NAG-ASN : angle 2.09630 / 1.30 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 175 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 TYR cc_start: 0.7647 (m-80) cc_final: 0.7327 (m-80) REVERT: A 420 GLU cc_start: 0.7703 (tm-30) cc_final: 0.7387 (tm-30) REVERT: A 478 SER cc_start: 0.7902 (p) cc_final: 0.7368 (t) REVERT: A 674 GLN cc_start: 0.7571 (pm20) cc_final: 0.7231 (pt0) REVERT: B 80 ARG cc_start: 0.7206 (ttm110) cc_final: 0.6849 (tpp-160) REVERT: B 276 HIS cc_start: 0.4703 (OUTLIER) cc_final: 0.4127 (p90) REVERT: B 310 GLN cc_start: 0.8098 (tm-30) cc_final: 0.7765 (tm-30) REVERT: B 388 MET cc_start: 0.7126 (mtp) cc_final: 0.6770 (mtp) REVERT: B 436 LYS cc_start: 0.8147 (ttmt) cc_final: 0.7893 (mtmm) REVERT: B 452 GLN cc_start: 0.7162 (mp10) cc_final: 0.6934 (mp-120) REVERT: B 592 MET cc_start: 0.7597 (mtp) cc_final: 0.7335 (mtm) REVERT: B 624 MET cc_start: 0.7587 (mmm) cc_final: 0.7348 (mmm) outliers start: 34 outliers final: 20 residues processed: 199 average time/residue: 0.4386 time to fit residues: 94.9383 Evaluate side-chains 187 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 166 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 CYS Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 217 PHE Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 276 HIS Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 587 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 700 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 74 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 chunk 62 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 27 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 107 optimal weight: 0.3980 chunk 19 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 254 ASN A 431 GLN B 176 GLN ** B 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4883 r_free = 0.4883 target = 0.233312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4550 r_free = 0.4550 target = 0.200681 restraints weight = 11540.992| |-----------------------------------------------------------------------------| r_work (start): 0.4549 rms_B_bonded: 2.73 r_work: 0.4421 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.4421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.2770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 9599 Z= 0.158 Angle : 0.694 9.343 13061 Z= 0.345 Chirality : 0.046 0.326 1433 Planarity : 0.004 0.041 1650 Dihedral : 4.791 46.004 1261 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.04 % Favored : 93.69 % Rotamer: Outliers : 3.26 % Allowed : 21.07 % Favored : 75.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (0.25), residues: 1126 helix: 0.21 (0.27), residues: 374 sheet: -1.73 (0.50), residues: 114 loop : -0.90 (0.25), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 394 TYR 0.034 0.002 TYR A 467 PHE 0.014 0.001 PHE B 633 TRP 0.032 0.002 TRP A 200 HIS 0.004 0.001 HIS B 571 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.16 ( 9585) covalent geometry : angle 0.69046 / 0.34 (13029) SS BOND : bond 0.00352 / 0.21 ( 10) SS BOND : angle 1.26304 / 0.91 ( 20) hydrogen bonds : bond 0.04066 / 2.43 ( 294) hydrogen bonds : angle 5.04947 / 3.63 ( 813) link_BETA1-4 : bond 0.00302 / 0.15 ( 2) link_BETA1-4 : angle 1.69152 / 1.43 ( 6) link_NAG-ASN : bond 0.00115 / 0.05 ( 2) link_NAG-ASN : angle 2.14563 / 1.34 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 171 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 GLN cc_start: 0.7254 (tp-100) cc_final: 0.6662 (tp-100) REVERT: A 262 TYR cc_start: 0.7615 (m-80) cc_final: 0.7349 (m-80) REVERT: A 420 GLU cc_start: 0.7768 (tm-30) cc_final: 0.7458 (tm-30) REVERT: A 478 SER cc_start: 0.7886 (p) cc_final: 0.7368 (t) REVERT: A 674 GLN cc_start: 0.7730 (pm20) cc_final: 0.7328 (pt0) REVERT: B 80 ARG cc_start: 0.7236 (ttm110) cc_final: 0.6876 (tpp-160) REVERT: B 276 HIS cc_start: 0.4627 (OUTLIER) cc_final: 0.4025 (p90) REVERT: B 310 GLN cc_start: 0.8158 (tm-30) cc_final: 0.7775 (tm-30) REVERT: B 313 GLN cc_start: 0.7711 (tt0) cc_final: 0.7315 (tm-30) REVERT: B 314 GLU cc_start: 0.7644 (mp0) cc_final: 0.7414 (mp0) REVERT: B 388 MET cc_start: 0.7065 (mtp) cc_final: 0.6744 (mtp) REVERT: B 592 MET cc_start: 0.7580 (mtp) cc_final: 0.7330 (mtm) REVERT: B 624 MET cc_start: 0.7612 (mmm) cc_final: 0.7378 (mmm) outliers start: 33 outliers final: 19 residues processed: 194 average time/residue: 0.3920 time to fit residues: 83.0123 Evaluate side-chains 187 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 167 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 CYS Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain B residue 217 PHE Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 276 HIS Chi-restraints excluded: chain B residue 297 ARG Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 587 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 700 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 5 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 100 optimal weight: 0.9990 chunk 86 optimal weight: 0.5980 chunk 54 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 41 optimal weight: 7.9990 chunk 88 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 254 ASN A 431 GLN B 176 GLN ** B 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4872 r_free = 0.4872 target = 0.232235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4538 r_free = 0.4538 target = 0.199593 restraints weight = 11557.513| |-----------------------------------------------------------------------------| r_work (start): 0.4535 rms_B_bonded: 2.72 r_work: 0.4406 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.4406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.2853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 9599 Z= 0.181 Angle : 0.715 9.436 13061 Z= 0.357 Chirality : 0.047 0.305 1433 Planarity : 0.005 0.041 1650 Dihedral : 4.915 46.310 1261 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.04 % Favored : 93.69 % Rotamer: Outliers : 2.57 % Allowed : 21.27 % Favored : 76.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.25), residues: 1126 helix: 0.19 (0.27), residues: 372 sheet: -1.53 (0.55), residues: 102 loop : -0.95 (0.25), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 394 TYR 0.042 0.002 TYR A 467 PHE 0.016 0.002 PHE B 98 TRP 0.035 0.002 TRP A 200 HIS 0.004 0.001 HIS B 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.18 ( 9585) covalent geometry : angle 0.71090 / 0.36 (13029) SS BOND : bond 0.00377 / 0.23 ( 10) SS BOND : angle 1.36067 / 0.98 ( 20) hydrogen bonds : bond 0.04254 / 2.54 ( 294) hydrogen bonds : angle 5.10407 / 3.66 ( 813) link_BETA1-4 : bond 0.00304 / 0.15 ( 2) link_BETA1-4 : angle 1.81153 / 1.57 ( 6) link_NAG-ASN : bond 0.00130 / 0.06 ( 2) link_NAG-ASN : angle 2.19529 / 1.38 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 166 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 GLN cc_start: 0.7258 (tp-100) cc_final: 0.6719 (tp-100) REVERT: A 262 TYR cc_start: 0.7638 (m-80) cc_final: 0.7367 (m-80) REVERT: A 420 GLU cc_start: 0.7789 (tm-30) cc_final: 0.7517 (tm-30) REVERT: A 478 SER cc_start: 0.7899 (p) cc_final: 0.7384 (t) REVERT: B 80 ARG cc_start: 0.7264 (ttm110) cc_final: 0.6902 (tpp-160) REVERT: B 276 HIS cc_start: 0.4653 (OUTLIER) cc_final: 0.4069 (p90) REVERT: B 310 GLN cc_start: 0.8173 (tm-30) cc_final: 0.7766 (tm-30) REVERT: B 313 GLN cc_start: 0.7770 (tt0) cc_final: 0.7536 (tm-30) REVERT: B 314 GLU cc_start: 0.7627 (mp0) cc_final: 0.7426 (mp0) REVERT: B 388 MET cc_start: 0.7088 (mtp) cc_final: 0.6770 (mtp) REVERT: B 436 LYS cc_start: 0.8184 (ttmt) cc_final: 0.7951 (mtmm) REVERT: B 592 MET cc_start: 0.7590 (mtp) cc_final: 0.7327 (mtm) REVERT: B 624 MET cc_start: 0.7616 (mmm) cc_final: 0.7390 (mmt) outliers start: 26 outliers final: 20 residues processed: 182 average time/residue: 0.3644 time to fit residues: 72.5444 Evaluate side-chains 186 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 165 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 CYS Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 625 ILE Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 217 PHE Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 276 HIS Chi-restraints excluded: chain B residue 297 ARG Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 587 THR Chi-restraints excluded: chain B residue 620 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 33 optimal weight: 0.2980 chunk 14 optimal weight: 0.0040 chunk 102 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 chunk 32 optimal weight: 0.5980 chunk 4 optimal weight: 0.5980 chunk 66 optimal weight: 4.9990 chunk 59 optimal weight: 0.0000 chunk 56 optimal weight: 3.9990 overall best weight: 0.2996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 254 ASN A 431 GLN A 721 GLN B 176 GLN ** B 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4923 r_free = 0.4923 target = 0.237675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4596 r_free = 0.4596 target = 0.205692 restraints weight = 11348.176| |-----------------------------------------------------------------------------| r_work (start): 0.4604 rms_B_bonded: 2.68 r_work: 0.4476 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.4476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.2901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9599 Z= 0.128 Angle : 0.686 9.230 13061 Z= 0.340 Chirality : 0.046 0.300 1433 Planarity : 0.004 0.042 1650 Dihedral : 4.708 46.910 1261 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.86 % Favored : 93.87 % Rotamer: Outliers : 2.08 % Allowed : 22.35 % Favored : 75.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.25), residues: 1126 helix: 0.35 (0.27), residues: 375 sheet: -1.56 (0.51), residues: 113 loop : -0.82 (0.25), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 394 TYR 0.031 0.001 TYR A 467 PHE 0.019 0.001 PHE B 680 TRP 0.031 0.002 TRP A 200 HIS 0.007 0.001 HIS B 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 ( 9585) covalent geometry : angle 0.68357 / 0.34 (13029) SS BOND : bond 0.00287 / 0.17 ( 10) SS BOND : angle 1.08894 / 0.79 ( 20) hydrogen bonds : bond 0.03581 / 2.16 ( 294) hydrogen bonds : angle 4.89969 / 3.52 ( 813) link_BETA1-4 : bond 0.00233 / 0.11 ( 2) link_BETA1-4 : angle 1.41371 / 1.10 ( 6) link_NAG-ASN : bond 0.00199 / 0.10 ( 2) link_NAG-ASN : angle 1.96051 / 1.21 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2847.21 seconds wall clock time: 49 minutes 19.74 seconds (2959.74 seconds total)