Starting phenix.real_space_refine on Sun May 3 08:48:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x0f_37977/05_2026/8x0f_37977.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x0f_37977/05_2026/8x0f_37977.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8x0f_37977/05_2026/8x0f_37977.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x0f_37977/05_2026/8x0f_37977.map" model { file = "/net/cci-nas-00/data/ceres_data/8x0f_37977/05_2026/8x0f_37977.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x0f_37977/05_2026/8x0f_37977.cif" } resolution = 3.3 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= 0.001 sd= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 114 5.16 5 C 7760 2.51 5 N 1998 2.21 5 O 2201 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12073 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 762, 5995 Classifications: {'peptide': 762} Link IDs: {'PTRANS': 32, 'TRANS': 729} Chain breaks: 2 Chain: "B" Number of atoms: 5995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 762, 5995 Classifications: {'peptide': 762} Link IDs: {'PTRANS': 32, 'TRANS': 729} Chain breaks: 2 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 56 Unusual residues: {'NAG': 1, 'QUS': 1, 'XRQ': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {'NAG': 1, 'QUS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.48, per 1000 atoms: 0.21 Number of scatterers: 12073 At special positions: 0 Unit cell: (85.059, 106.142, 175.934, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 114 16.00 O 2201 8.00 N 1998 7.00 C 7760 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=20, symmetry=0 Simple disulfide: pdb=" SG CYS A 57 " - pdb=" SG CYS A 99 " distance=2.04 Simple disulfide: pdb=" SG CYS A 241 " - pdb=" SG CYS A 530 " distance=2.03 Simple disulfide: pdb=" SG CYS A 276 " - pdb=" SG CYS A 278 " distance=2.03 Simple disulfide: pdb=" SG CYS A 365 " - pdb=" SG CYS A 381 " distance=2.02 Simple disulfide: pdb=" SG CYS A 419 " - pdb=" SG CYS A 426 " distance=2.03 Simple disulfide: pdb=" SG CYS A 511 " - pdb=" SG CYS A 531 " distance=2.03 Simple disulfide: pdb=" SG CYS A 515 " - pdb=" SG CYS A 534 " distance=2.02 Simple disulfide: pdb=" SG CYS A 537 " - pdb=" SG CYS A 549 " distance=2.04 Simple disulfide: pdb=" SG CYS A 552 " - pdb=" SG CYS A 565 " distance=2.03 Simple disulfide: pdb=" SG CYS A 644 " - pdb=" SG CYS A 733 " distance=2.03 Simple disulfide: pdb=" SG CYS B 57 " - pdb=" SG CYS B 99 " distance=2.03 Simple disulfide: pdb=" SG CYS B 241 " - pdb=" SG CYS B 530 " distance=2.02 Simple disulfide: pdb=" SG CYS B 276 " - pdb=" SG CYS B 278 " distance=2.03 Simple disulfide: pdb=" SG CYS B 365 " - pdb=" SG CYS B 381 " distance=2.03 Simple disulfide: pdb=" SG CYS B 419 " - pdb=" SG CYS B 426 " distance=2.02 Simple disulfide: pdb=" SG CYS B 511 " - pdb=" SG CYS B 531 " distance=2.03 Simple disulfide: pdb=" SG CYS B 515 " - pdb=" SG CYS B 534 " distance=2.03 Simple disulfide: pdb=" SG CYS B 537 " - pdb=" SG CYS B 549 " distance=2.03 Simple disulfide: pdb=" SG CYS B 552 " - pdb=" SG CYS B 565 " distance=2.03 Simple disulfide: pdb=" SG CYS B 644 " - pdb=" SG CYS B 733 " 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 NAG-ASN " NAG A 901 " - " ASN A 210 " " NAG B 901 " - " ASN B 210 " Time building additional restraints: 1.11 Conformation dependent library (CDL) restraints added in 603.2 milliseconds 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2844 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 14 sheets defined 48.6% alpha, 9.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 48 through 52 removed outlier: 3.512A pdb=" N VAL A 52 " --> pdb=" O VAL A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 82 Processing helix chain 'A' and resid 101 through 113 Processing helix chain 'A' and resid 151 through 163 removed outlier: 3.770A pdb=" N LEU A 161 " --> pdb=" O GLN A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 166 No H-bonds generated for 'chain 'A' and resid 164 through 166' Processing helix chain 'A' and resid 176 through 181 removed outlier: 3.571A pdb=" N LEU A 179 " --> pdb=" O SER A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 209 removed outlier: 4.190A pdb=" N GLN A 198 " --> pdb=" O SER A 194 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR A 209 " --> pdb=" O ILE A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 237 removed outlier: 3.562A pdb=" N SER A 226 " --> pdb=" O ASN A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 266 Processing helix chain 'A' and resid 279 through 293 Processing helix chain 'A' and resid 317 through 322 Processing helix chain 'A' and resid 334 through 342 Processing helix chain 'A' and resid 354 through 363 Processing helix chain 'A' and resid 396 through 419 removed outlier: 3.763A pdb=" N VAL A 400 " --> pdb=" O LYS A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 443 removed outlier: 3.791A pdb=" N LYS A 443 " --> pdb=" O GLU A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 604 Processing helix chain 'A' and resid 614 through 635 removed outlier: 3.501A pdb=" N TYR A 619 " --> pdb=" O ARG A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 643 through 670 Proline residue: A 655 - end of helix removed outlier: 3.623A pdb=" N SER A 658 " --> pdb=" O SER A 654 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N TYR A 659 " --> pdb=" O PRO A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 691 through 715 removed outlier: 4.284A pdb=" N VAL A 695 " --> pdb=" O CYS A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 736 through 762 Proline residue: A 743 - end of helix Processing helix chain 'A' and resid 770 through 795 removed outlier: 4.062A pdb=" N VAL A 789 " --> pdb=" O TRP A 785 " (cutoff:3.500A) Proline residue: A 790 - end of helix Processing helix chain 'A' and resid 798 through 827 removed outlier: 3.549A pdb=" N LEU A 813 " --> pdb=" O SER A 809 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY A 815 " --> pdb=" O THR A 811 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N CYS A 816 " --> pdb=" O VAL A 812 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N MET A 817 " --> pdb=" O LEU A 813 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N PHE A 818 " --> pdb=" O LEU A 814 " (cutoff:3.500A) Proline residue: A 820 - end of helix Processing helix chain 'B' and resid 65 through 81 removed outlier: 4.022A pdb=" N GLU B 77 " --> pdb=" O LEU B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 114 Processing helix chain 'B' and resid 115 through 117 No H-bonds generated for 'chain 'B' and resid 115 through 117' Processing helix chain 'B' and resid 151 through 163 removed outlier: 3.866A pdb=" N LEU B 161 " --> pdb=" O GLN B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 166 No H-bonds generated for 'chain 'B' and resid 164 through 166' Processing helix chain 'B' and resid 176 through 181 removed outlier: 3.714A pdb=" N LEU B 179 " --> pdb=" O SER B 176 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASP B 181 " --> pdb=" O ASP B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 209 Processing helix chain 'B' and resid 222 through 237 Processing helix chain 'B' and resid 253 through 267 removed outlier: 4.215A pdb=" N HIS B 267 " --> pdb=" O LYS B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 293 Processing helix chain 'B' and resid 317 through 321 Processing helix chain 'B' and resid 334 through 342 Processing helix chain 'B' and resid 354 through 363 Processing helix chain 'B' and resid 396 through 419 removed outlier: 3.868A pdb=" N VAL B 400 " --> pdb=" O LYS B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 442 Processing helix chain 'B' and resid 560 through 563 Processing helix chain 'B' and resid 577 through 604 Processing helix chain 'B' and resid 607 through 611 Processing helix chain 'B' and resid 616 through 636 removed outlier: 5.199A pdb=" N LEU B 622 " --> pdb=" O CYS B 618 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ILE B 636 " --> pdb=" O THR B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 640 through 670 Proline residue: B 655 - end of helix removed outlier: 3.724A pdb=" N ALA B 661 " --> pdb=" O MET B 657 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU B 662 " --> pdb=" O SER B 658 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ALA B 670 " --> pdb=" O THR B 666 " (cutoff:3.500A) Processing helix chain 'B' and resid 692 through 715 removed outlier: 4.143A pdb=" N LEU B 700 " --> pdb=" O ILE B 696 " (cutoff:3.500A) Processing helix chain 'B' and resid 736 through 764 Proline residue: B 743 - end of helix removed outlier: 3.891A pdb=" N PHE B 759 " --> pdb=" O THR B 755 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N LYS B 760 " --> pdb=" O PHE B 756 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N THR B 761 " --> pdb=" O TYR B 757 " (cutoff:3.500A) Processing helix chain 'B' and resid 769 through 787 removed outlier: 3.919A pdb=" N TYR B 773 " --> pdb=" O ASN B 769 " (cutoff:3.500A) Processing helix chain 'B' and resid 787 through 795 removed outlier: 4.263A pdb=" N ILE B 791 " --> pdb=" O ALA B 787 " (cutoff:3.500A) Processing helix chain 'B' and resid 798 through 827 removed outlier: 3.851A pdb=" N LEU B 813 " --> pdb=" O SER B 809 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU B 814 " --> pdb=" O ALA B 810 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N VAL B 819 " --> pdb=" O GLY B 815 " (cutoff:3.500A) Proline residue: B 820 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 91 through 97 removed outlier: 6.546A pdb=" N ILE A 35 " --> pdb=" O GLY A 92 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N GLU A 94 " --> pdb=" O ILE A 35 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N ILE A 37 " --> pdb=" O GLU A 94 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N ARG A 96 " --> pdb=" O ILE A 37 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N ALA A 39 " --> pdb=" O ARG A 96 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N ILE A 36 " --> pdb=" O VAL A 144 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N VAL A 146 " --> pdb=" O ILE A 36 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N GLY A 38 " --> pdb=" O VAL A 146 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N GLY A 148 " --> pdb=" O GLY A 38 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N LEU A 40 " --> pdb=" O GLY A 148 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N GLN A 169 " --> pdb=" O MET A 189 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 241 through 248 removed outlier: 8.000A pdb=" N VAL A 214 " --> pdb=" O HIS A 244 " (cutoff:3.500A) removed outlier: 9.098A pdb=" N TYR A 246 " --> pdb=" O VAL A 214 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ALA A 216 " --> pdb=" O TYR A 246 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N ILE A 248 " --> pdb=" O ALA A 216 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N HIS A 218 " --> pdb=" O ILE A 248 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N TYR A 213 " --> pdb=" O VAL A 273 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N ALA A 275 " --> pdb=" O TYR A 213 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N SER A 215 " --> pdb=" O ALA A 275 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N PHE A 277 " --> pdb=" O SER A 215 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N VAL A 217 " --> pdb=" O PHE A 277 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N VAL A 274 " --> pdb=" O LEU A 302 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 325 through 329 removed outlier: 3.709A pdb=" N GLY A 485 " --> pdb=" O ILE A 468 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ASN A 470 " --> pdb=" O ASN A 483 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N ASN A 483 " --> pdb=" O ASN A 470 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LYS A 472 " --> pdb=" O TYR A 481 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N TYR A 481 " --> pdb=" O LYS A 472 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 446 through 447 Processing sheet with id=AA5, first strand: chain 'A' and resid 719 through 720 Processing sheet with id=AA6, first strand: chain 'B' and resid 91 through 97 removed outlier: 5.884A pdb=" N ILE B 35 " --> pdb=" O GLY B 92 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N GLU B 94 " --> pdb=" O ILE B 35 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ILE B 37 " --> pdb=" O GLU B 94 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N ARG B 96 " --> pdb=" O ILE B 37 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ALA B 39 " --> pdb=" O ARG B 96 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N ILE B 36 " --> pdb=" O ILE B 143 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N GLY B 145 " --> pdb=" O ILE B 36 " (cutoff:3.500A) removed outlier: 8.506A pdb=" N ILE B 170 " --> pdb=" O VAL B 144 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N VAL B 146 " --> pdb=" O ILE B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 241 through 248 removed outlier: 8.009A pdb=" N VAL B 214 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N SER B 245 " --> pdb=" O VAL B 214 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ALA B 216 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N LYS B 247 " --> pdb=" O ALA B 216 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N HIS B 218 " --> pdb=" O LYS B 247 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N TYR B 213 " --> pdb=" O VAL B 273 " (cutoff:3.500A) removed outlier: 8.375A pdb=" N ALA B 275 " --> pdb=" O TYR B 213 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N SER B 215 " --> pdb=" O ALA B 275 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N PHE B 277 " --> pdb=" O SER B 215 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N VAL B 217 " --> pdb=" O PHE B 277 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N VAL B 274 " --> pdb=" O LEU B 302 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.543A pdb=" N LYS B 472 " --> pdb=" O ASP B 480 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N TYR B 478 " --> pdb=" O MET B 474 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 446 through 447 Processing sheet with id=AB1, first strand: chain 'B' and resid 485 through 487 Processing sheet with id=AB2, first strand: chain 'B' and resid 520 through 521 Processing sheet with id=AB3, first strand: chain 'B' and resid 541 through 543 removed outlier: 3.674A pdb=" N TYR B 542 " --> pdb=" O LYS B 550 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 557 through 558 Processing sheet with id=AB5, first strand: chain 'B' and resid 719 through 722 545 hydrogen bonds defined for protein. 1581 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.00 Time building geometry restraints manager: 1.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2288 1.33 - 1.45: 3069 1.45 - 1.57: 6831 1.57 - 1.70: 0 1.70 - 1.82: 164 Bond restraints: 12352 Sorted by residual: bond pdb=" C8 XRQ A 903 " pdb=" N4 XRQ A 903 " ideal model delta sigma weight residual 1.416 1.360 0.056 2.00e-02 2.50e+03 7.89e+00 bond pdb=" C10 XRQ A 903 " pdb=" N3 XRQ A 903 " ideal model delta sigma weight residual 1.375 1.336 0.039 2.00e-02 2.50e+03 3.89e+00 bond pdb=" C04 QUS B 902 " pdb=" N14 QUS B 902 " ideal model delta sigma weight residual 1.380 1.341 0.039 2.00e-02 2.50e+03 3.73e+00 bond pdb=" C04 QUS A 902 " pdb=" N14 QUS A 902 " ideal model delta sigma weight residual 1.380 1.342 0.038 2.00e-02 2.50e+03 3.59e+00 bond pdb=" C SER A 529 " pdb=" N CYS A 530 " ideal model delta sigma weight residual 1.332 1.307 0.025 1.40e-02 5.10e+03 3.27e+00 ... (remaining 12347 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 16422 2.03 - 4.07: 264 4.07 - 6.10: 32 6.10 - 8.13: 16 8.13 - 10.17: 8 Bond angle restraints: 16742 Sorted by residual: angle pdb=" N VAL B 740 " pdb=" CA VAL B 740 " pdb=" C VAL B 740 " ideal model delta sigma weight residual 112.96 109.10 3.86 1.00e+00 1.00e+00 1.49e+01 angle pdb=" C03 QUS A 902 " pdb=" N14 QUS A 902 " pdb=" O20 QUS A 902 " ideal model delta sigma weight residual 112.77 122.94 -10.17 3.00e+00 1.11e-01 1.15e+01 angle pdb=" CB MET B 802 " pdb=" CG MET B 802 " pdb=" SD MET B 802 " ideal model delta sigma weight residual 112.70 122.72 -10.02 3.00e+00 1.11e-01 1.11e+01 angle pdb=" C03 QUS B 902 " pdb=" N14 QUS B 902 " pdb=" O20 QUS B 902 " ideal model delta sigma weight residual 112.77 122.41 -9.64 3.00e+00 1.11e-01 1.03e+01 angle pdb=" CB MET B 397 " pdb=" CG MET B 397 " pdb=" SD MET B 397 " ideal model delta sigma weight residual 112.70 122.18 -9.48 3.00e+00 1.11e-01 9.98e+00 ... (remaining 16737 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.48: 6477 21.48 - 42.97: 784 42.97 - 64.45: 139 64.45 - 85.94: 29 85.94 - 107.42: 9 Dihedral angle restraints: 7438 sinusoidal: 3002 harmonic: 4436 Sorted by residual: dihedral pdb=" CB CYS B 57 " pdb=" SG CYS B 57 " pdb=" SG CYS B 99 " pdb=" CB CYS B 99 " ideal model delta sinusoidal sigma weight residual 93.00 4.71 88.29 1 1.00e+01 1.00e-02 9.31e+01 dihedral pdb=" CB CYS A 57 " pdb=" SG CYS A 57 " pdb=" SG CYS A 99 " pdb=" CB CYS A 99 " ideal model delta sinusoidal sigma weight residual 93.00 10.65 82.35 1 1.00e+01 1.00e-02 8.32e+01 dihedral pdb=" CB CYS A 537 " pdb=" SG CYS A 537 " pdb=" SG CYS A 549 " pdb=" CB CYS A 549 " ideal model delta sinusoidal sigma weight residual -86.00 -159.08 73.08 1 1.00e+01 1.00e-02 6.81e+01 ... (remaining 7435 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1539 0.059 - 0.119: 311 0.119 - 0.178: 21 0.178 - 0.237: 1 0.237 - 0.296: 4 Chirality restraints: 1876 Sorted by residual: chirality pdb=" CG LEU B 711 " pdb=" CB LEU B 711 " pdb=" CD1 LEU B 711 " pdb=" CD2 LEU B 711 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.19e+00 chirality pdb=" CG LEU B 627 " pdb=" CB LEU B 627 " pdb=" CD1 LEU B 627 " pdb=" CD2 LEU B 627 " both_signs ideal model delta sigma weight residual False -2.59 -2.31 -0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" C1 NAG B 901 " pdb=" ND2 ASN B 210 " pdb=" C2 NAG B 901 " pdb=" O5 NAG B 901 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-01 2.50e+01 1.72e+00 ... (remaining 1873 not shown) Planarity restraints: 2112 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 XRQ A 903 " 0.108 2.00e-02 2.50e+03 2.40e-01 7.17e+02 pdb=" C2 XRQ A 903 " -0.189 2.00e-02 2.50e+03 pdb=" C8 XRQ A 903 " -0.291 2.00e-02 2.50e+03 pdb=" N2 XRQ A 903 " 0.393 2.00e-02 2.50e+03 pdb=" O1 XRQ A 903 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A 579 " -0.027 5.00e-02 4.00e+02 4.13e-02 2.74e+00 pdb=" N PRO A 580 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO A 580 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 580 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 577 " 0.027 5.00e-02 4.00e+02 4.08e-02 2.67e+00 pdb=" N PRO A 578 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 578 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 578 " 0.023 5.00e-02 4.00e+02 ... (remaining 2109 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1176 2.73 - 3.27: 12859 3.27 - 3.82: 20597 3.82 - 4.36: 23748 4.36 - 4.90: 40836 Nonbonded interactions: 99216 Sorted by model distance: nonbonded pdb=" O SER A 529 " pdb=" OG SER A 529 " model vdw 2.190 3.040 nonbonded pdb=" OD2 ASP A 561 " pdb=" OG1 THR A 563 " model vdw 2.196 3.040 nonbonded pdb=" OE1 GLN B 198 " pdb=" OG SER B 304 " model vdw 2.206 3.040 nonbonded pdb=" OE2 GLU B 70 " pdb=" ND2 ASN B 352 " model vdw 2.209 3.120 nonbonded pdb=" N GLN A 553 " pdb=" OE1 GLN A 553 " model vdw 2.228 3.120 ... (remaining 99211 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 Found NCS groups: ncs_group { reference = (chain 'A' and resid 25 through 902) selection = chain 'B' } 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: 9.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.390 Find NCS groups from input model: 0.300 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:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 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 : 0.006 0.059 12374 Z= 0.282 Angle : 0.695 10.166 16788 Z= 0.344 Chirality : 0.046 0.296 1876 Planarity : 0.006 0.240 2110 Dihedral : 18.217 107.420 4534 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.53 % Favored : 91.47 % Rotamer: Outliers : 0.23 % Allowed : 32.75 % Favored : 67.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.42 (0.22), residues: 1512 helix: 1.21 (0.20), residues: 681 sheet: -1.40 (0.40), residues: 178 loop : -1.58 (0.24), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 310 TYR 0.012 0.001 TYR A 341 PHE 0.017 0.002 PHE B 337 TRP 0.008 0.001 TRP B 336 HIS 0.003 0.001 HIS A 74 Details of bonding type rmsd covalent geometry : bond 0.00638 (12352) covalent geometry : angle 0.69047 (16742) SS BOND : bond 0.00456 ( 20) SS BOND : angle 1.63605 ( 40) hydrogen bonds : bond 0.15962 ( 545) hydrogen bonds : angle 5.63352 ( 1581) link_NAG-ASN : bond 0.00390 ( 2) link_NAG-ASN : angle 2.17870 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 93 time to evaluate : 0.359 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 96 average time/residue: 0.0893 time to fit residues: 13.0795 Evaluate side-chains 95 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 93 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ASP Chi-restraints excluded: chain A residue 385 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 5.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.103970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.071826 restraints weight = 32595.088| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 2.51 r_work: 0.3183 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.0836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12374 Z= 0.142 Angle : 0.622 14.200 16788 Z= 0.306 Chirality : 0.044 0.276 1876 Planarity : 0.004 0.040 2110 Dihedral : 7.720 71.146 1722 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 3.12 % Allowed : 29.86 % Favored : 67.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.32 (0.22), residues: 1512 helix: 1.22 (0.20), residues: 700 sheet: -1.36 (0.41), residues: 177 loop : -1.52 (0.25), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 55 TYR 0.008 0.001 TYR A 645 PHE 0.034 0.001 PHE B 776 TRP 0.012 0.001 TRP B 336 HIS 0.003 0.001 HIS B 391 Details of bonding type rmsd covalent geometry : bond 0.00306 (12352) covalent geometry : angle 0.62037 (16742) SS BOND : bond 0.00390 ( 20) SS BOND : angle 1.07185 ( 40) hydrogen bonds : bond 0.04594 ( 545) hydrogen bonds : angle 4.40169 ( 1581) link_NAG-ASN : bond 0.00108 ( 2) link_NAG-ASN : angle 1.35407 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 99 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 647 GLN cc_start: 0.7436 (tt0) cc_final: 0.7085 (mm-40) REVERT: B 372 GLN cc_start: 0.8281 (OUTLIER) cc_final: 0.8023 (mp10) REVERT: B 553 GLN cc_start: 0.8919 (pm20) cc_final: 0.8689 (pm20) outliers start: 41 outliers final: 21 residues processed: 133 average time/residue: 0.0827 time to fit residues: 17.0050 Evaluate side-chains 116 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 94 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 112 PHE Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 778 MET Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 267 HIS Chi-restraints excluded: chain B residue 277 PHE Chi-restraints excluded: chain B residue 281 MET Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 372 GLN Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 530 CYS Chi-restraints excluded: chain B residue 627 LEU Chi-restraints excluded: chain B residue 801 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 95 optimal weight: 5.9990 chunk 71 optimal weight: 8.9990 chunk 107 optimal weight: 0.8980 chunk 148 optimal weight: 6.9990 chunk 59 optimal weight: 8.9990 chunk 99 optimal weight: 3.9990 chunk 56 optimal weight: 6.9990 chunk 147 optimal weight: 7.9990 chunk 17 optimal weight: 4.9990 chunk 150 optimal weight: 8.9990 chunk 25 optimal weight: 5.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 GLN B 459 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.100125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.067062 restraints weight = 33233.011| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 2.60 r_work: 0.3073 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.0869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.059 12374 Z= 0.413 Angle : 0.769 12.894 16788 Z= 0.387 Chirality : 0.049 0.292 1876 Planarity : 0.005 0.041 2110 Dihedral : 6.681 59.243 1718 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.60 % Favored : 91.40 % Rotamer: Outliers : 4.94 % Allowed : 29.79 % Favored : 65.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.67 (0.22), residues: 1512 helix: 0.92 (0.20), residues: 701 sheet: -1.44 (0.40), residues: 177 loop : -1.72 (0.24), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 508 TYR 0.017 0.002 TYR A 341 PHE 0.021 0.002 PHE B 337 TRP 0.011 0.002 TRP A 336 HIS 0.004 0.001 HIS B 53 Details of bonding type rmsd covalent geometry : bond 0.00947 (12352) covalent geometry : angle 0.76414 (16742) SS BOND : bond 0.00580 ( 20) SS BOND : angle 1.58223 ( 40) hydrogen bonds : bond 0.05380 ( 545) hydrogen bonds : angle 4.64450 ( 1581) link_NAG-ASN : bond 0.00486 ( 2) link_NAG-ASN : angle 3.00087 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 96 time to evaluate : 0.453 Fit side-chains revert: symmetry clash REVERT: A 319 ARG cc_start: 0.8496 (OUTLIER) cc_final: 0.7958 (tpp-160) REVERT: B 372 GLN cc_start: 0.8226 (OUTLIER) cc_final: 0.8006 (mp10) REVERT: B 596 PHE cc_start: 0.6980 (OUTLIER) cc_final: 0.5833 (m-80) REVERT: B 788 PHE cc_start: 0.5917 (OUTLIER) cc_final: 0.4504 (t80) outliers start: 65 outliers final: 35 residues processed: 147 average time/residue: 0.0909 time to fit residues: 20.3339 Evaluate side-chains 134 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 95 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 611 LYS Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 703 ILE Chi-restraints excluded: chain A residue 778 MET Chi-restraints excluded: chain A residue 788 PHE Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 814 LEU Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 57 CYS Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 277 PHE Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 372 GLN Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 596 PHE Chi-restraints excluded: chain B residue 625 ILE Chi-restraints excluded: chain B residue 627 LEU Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 657 MET Chi-restraints excluded: chain B residue 713 ILE Chi-restraints excluded: chain B residue 788 PHE Chi-restraints excluded: chain B residue 801 THR Chi-restraints excluded: chain B residue 812 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 8 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 99 optimal weight: 0.7980 chunk 59 optimal weight: 7.9990 chunk 57 optimal weight: 0.9990 chunk 130 optimal weight: 9.9990 chunk 4 optimal weight: 0.6980 chunk 124 optimal weight: 8.9990 chunk 90 optimal weight: 0.9980 chunk 103 optimal weight: 0.7980 chunk 51 optimal weight: 7.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.103666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.071257 restraints weight = 32734.637| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 2.56 r_work: 0.3168 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.1054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.105 12374 Z= 0.140 Angle : 0.612 12.088 16788 Z= 0.302 Chirality : 0.043 0.263 1876 Planarity : 0.004 0.042 2110 Dihedral : 5.614 52.522 1718 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 4.64 % Allowed : 29.79 % Favored : 65.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.41 (0.22), residues: 1512 helix: 1.14 (0.20), residues: 702 sheet: -1.50 (0.42), residues: 158 loop : -1.55 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 508 TYR 0.008 0.001 TYR A 645 PHE 0.014 0.001 PHE B 586 TRP 0.013 0.001 TRP B 336 HIS 0.002 0.001 HIS B 218 Details of bonding type rmsd covalent geometry : bond 0.00311 (12352) covalent geometry : angle 0.60681 (16742) SS BOND : bond 0.00501 ( 20) SS BOND : angle 1.62425 ( 40) hydrogen bonds : bond 0.04344 ( 545) hydrogen bonds : angle 4.23623 ( 1581) link_NAG-ASN : bond 0.00042 ( 2) link_NAG-ASN : angle 2.04142 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 97 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 319 ARG cc_start: 0.8548 (OUTLIER) cc_final: 0.8051 (tpp-160) REVERT: A 627 LEU cc_start: 0.8812 (tt) cc_final: 0.8502 (mm) REVERT: B 372 GLN cc_start: 0.8276 (OUTLIER) cc_final: 0.8005 (mp10) REVERT: B 596 PHE cc_start: 0.6988 (OUTLIER) cc_final: 0.5736 (m-80) REVERT: B 778 MET cc_start: 0.8140 (tpp) cc_final: 0.7918 (tpp) REVERT: B 788 PHE cc_start: 0.6058 (OUTLIER) cc_final: 0.4573 (t80) REVERT: B 802 MET cc_start: 0.8064 (tpp) cc_final: 0.7859 (tpp) outliers start: 61 outliers final: 35 residues processed: 145 average time/residue: 0.0904 time to fit residues: 20.2601 Evaluate side-chains 134 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 95 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 MET Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 112 PHE Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain A residue 395 SER Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 659 TYR Chi-restraints excluded: chain A residue 703 ILE Chi-restraints excluded: chain A residue 788 PHE Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 267 HIS Chi-restraints excluded: chain B residue 277 PHE Chi-restraints excluded: chain B residue 372 GLN Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 596 PHE Chi-restraints excluded: chain B residue 625 ILE Chi-restraints excluded: chain B residue 627 LEU Chi-restraints excluded: chain B residue 636 ILE Chi-restraints excluded: chain B residue 657 MET Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 713 ILE Chi-restraints excluded: chain B residue 788 PHE Chi-restraints excluded: chain B residue 801 THR Chi-restraints excluded: chain B residue 814 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 149 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 91 optimal weight: 0.6980 chunk 108 optimal weight: 3.9990 chunk 102 optimal weight: 0.4980 chunk 89 optimal weight: 4.9990 chunk 56 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 57 optimal weight: 9.9990 chunk 123 optimal weight: 0.9980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.104226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.071966 restraints weight = 32817.622| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 2.57 r_work: 0.3187 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.1215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 12374 Z= 0.128 Angle : 0.583 10.585 16788 Z= 0.287 Chirality : 0.043 0.257 1876 Planarity : 0.003 0.040 2110 Dihedral : 5.091 52.601 1718 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 4.41 % Allowed : 29.48 % Favored : 66.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.29 (0.22), residues: 1512 helix: 1.28 (0.20), residues: 703 sheet: -1.50 (0.42), residues: 164 loop : -1.50 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 508 TYR 0.006 0.001 TYR A 645 PHE 0.013 0.001 PHE B 818 TRP 0.013 0.001 TRP B 336 HIS 0.002 0.000 HIS B 267 Details of bonding type rmsd covalent geometry : bond 0.00287 (12352) covalent geometry : angle 0.57944 (16742) SS BOND : bond 0.00382 ( 20) SS BOND : angle 1.44446 ( 40) hydrogen bonds : bond 0.04040 ( 545) hydrogen bonds : angle 4.11259 ( 1581) link_NAG-ASN : bond 0.00243 ( 2) link_NAG-ASN : angle 1.20515 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 101 time to evaluate : 0.325 Fit side-chains revert: symmetry clash REVERT: A 319 ARG cc_start: 0.8488 (OUTLIER) cc_final: 0.7984 (tpp-160) REVERT: B 372 GLN cc_start: 0.8286 (OUTLIER) cc_final: 0.8019 (mp10) REVERT: B 596 PHE cc_start: 0.6965 (OUTLIER) cc_final: 0.5796 (m-80) REVERT: B 778 MET cc_start: 0.8119 (tpp) cc_final: 0.7907 (tpp) REVERT: B 788 PHE cc_start: 0.5832 (OUTLIER) cc_final: 0.4319 (t80) REVERT: B 802 MET cc_start: 0.7975 (tpp) cc_final: 0.7765 (tpp) outliers start: 58 outliers final: 35 residues processed: 147 average time/residue: 0.0888 time to fit residues: 20.2438 Evaluate side-chains 132 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 93 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 MET Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 112 PHE Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 395 SER Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 659 TYR Chi-restraints excluded: chain A residue 703 ILE Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 814 LEU Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 57 CYS Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 277 PHE Chi-restraints excluded: chain B residue 281 MET Chi-restraints excluded: chain B residue 372 GLN Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 596 PHE Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 625 ILE Chi-restraints excluded: chain B residue 636 ILE Chi-restraints excluded: chain B residue 657 MET Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 788 PHE Chi-restraints excluded: chain B residue 801 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 47 optimal weight: 0.7980 chunk 85 optimal weight: 3.9990 chunk 146 optimal weight: 8.9990 chunk 126 optimal weight: 20.0000 chunk 121 optimal weight: 6.9990 chunk 42 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 99 optimal weight: 0.0000 chunk 98 optimal weight: 1.9990 chunk 64 optimal weight: 10.0000 chunk 102 optimal weight: 0.7980 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.103529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.071199 restraints weight = 32706.379| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 2.56 r_work: 0.3169 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.1307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 12374 Z= 0.157 Angle : 0.594 9.733 16788 Z= 0.294 Chirality : 0.043 0.203 1876 Planarity : 0.003 0.040 2110 Dihedral : 5.135 52.623 1718 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 3.88 % Allowed : 30.55 % Favored : 65.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.30 (0.22), residues: 1512 helix: 1.30 (0.20), residues: 703 sheet: -1.55 (0.42), residues: 165 loop : -1.53 (0.24), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 508 TYR 0.022 0.001 TYR A 823 PHE 0.020 0.001 PHE B 544 TRP 0.011 0.001 TRP B 336 HIS 0.002 0.000 HIS B 267 Details of bonding type rmsd covalent geometry : bond 0.00359 (12352) covalent geometry : angle 0.59021 (16742) SS BOND : bond 0.00369 ( 20) SS BOND : angle 1.41831 ( 40) hydrogen bonds : bond 0.04067 ( 545) hydrogen bonds : angle 4.11153 ( 1581) link_NAG-ASN : bond 0.00060 ( 2) link_NAG-ASN : angle 1.30097 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 97 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 647 GLN cc_start: 0.7364 (tt0) cc_final: 0.6975 (mm-40) REVERT: B 372 GLN cc_start: 0.8262 (OUTLIER) cc_final: 0.7994 (mp10) REVERT: B 596 PHE cc_start: 0.6960 (OUTLIER) cc_final: 0.5784 (m-80) REVERT: B 778 MET cc_start: 0.8123 (tpp) cc_final: 0.7904 (tpp) REVERT: B 788 PHE cc_start: 0.5866 (OUTLIER) cc_final: 0.4252 (t80) outliers start: 51 outliers final: 41 residues processed: 137 average time/residue: 0.0849 time to fit residues: 18.3888 Evaluate side-chains 136 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 92 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 MET Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 112 PHE Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 395 SER Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 659 TYR Chi-restraints excluded: chain A residue 703 ILE Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 814 LEU Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 57 CYS Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 277 PHE Chi-restraints excluded: chain B residue 281 MET Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 372 GLN Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 596 PHE Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 625 ILE Chi-restraints excluded: chain B residue 627 LEU Chi-restraints excluded: chain B residue 636 ILE Chi-restraints excluded: chain B residue 657 MET Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 788 PHE Chi-restraints excluded: chain B residue 801 THR Chi-restraints excluded: chain B residue 814 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 91 optimal weight: 0.6980 chunk 149 optimal weight: 10.0000 chunk 88 optimal weight: 3.9990 chunk 50 optimal weight: 9.9990 chunk 61 optimal weight: 10.0000 chunk 95 optimal weight: 1.9990 chunk 133 optimal weight: 7.9990 chunk 148 optimal weight: 7.9990 chunk 16 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.102152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.069601 restraints weight = 32906.159| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 2.56 r_work: 0.3133 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.1233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 12374 Z= 0.248 Angle : 0.639 8.887 16788 Z= 0.319 Chirality : 0.044 0.202 1876 Planarity : 0.004 0.039 2110 Dihedral : 5.342 54.305 1718 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 4.79 % Allowed : 30.02 % Favored : 65.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.36 (0.22), residues: 1512 helix: 1.22 (0.20), residues: 706 sheet: -1.48 (0.42), residues: 158 loop : -1.57 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 310 TYR 0.015 0.001 TYR A 823 PHE 0.017 0.002 PHE B 544 TRP 0.010 0.001 TRP B 336 HIS 0.003 0.001 HIS B 267 Details of bonding type rmsd covalent geometry : bond 0.00574 (12352) covalent geometry : angle 0.63398 (16742) SS BOND : bond 0.00444 ( 20) SS BOND : angle 1.64069 ( 40) hydrogen bonds : bond 0.04401 ( 545) hydrogen bonds : angle 4.24426 ( 1581) link_NAG-ASN : bond 0.00207 ( 2) link_NAG-ASN : angle 1.66648 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 96 time to evaluate : 0.290 Fit side-chains revert: symmetry clash REVERT: B 372 GLN cc_start: 0.8308 (OUTLIER) cc_final: 0.8041 (mp10) REVERT: B 596 PHE cc_start: 0.6999 (OUTLIER) cc_final: 0.5756 (m-80) REVERT: B 778 MET cc_start: 0.8127 (tpp) cc_final: 0.7901 (tpp) REVERT: B 788 PHE cc_start: 0.5825 (OUTLIER) cc_final: 0.4524 (t80) outliers start: 63 outliers final: 48 residues processed: 144 average time/residue: 0.0879 time to fit residues: 19.6629 Evaluate side-chains 146 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 95 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 31 MET Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 112 PHE Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain A residue 381 CYS Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 395 SER Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 659 TYR Chi-restraints excluded: chain A residue 703 ILE Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 814 LEU Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 57 CYS Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 277 PHE Chi-restraints excluded: chain B residue 281 MET Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 372 GLN Chi-restraints excluded: chain B residue 405 TYR Chi-restraints excluded: chain B residue 419 CYS Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 596 PHE Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 625 ILE Chi-restraints excluded: chain B residue 627 LEU Chi-restraints excluded: chain B residue 636 ILE Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 657 MET Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 713 ILE Chi-restraints excluded: chain B residue 788 PHE Chi-restraints excluded: chain B residue 789 VAL Chi-restraints excluded: chain B residue 801 THR Chi-restraints excluded: chain B residue 814 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 41 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 126 optimal weight: 10.0000 chunk 113 optimal weight: 9.9990 chunk 150 optimal weight: 9.9990 chunk 117 optimal weight: 0.7980 chunk 133 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 100 optimal weight: 0.7980 chunk 70 optimal weight: 8.9990 chunk 73 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.103656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.071233 restraints weight = 32886.939| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.65 r_work: 0.3169 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.1391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12374 Z= 0.143 Angle : 0.597 8.151 16788 Z= 0.295 Chirality : 0.043 0.194 1876 Planarity : 0.003 0.040 2110 Dihedral : 5.219 55.979 1718 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 4.64 % Allowed : 30.24 % Favored : 65.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.24 (0.22), residues: 1512 helix: 1.32 (0.20), residues: 703 sheet: -1.46 (0.42), residues: 158 loop : -1.48 (0.24), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 508 TYR 0.012 0.001 TYR A 823 PHE 0.018 0.001 PHE B 544 TRP 0.013 0.001 TRP B 336 HIS 0.002 0.000 HIS B 218 Details of bonding type rmsd covalent geometry : bond 0.00326 (12352) covalent geometry : angle 0.59423 (16742) SS BOND : bond 0.00342 ( 20) SS BOND : angle 1.31877 ( 40) hydrogen bonds : bond 0.04032 ( 545) hydrogen bonds : angle 4.10838 ( 1581) link_NAG-ASN : bond 0.00103 ( 2) link_NAG-ASN : angle 1.17995 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 99 time to evaluate : 0.487 Fit side-chains revert: symmetry clash REVERT: A 559 THR cc_start: 0.6237 (OUTLIER) cc_final: 0.5949 (p) REVERT: B 372 GLN cc_start: 0.8140 (OUTLIER) cc_final: 0.7932 (mp10) REVERT: B 596 PHE cc_start: 0.6957 (OUTLIER) cc_final: 0.5795 (m-80) REVERT: B 778 MET cc_start: 0.8078 (tpp) cc_final: 0.7860 (tpp) REVERT: B 788 PHE cc_start: 0.5723 (OUTLIER) cc_final: 0.4437 (t80) outliers start: 61 outliers final: 48 residues processed: 148 average time/residue: 0.0832 time to fit residues: 19.6541 Evaluate side-chains 146 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 94 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 MET Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 112 PHE Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 395 SER Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 559 THR Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 636 ILE Chi-restraints excluded: chain A residue 659 TYR Chi-restraints excluded: chain A residue 703 ILE Chi-restraints excluded: chain A residue 784 ILE Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 57 CYS Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 277 PHE Chi-restraints excluded: chain B residue 281 MET Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 372 GLN Chi-restraints excluded: chain B residue 405 TYR Chi-restraints excluded: chain B residue 419 CYS Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 596 PHE Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 625 ILE Chi-restraints excluded: chain B residue 627 LEU Chi-restraints excluded: chain B residue 635 LEU Chi-restraints excluded: chain B residue 636 ILE Chi-restraints excluded: chain B residue 657 MET Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 788 PHE Chi-restraints excluded: chain B residue 789 VAL Chi-restraints excluded: chain B residue 801 THR Chi-restraints excluded: chain B residue 814 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 138 optimal weight: 30.0000 chunk 14 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 110 optimal weight: 3.9990 chunk 75 optimal weight: 0.3980 chunk 127 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 117 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 chunk 123 optimal weight: 5.9990 chunk 33 optimal weight: 7.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.103846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.071353 restraints weight = 32899.221| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 2.65 r_work: 0.3172 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.1472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12374 Z= 0.142 Angle : 0.603 9.189 16788 Z= 0.297 Chirality : 0.043 0.198 1876 Planarity : 0.003 0.040 2110 Dihedral : 5.209 58.660 1718 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 4.48 % Allowed : 31.00 % Favored : 64.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.23 (0.22), residues: 1512 helix: 1.37 (0.20), residues: 702 sheet: -1.55 (0.42), residues: 165 loop : -1.49 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 508 TYR 0.010 0.001 TYR A 823 PHE 0.018 0.001 PHE B 633 TRP 0.013 0.001 TRP B 336 HIS 0.002 0.000 HIS B 267 Details of bonding type rmsd covalent geometry : bond 0.00325 (12352) covalent geometry : angle 0.60060 (16742) SS BOND : bond 0.00323 ( 20) SS BOND : angle 1.27172 ( 40) hydrogen bonds : bond 0.03963 ( 545) hydrogen bonds : angle 4.08077 ( 1581) link_NAG-ASN : bond 0.00048 ( 2) link_NAG-ASN : angle 1.06774 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 96 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 559 THR cc_start: 0.6263 (OUTLIER) cc_final: 0.5986 (p) REVERT: B 372 GLN cc_start: 0.8143 (OUTLIER) cc_final: 0.7932 (mp10) REVERT: B 596 PHE cc_start: 0.6904 (OUTLIER) cc_final: 0.5793 (m-80) REVERT: B 778 MET cc_start: 0.8091 (tpp) cc_final: 0.7876 (tpp) REVERT: B 788 PHE cc_start: 0.5778 (OUTLIER) cc_final: 0.4348 (t80) REVERT: B 801 THR cc_start: 0.8703 (p) cc_final: 0.8459 (t) outliers start: 59 outliers final: 48 residues processed: 145 average time/residue: 0.0818 time to fit residues: 19.1407 Evaluate side-chains 146 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 94 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 MET Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 112 PHE Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain A residue 381 CYS Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 395 SER Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 559 THR Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 636 ILE Chi-restraints excluded: chain A residue 659 TYR Chi-restraints excluded: chain A residue 703 ILE Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 57 CYS Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 277 PHE Chi-restraints excluded: chain B residue 281 MET Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 372 GLN Chi-restraints excluded: chain B residue 405 TYR Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 596 PHE Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 625 ILE Chi-restraints excluded: chain B residue 627 LEU Chi-restraints excluded: chain B residue 635 LEU Chi-restraints excluded: chain B residue 636 ILE Chi-restraints excluded: chain B residue 657 MET Chi-restraints excluded: chain B residue 788 PHE Chi-restraints excluded: chain B residue 789 VAL Chi-restraints excluded: chain B residue 814 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 41 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 chunk 145 optimal weight: 7.9990 chunk 134 optimal weight: 8.9990 chunk 87 optimal weight: 2.9990 chunk 140 optimal weight: 8.9990 chunk 116 optimal weight: 4.9990 chunk 108 optimal weight: 2.9990 chunk 54 optimal weight: 20.0000 chunk 81 optimal weight: 0.8980 chunk 110 optimal weight: 0.0970 overall best weight: 1.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 519 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.103374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.070647 restraints weight = 33152.478| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 2.69 r_work: 0.3153 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 12374 Z= 0.175 Angle : 0.634 10.805 16788 Z= 0.309 Chirality : 0.043 0.204 1876 Planarity : 0.004 0.040 2110 Dihedral : 5.273 58.157 1718 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 4.41 % Allowed : 31.08 % Favored : 64.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.25 (0.22), residues: 1512 helix: 1.31 (0.20), residues: 705 sheet: -1.51 (0.42), residues: 158 loop : -1.50 (0.24), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 208 TYR 0.009 0.001 TYR A 823 PHE 0.016 0.001 PHE B 544 TRP 0.011 0.001 TRP B 336 HIS 0.002 0.001 HIS B 267 Details of bonding type rmsd covalent geometry : bond 0.00403 (12352) covalent geometry : angle 0.62150 (16742) SS BOND : bond 0.00364 ( 20) SS BOND : angle 1.36577 ( 40) hydrogen bonds : bond 0.04026 ( 545) hydrogen bonds : angle 4.10274 ( 1581) link_NAG-ASN : bond 0.00132 ( 2) link_NAG-ASN : angle 5.81395 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 93 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 559 THR cc_start: 0.6376 (OUTLIER) cc_final: 0.6099 (p) REVERT: B 372 GLN cc_start: 0.8147 (OUTLIER) cc_final: 0.7937 (mp10) REVERT: B 596 PHE cc_start: 0.6896 (OUTLIER) cc_final: 0.5785 (m-80) REVERT: B 778 MET cc_start: 0.8082 (tpp) cc_final: 0.7868 (tpp) REVERT: B 788 PHE cc_start: 0.5916 (OUTLIER) cc_final: 0.4695 (t80) outliers start: 58 outliers final: 50 residues processed: 141 average time/residue: 0.0786 time to fit residues: 17.8465 Evaluate side-chains 145 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 91 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 MET Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 112 PHE Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain A residue 381 CYS Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 395 SER Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 559 THR Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 636 ILE Chi-restraints excluded: chain A residue 659 TYR Chi-restraints excluded: chain A residue 703 ILE Chi-restraints excluded: chain A residue 784 ILE Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 814 LEU Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 57 CYS Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 277 PHE Chi-restraints excluded: chain B residue 281 MET Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 372 GLN Chi-restraints excluded: chain B residue 405 TYR Chi-restraints excluded: chain B residue 419 CYS Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 596 PHE Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 625 ILE Chi-restraints excluded: chain B residue 627 LEU Chi-restraints excluded: chain B residue 635 LEU Chi-restraints excluded: chain B residue 636 ILE Chi-restraints excluded: chain B residue 657 MET Chi-restraints excluded: chain B residue 788 PHE Chi-restraints excluded: chain B residue 789 VAL Chi-restraints excluded: chain B residue 814 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 62 optimal weight: 30.0000 chunk 150 optimal weight: 8.9990 chunk 72 optimal weight: 6.9990 chunk 114 optimal weight: 2.9990 chunk 116 optimal weight: 0.0970 chunk 124 optimal weight: 0.9980 chunk 66 optimal weight: 9.9990 chunk 117 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 132 optimal weight: 7.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.103826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.071449 restraints weight = 32800.332| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 2.63 r_work: 0.3175 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.1543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12374 Z= 0.149 Angle : 0.621 10.195 16788 Z= 0.302 Chirality : 0.043 0.196 1876 Planarity : 0.003 0.040 2110 Dihedral : 5.175 55.435 1718 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 4.33 % Allowed : 30.93 % Favored : 64.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.24 (0.22), residues: 1512 helix: 1.33 (0.19), residues: 707 sheet: -1.61 (0.41), residues: 165 loop : -1.46 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 524 TYR 0.009 0.001 TYR A 823 PHE 0.017 0.001 PHE B 544 TRP 0.012 0.001 TRP B 336 HIS 0.002 0.000 HIS B 267 Details of bonding type rmsd covalent geometry : bond 0.00343 (12352) covalent geometry : angle 0.61280 (16742) SS BOND : bond 0.00343 ( 20) SS BOND : angle 1.26187 ( 40) hydrogen bonds : bond 0.03941 ( 545) hydrogen bonds : angle 4.08239 ( 1581) link_NAG-ASN : bond 0.00247 ( 2) link_NAG-ASN : angle 4.50994 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3364.88 seconds wall clock time: 58 minutes 20.56 seconds (3500.56 seconds total)