Starting phenix.real_space_refine on Sun Sep 13 06:48:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9roj_54121/09_2026/9roj_54121_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9roj_54121/09_2026/9roj_54121.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9roj_54121/09_2026/9roj_54121.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9roj_54121/09_2026/9roj_54121.map" model { file = "/net/cci-nas-00/data/ceres_data/9roj_54121/09_2026/9roj_54121_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9roj_54121/09_2026/9roj_54121_trim.cif" } resolution = 3.58 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= 0.024 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: 6 Type Number sf(0) Gaussians S 61 5.16 5 Na 1 4.78 5 C 6586 2.51 5 N 1695 2.21 5 O 1923 1.98 5 H 10153 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20419 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 15231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 984, 15231 Classifications: {'peptide': 984} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 41, 'TRANS': 942} Chain: "B" Number of atoms: 4518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 4518 Classifications: {'peptide': 279} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 258} Chain: "C" Number of atoms: 543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 543 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "A" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 57 Unusual residues: {' NA': 1, 'CLR': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 70 Unusual residues: {'CLR': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 3.19, per 1000 atoms: 0.16 Number of scatterers: 20419 At special positions: 0 Unit cell: (83.584, 87.502, 173.698, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 61 16.00 Na 1 11.00 O 1923 8.00 N 1695 7.00 C 6586 6.00 H 10153 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 42 " - pdb=" SG CYS A 49 " distance=2.03 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 149 " distance=2.03 Simple disulfide: pdb=" SG CYS B 159 " - pdb=" SG CYS B 175 " distance=2.03 Simple disulfide: pdb=" SG CYS B 213 " - pdb=" SG CYS B 276 " 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 B1102 " - " ASN B 158 " " NAG B1103 " - " ASN B 193 " " NAG B1104 " - " ASN B 265 " Time building additional restraints: 1.42 Conformation dependent library (CDL) restraints added in 423.7 milliseconds 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2390 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 11 sheets defined 49.1% alpha, 15.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 37 through 45 removed outlier: 3.912A pdb=" N TYR A 45 " --> pdb=" O VAL A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 66 Processing helix chain 'A' and resid 78 through 88 removed outlier: 3.680A pdb=" N GLY A 88 " --> pdb=" O ARG A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 105 removed outlier: 3.519A pdb=" N ILE A 99 " --> pdb=" O TRP A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 152 removed outlier: 3.847A pdb=" N ILE A 147 " --> pdb=" O LYS A 143 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N MET A 148 " --> pdb=" O SER A 144 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLU A 149 " --> pdb=" O SER A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 175 No H-bonds generated for 'chain 'A' and resid 173 through 175' Processing helix chain 'A' and resid 272 through 303 Processing helix chain 'A' and resid 306 through 322 removed outlier: 3.508A pdb=" N VAL A 322 " --> pdb=" O ILE A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 344 removed outlier: 3.866A pdb=" N THR A 331 " --> pdb=" O LEU A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 358 removed outlier: 4.229A pdb=" N VAL A 354 " --> pdb=" O ASN A 350 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLU A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N THR A 356 " --> pdb=" O GLU A 352 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLY A 358 " --> pdb=" O VAL A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 419 removed outlier: 3.542A pdb=" N VAL A 409 " --> pdb=" O SER A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 454 removed outlier: 3.734A pdb=" N LEU A 452 " --> pdb=" O LYS A 448 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N SER A 453 " --> pdb=" O CYS A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 464 removed outlier: 4.111A pdb=" N MET A 460 " --> pdb=" O SER A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 506 Processing helix chain 'A' and resid 521 through 538 removed outlier: 3.949A pdb=" N LEU A 538 " --> pdb=" O GLU A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 599 Processing helix chain 'A' and resid 610 through 622 Processing helix chain 'A' and resid 630 through 639 Processing helix chain 'A' and resid 641 through 645 Processing helix chain 'A' and resid 646 through 650 Processing helix chain 'A' and resid 657 through 663 removed outlier: 3.605A pdb=" N ASP A 662 " --> pdb=" O THR A 658 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 675 Processing helix chain 'A' and resid 684 through 698 removed outlier: 3.716A pdb=" N GLN A 698 " --> pdb=" O GLY A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 711 through 718 Processing helix chain 'A' and resid 729 through 736 Processing helix chain 'A' and resid 744 through 769 removed outlier: 3.824A pdb=" N ILE A 748 " --> pdb=" O ASN A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 774 Processing helix chain 'A' and resid 777 through 786 Processing helix chain 'A' and resid 793 through 805 Processing helix chain 'A' and resid 806 through 812 removed outlier: 3.997A pdb=" N ILE A 810 " --> pdb=" O MET A 806 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 815 No H-bonds generated for 'chain 'A' and resid 813 through 815' Processing helix chain 'A' and resid 836 through 846 removed outlier: 3.675A pdb=" N GLN A 846 " --> pdb=" O MET A 842 " (cutoff:3.500A) Processing helix chain 'A' and resid 847 through 867 Processing helix chain 'A' and resid 869 through 874 removed outlier: 4.038A pdb=" N VAL A 874 " --> pdb=" O PRO A 870 " (cutoff:3.500A) Processing helix chain 'A' and resid 876 through 882 Processing helix chain 'A' and resid 897 through 927 removed outlier: 3.576A pdb=" N ARG A 901 " --> pdb=" O THR A 897 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ALA A 922 " --> pdb=" O VAL A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 933 through 938 Processing helix chain 'A' and resid 941 through 961 Processing helix chain 'A' and resid 963 through 968 Processing helix chain 'A' and resid 974 through 979 removed outlier: 4.071A pdb=" N TRP A 978 " --> pdb=" O LYS A 974 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N PHE A 979 " --> pdb=" O PRO A 975 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 974 through 979' Processing helix chain 'A' and resid 981 through 1002 Processing helix chain 'A' and resid 1005 through 1012 Processing helix chain 'B' and resid 28 through 61 Processing helix chain 'B' and resid 98 through 109 Processing helix chain 'B' and resid 115 through 119 removed outlier: 3.623A pdb=" N ARG B 118 " --> pdb=" O SER B 115 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ASP B 119 " --> pdb=" O ALA B 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 115 through 119' Processing helix chain 'B' and resid 152 through 156 Processing helix chain 'B' and resid 204 through 206 No H-bonds generated for 'chain 'B' and resid 204 through 206' Processing helix chain 'B' and resid 217 through 225 removed outlier: 4.506A pdb=" N GLY B 225 " --> pdb=" O LYS B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 235 Processing helix chain 'B' and resid 246 through 251 removed outlier: 4.075A pdb=" N LEU B 250 " --> pdb=" O TYR B 246 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN B 251 " --> pdb=" O GLY B 247 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 246 through 251' Processing helix chain 'C' and resid 33 through 57 removed outlier: 3.558A pdb=" N SER C 57 " --> pdb=" O LEU C 53 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 166 through 171 removed outlier: 12.013A pdb=" N GLN A 158 " --> pdb=" O LYS A 184 " (cutoff:3.500A) removed outlier: 9.327A pdb=" N LYS A 184 " --> pdb=" O GLN A 158 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N LEU A 160 " --> pdb=" O GLU A 182 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU A 180 " --> pdb=" O ILE A 162 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N THR A 237 " --> pdb=" O ASP A 204 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ASP A 204 " --> pdb=" O THR A 237 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N CYS A 239 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N LYS A 202 " --> pdb=" O CYS A 239 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N GLU A 241 " --> pdb=" O GLY A 200 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N GLY A 200 " --> pdb=" O GLU A 241 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N THR A 243 " --> pdb=" O ALA A 198 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N ALA A 198 " --> pdb=" O THR A 243 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ARG A 245 " --> pdb=" O ILE A 196 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ASP A 192 " --> pdb=" O VAL A 249 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 187 through 189 removed outlier: 4.077A pdb=" N THR A 237 " --> pdb=" O VAL A 189 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N THR A 237 " --> pdb=" O ASP A 204 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ASP A 204 " --> pdb=" O THR A 237 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N CYS A 239 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N LYS A 202 " --> pdb=" O CYS A 239 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N GLU A 241 " --> pdb=" O GLY A 200 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N GLY A 200 " --> pdb=" O GLU A 241 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N THR A 243 " --> pdb=" O ALA A 198 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N ALA A 198 " --> pdb=" O THR A 243 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ARG A 245 " --> pdb=" O ILE A 196 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ASP A 192 " --> pdb=" O VAL A 249 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU A 193 " --> pdb=" O THR A 233 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 346 through 347 removed outlier: 7.615A pdb=" N VAL A 702 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N VAL A 722 " --> pdb=" O VAL A 702 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N VAL A 704 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N MET A 724 " --> pdb=" O VAL A 704 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N THR A 362 " --> pdb=" O ALA A 703 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N ILE A 363 " --> pdb=" O ILE A 604 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 386 through 389 removed outlier: 5.432A pdb=" N VAL A 378 " --> pdb=" O ILE A 582 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N ILE A 582 " --> pdb=" O VAL A 378 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N PHE A 545 " --> pdb=" O VAL A 576 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N LEU A 578 " --> pdb=" O LEU A 543 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N LEU A 543 " --> pdb=" O LEU A 578 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N SER A 580 " --> pdb=" O ARG A 541 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ARG A 541 " --> pdb=" O SER A 580 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LYS A 498 " --> pdb=" O GLN A 479 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLN A 479 " --> pdb=" O LYS A 498 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 386 through 389 removed outlier: 5.432A pdb=" N VAL A 378 " --> pdb=" O ILE A 582 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N ILE A 582 " --> pdb=" O VAL A 378 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N PHE A 575 " --> pdb=" O SER A 509 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ILE A 511 " --> pdb=" O PHE A 575 " (cutoff:3.500A) removed outlier: 8.895A pdb=" N GLY A 577 " --> pdb=" O ILE A 511 " (cutoff:3.500A) removed outlier: 11.286A pdb=" N LEU A 513 " --> pdb=" O GLY A 577 " (cutoff:3.500A) removed outlier: 17.073A pdb=" N MET A 579 " --> pdb=" O LEU A 513 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 652 through 656 Processing sheet with id=AA7, first strand: chain 'A' and resid 888 through 889 Processing sheet with id=AA8, first strand: chain 'B' and resid 77 through 79 Processing sheet with id=AA9, first strand: chain 'B' and resid 87 through 89 removed outlier: 6.226A pdb=" N ILE B 88 " --> pdb=" O GLU B 300 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 123 through 124 Processing sheet with id=AB2, first strand: chain 'B' and resid 208 through 210 505 hydrogen bonds defined for protein. 1455 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: 5.39 Time building geometry restraints manager: 1.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 10130 1.03 - 1.23: 29 1.23 - 1.42: 4250 1.42 - 1.62: 6136 1.62 - 1.82: 90 Bond restraints: 20635 Sorted by residual: bond pdb=" C1 NAG B1103 " pdb=" O5 NAG B1103 " ideal model delta sigma weight residual 1.406 1.431 -0.025 2.00e-02 2.50e+03 1.57e+00 bond pdb=" C1 NAG B1104 " pdb=" O5 NAG B1104 " ideal model delta sigma weight residual 1.406 1.431 -0.025 2.00e-02 2.50e+03 1.54e+00 bond pdb=" C1 NAG B1102 " pdb=" O5 NAG B1102 " ideal model delta sigma weight residual 1.406 1.429 -0.023 2.00e-02 2.50e+03 1.35e+00 bond pdb=" C5 NAG B1103 " pdb=" O5 NAG B1103 " ideal model delta sigma weight residual 1.413 1.436 -0.023 2.00e-02 2.50e+03 1.31e+00 bond pdb=" C5 NAG B1102 " pdb=" O5 NAG B1102 " ideal model delta sigma weight residual 1.413 1.436 -0.023 2.00e-02 2.50e+03 1.30e+00 ... (remaining 20630 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.13: 35477 1.13 - 2.26: 1735 2.26 - 3.39: 99 3.39 - 4.52: 38 4.52 - 5.66: 5 Bond angle restraints: 37354 Sorted by residual: angle pdb=" C ASN A 491 " pdb=" N ARG A 492 " pdb=" CA ARG A 492 " ideal model delta sigma weight residual 121.54 125.84 -4.30 1.91e+00 2.74e-01 5.06e+00 angle pdb=" N ASN B 158 " pdb=" CA ASN B 158 " pdb=" CB ASN B 158 " ideal model delta sigma weight residual 113.65 110.41 3.24 1.47e+00 4.63e-01 4.86e+00 angle pdb=" CB ARG B 27 " pdb=" CG ARG B 27 " pdb=" CD ARG B 27 " ideal model delta sigma weight residual 111.30 116.03 -4.73 2.30e+00 1.89e-01 4.23e+00 angle pdb=" CG ARG B 27 " pdb=" CD ARG B 27 " pdb=" NE ARG B 27 " ideal model delta sigma weight residual 112.00 116.46 -4.46 2.20e+00 2.07e-01 4.11e+00 angle pdb=" CA SER C 57 " pdb=" C SER C 57 " pdb=" O SER C 57 " ideal model delta sigma weight residual 122.27 120.08 2.19 1.16e+00 7.43e-01 3.56e+00 ... (remaining 37349 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 8731 17.70 - 35.41: 812 35.41 - 53.11: 267 53.11 - 70.81: 72 70.81 - 88.52: 14 Dihedral angle restraints: 9896 sinusoidal: 5553 harmonic: 4343 Sorted by residual: dihedral pdb=" CB CYS B 126 " pdb=" SG CYS B 126 " pdb=" SG CYS B 149 " pdb=" CB CYS B 149 " ideal model delta sinusoidal sigma weight residual 93.00 155.99 -62.99 1 1.00e+01 1.00e-02 5.24e+01 dihedral pdb=" CA ASP A 490 " pdb=" C ASP A 490 " pdb=" N ASN A 491 " pdb=" CA ASN A 491 " ideal model delta harmonic sigma weight residual 180.00 156.35 23.65 0 5.00e+00 4.00e-02 2.24e+01 dihedral pdb=" CA LEU C 56 " pdb=" C LEU C 56 " pdb=" N SER C 57 " pdb=" CA SER C 57 " ideal model delta harmonic sigma weight residual 180.00 160.10 19.90 0 5.00e+00 4.00e-02 1.58e+01 ... (remaining 9893 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1117 0.033 - 0.066: 348 0.066 - 0.099: 105 0.099 - 0.132: 55 0.132 - 0.165: 3 Chirality restraints: 1628 Sorted by residual: chirality pdb=" C1 NAG B1102 " pdb=" ND2 ASN B 158 " pdb=" C2 NAG B1102 " pdb=" O5 NAG B1102 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-01 2.50e+01 6.77e-01 chirality pdb=" C1 NAG B1104 " pdb=" ND2 ASN B 265 " pdb=" C2 NAG B1104 " pdb=" O5 NAG B1104 " both_signs ideal model delta sigma weight residual False -2.40 -2.27 -0.13 2.00e-01 2.50e+01 4.45e-01 chirality pdb=" CA ILE A 430 " pdb=" N ILE A 430 " pdb=" C ILE A 430 " pdb=" CB ILE A 430 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.36e-01 ... (remaining 1625 not shown) Planarity restraints: 3050 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 94 " -0.040 5.00e-02 4.00e+02 6.08e-02 5.92e+00 pdb=" N PRO B 95 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO B 95 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 95 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 610 " -0.026 5.00e-02 4.00e+02 4.03e-02 2.59e+00 pdb=" N PRO A 611 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 611 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 611 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 76 " 0.023 5.00e-02 4.00e+02 3.43e-02 1.88e+00 pdb=" N PRO A 77 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 77 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 77 " 0.019 5.00e-02 4.00e+02 ... (remaining 3047 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.15: 876 2.15 - 2.77: 39496 2.77 - 3.38: 58764 3.38 - 3.99: 73461 3.99 - 4.60: 113949 Nonbonded interactions: 286546 Sorted by model distance: nonbonded pdb=" OE1 GLU A 837 " pdb=" H GLU A 837 " model vdw 1.542 2.450 nonbonded pdb=" H VAL A 702 " pdb=" OD2 ASP A 719 " model vdw 1.559 2.450 nonbonded pdb=" H ILE A 195 " pdb=" O ASN A 231 " model vdw 1.583 2.450 nonbonded pdb=" H GLY A1004 " pdb=" OE1 GLU A1008 " model vdw 1.594 2.450 nonbonded pdb=" OE1 GLN B 79 " pdb=" H GLN B 79 " model vdw 1.602 2.450 ... (remaining 286541 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.910 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: 0.090 Extract box with map and model: 0.270 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 18.400 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 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:0.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 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 : 0.002 0.025 10489 Z= 0.100 Angle : 0.495 5.655 14243 Z= 0.245 Chirality : 0.039 0.165 1628 Planarity : 0.003 0.061 1815 Dihedral : 15.336 88.516 4092 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.03 % Favored : 94.89 % Rotamer: Outliers : 0.18 % Allowed : 18.62 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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: 0.47 (0.25), residues: 1291 helix: 2.28 (0.23), residues: 543 sheet: -1.17 (0.42), residues: 156 loop : -1.19 (0.27), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 27 TYR 0.010 0.001 TYR A 859 PHE 0.014 0.001 PHE A 234 TRP 0.011 0.001 TRP B 32 HIS 0.003 0.001 HIS A 388 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.10 (10482) covalent geometry : angle 0.49408 / 0.24 (14226) SS BOND : bond 0.00171 / 0.07 ( 4) SS BOND : angle 0.98839 / 0.55 ( 8) hydrogen bonds : bond 0.14684 / 10.06 ( 493) hydrogen bonds : angle 6.38994 / 4.62 ( 1455) link_NAG-ASN : bond 0.00153 / 0.06 ( 3) link_NAG-ASN : angle 0.66189 / 0.33 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 81 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 83 average time/residue: 0.2528 time to fit residues: 29.1076 Evaluate side-chains 80 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 78 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 ARG Chi-restraints excluded: chain B residue 193 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.0770 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 overall best weight: 0.9740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 158 GLN A 696 GLN A 851 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.106812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.075966 restraints weight = 81085.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.079302 restraints weight = 30235.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.081413 restraints weight = 17444.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.082650 restraints weight = 12860.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.083314 restraints weight = 10848.174| |-----------------------------------------------------------------------------| r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.0596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10489 Z= 0.126 Angle : 0.502 5.451 14243 Z= 0.261 Chirality : 0.040 0.136 1628 Planarity : 0.004 0.052 1815 Dihedral : 5.795 57.878 1660 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.65 % Favored : 94.27 % Rotamer: Outliers : 1.17 % Allowed : 17.72 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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: 0.31 (0.25), residues: 1291 helix: 2.13 (0.22), residues: 555 sheet: -1.34 (0.42), residues: 149 loop : -1.31 (0.27), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 756 TYR 0.011 0.001 TYR A 859 PHE 0.012 0.001 PHE B 108 TRP 0.003 0.000 TRP B 32 HIS 0.003 0.001 HIS A 380 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (10482) covalent geometry : angle 0.50119 / 0.26 (14226) SS BOND : bond 0.00292 / 0.10 ( 4) SS BOND : angle 0.45901 / 0.28 ( 8) hydrogen bonds : bond 0.04650 / 3.14 ( 493) hydrogen bonds : angle 4.86082 / 3.52 ( 1455) link_NAG-ASN : bond 0.00128 / 0.06 ( 3) link_NAG-ASN : angle 0.96603 / 0.49 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 86 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1010 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.7970 (mp0) REVERT: B 266 LEU cc_start: 0.8199 (OUTLIER) cc_final: 0.7985 (mp) outliers start: 13 outliers final: 7 residues processed: 96 average time/residue: 0.2442 time to fit residues: 32.7268 Evaluate side-chains 89 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 80 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 CYS Chi-restraints excluded: chain A residue 610 HIS Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 1010 GLU Chi-restraints excluded: chain B residue 27 ARG Chi-restraints excluded: chain B residue 193 ASN Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 55 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 23 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 117 optimal weight: 4.9990 chunk 112 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 chunk 78 optimal weight: 1.9990 chunk 45 optimal weight: 9.9990 chunk 29 optimal weight: 0.5980 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 158 GLN A 686 GLN A 851 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.105185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.074134 restraints weight = 81856.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.077621 restraints weight = 30265.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.079794 restraints weight = 17257.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.081095 restraints weight = 12557.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.081657 restraints weight = 10517.496| |-----------------------------------------------------------------------------| r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.0844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 10489 Z= 0.192 Angle : 0.522 5.671 14243 Z= 0.275 Chirality : 0.040 0.149 1628 Planarity : 0.004 0.041 1815 Dihedral : 5.822 59.721 1660 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.74 % Favored : 93.18 % Rotamer: Outliers : 1.71 % Allowed : 18.17 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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: 0.04 (0.24), residues: 1291 helix: 1.89 (0.22), residues: 557 sheet: -1.52 (0.41), residues: 149 loop : -1.44 (0.26), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 27 TYR 0.015 0.001 TYR A 859 PHE 0.009 0.001 PHE A 857 TRP 0.004 0.001 TRP A 408 HIS 0.003 0.001 HIS A 610 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.19 (10482) covalent geometry : angle 0.52118 / 0.27 (14226) SS BOND : bond 0.00401 / 0.14 ( 4) SS BOND : angle 0.42030 / 0.26 ( 8) hydrogen bonds : bond 0.04263 / 2.89 ( 493) hydrogen bonds : angle 4.74312 / 3.43 ( 1455) link_NAG-ASN : bond 0.00151 / 0.07 ( 3) link_NAG-ASN : angle 1.19745 / 0.56 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 80 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 266 LEU cc_start: 0.8214 (OUTLIER) cc_final: 0.7989 (mp) outliers start: 19 outliers final: 13 residues processed: 94 average time/residue: 0.2334 time to fit residues: 31.0462 Evaluate side-chains 93 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 79 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 CYS Chi-restraints excluded: chain A residue 443 GLU Chi-restraints excluded: chain A residue 610 HIS Chi-restraints excluded: chain A residue 766 ILE Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 858 SER Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain B residue 27 ARG Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 193 ASN Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain C residue 46 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 121 optimal weight: 1.9990 chunk 39 optimal weight: 9.9990 chunk 34 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 46 optimal weight: 10.0000 chunk 51 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 108 optimal weight: 0.0980 chunk 96 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 158 GLN A 851 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.106382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.075386 restraints weight = 81492.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.078900 restraints weight = 30631.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.081095 restraints weight = 17545.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.082395 restraints weight = 12800.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.082953 restraints weight = 10728.676| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.0988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10489 Z= 0.118 Angle : 0.492 5.350 14243 Z= 0.254 Chirality : 0.040 0.137 1628 Planarity : 0.003 0.038 1815 Dihedral : 5.683 59.778 1660 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 1.35 % Allowed : 18.08 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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: 0.16 (0.24), residues: 1291 helix: 2.02 (0.22), residues: 557 sheet: -1.59 (0.41), residues: 152 loop : -1.37 (0.26), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 27 TYR 0.013 0.001 TYR A 859 PHE 0.011 0.001 PHE B 108 TRP 0.003 0.001 TRP A1006 HIS 0.002 0.001 HIS A 380 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (10482) covalent geometry : angle 0.49132 / 0.25 (14226) SS BOND : bond 0.00289 / 0.10 ( 4) SS BOND : angle 0.35632 / 0.23 ( 8) hydrogen bonds : bond 0.03873 / 2.62 ( 493) hydrogen bonds : angle 4.51358 / 3.26 ( 1455) link_NAG-ASN : bond 0.00135 / 0.06 ( 3) link_NAG-ASN : angle 0.98134 / 0.45 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 88 time to evaluate : 0.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 266 LEU cc_start: 0.8254 (OUTLIER) cc_final: 0.8039 (mp) outliers start: 15 outliers final: 13 residues processed: 100 average time/residue: 0.2479 time to fit residues: 34.7175 Evaluate side-chains 96 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 82 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 346 CYS Chi-restraints excluded: chain A residue 442 SER Chi-restraints excluded: chain A residue 443 GLU Chi-restraints excluded: chain A residue 766 ILE Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 193 ASN Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain C residue 46 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 46 optimal weight: 9.9990 chunk 75 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 124 optimal weight: 4.9990 chunk 76 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 81 optimal weight: 0.6980 chunk 53 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 158 GLN A 851 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.106010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.074810 restraints weight = 82842.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.078380 restraints weight = 30891.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.080647 restraints weight = 17685.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.081979 restraints weight = 12861.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.082689 restraints weight = 10764.309| |-----------------------------------------------------------------------------| r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.1085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10489 Z= 0.142 Angle : 0.495 5.418 14243 Z= 0.257 Chirality : 0.040 0.136 1628 Planarity : 0.003 0.038 1815 Dihedral : 5.486 59.703 1656 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 2.07 % Allowed : 17.72 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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: 0.08 (0.24), residues: 1291 helix: 1.92 (0.22), residues: 560 sheet: -1.60 (0.41), residues: 152 loop : -1.39 (0.26), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 901 TYR 0.020 0.001 TYR A 859 PHE 0.010 0.001 PHE B 108 TRP 0.003 0.001 TRP A1006 HIS 0.009 0.001 HIS A 610 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (10482) covalent geometry : angle 0.49433 / 0.26 (14226) SS BOND : bond 0.00330 / 0.11 ( 4) SS BOND : angle 0.37861 / 0.23 ( 8) hydrogen bonds : bond 0.03789 / 2.57 ( 493) hydrogen bonds : angle 4.46268 / 3.22 ( 1455) link_NAG-ASN : bond 0.00120 / 0.06 ( 3) link_NAG-ASN : angle 1.06275 / 0.50 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 86 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 266 LEU cc_start: 0.8223 (OUTLIER) cc_final: 0.7984 (mp) outliers start: 23 outliers final: 18 residues processed: 105 average time/residue: 0.2430 time to fit residues: 35.3222 Evaluate side-chains 100 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 81 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 346 CYS Chi-restraints excluded: chain A residue 355 GLU Chi-restraints excluded: chain A residue 442 SER Chi-restraints excluded: chain A residue 443 GLU Chi-restraints excluded: chain A residue 528 PHE Chi-restraints excluded: chain A residue 596 CYS Chi-restraints excluded: chain A residue 766 ILE Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 858 SER Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 193 ASN Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain C residue 46 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 102 optimal weight: 1.9990 chunk 125 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 19 optimal weight: 10.0000 chunk 113 optimal weight: 0.8980 chunk 82 optimal weight: 1.9990 chunk 114 optimal weight: 0.0570 chunk 45 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 overall best weight: 1.1904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 158 GLN A 696 GLN A 851 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.105503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.074506 restraints weight = 82551.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.078068 restraints weight = 30583.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.080291 restraints weight = 17370.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.081615 restraints weight = 12606.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.082235 restraints weight = 10522.817| |-----------------------------------------------------------------------------| r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.1176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 10489 Z= 0.132 Angle : 0.490 5.365 14243 Z= 0.254 Chirality : 0.040 0.137 1628 Planarity : 0.004 0.071 1815 Dihedral : 5.417 59.051 1656 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 1.98 % Allowed : 18.08 % Favored : 79.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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: 0.12 (0.24), residues: 1291 helix: 1.95 (0.22), residues: 560 sheet: -1.61 (0.41), residues: 152 loop : -1.36 (0.26), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 756 TYR 0.024 0.001 TYR A 859 PHE 0.010 0.001 PHE B 108 TRP 0.003 0.001 TRP A1006 HIS 0.002 0.001 HIS B 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (10482) covalent geometry : angle 0.48926 / 0.25 (14226) SS BOND : bond 0.00321 / 0.11 ( 4) SS BOND : angle 0.35676 / 0.22 ( 8) hydrogen bonds : bond 0.03740 / 2.52 ( 493) hydrogen bonds : angle 4.38988 / 3.16 ( 1455) link_NAG-ASN : bond 0.00122 / 0.05 ( 3) link_NAG-ASN : angle 1.01258 / 0.48 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 84 time to evaluate : 0.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 266 LEU cc_start: 0.8207 (OUTLIER) cc_final: 0.7973 (mp) outliers start: 22 outliers final: 19 residues processed: 102 average time/residue: 0.2523 time to fit residues: 35.7750 Evaluate side-chains 102 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 82 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 346 CYS Chi-restraints excluded: chain A residue 355 GLU Chi-restraints excluded: chain A residue 442 SER Chi-restraints excluded: chain A residue 443 GLU Chi-restraints excluded: chain A residue 528 PHE Chi-restraints excluded: chain A residue 596 CYS Chi-restraints excluded: chain A residue 766 ILE Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 858 SER Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 193 ASN Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain C residue 46 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 116 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 23 optimal weight: 0.3980 chunk 41 optimal weight: 10.0000 chunk 85 optimal weight: 3.9990 chunk 21 optimal weight: 8.9990 chunk 108 optimal weight: 0.7980 chunk 49 optimal weight: 0.7980 chunk 6 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 158 GLN A 851 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.105176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.073990 restraints weight = 83125.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.077540 restraints weight = 31037.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.079773 restraints weight = 17752.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.081087 restraints weight = 12886.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.081663 restraints weight = 10781.211| |-----------------------------------------------------------------------------| r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.1284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 10489 Z= 0.163 Angle : 0.510 7.709 14243 Z= 0.264 Chirality : 0.040 0.148 1628 Planarity : 0.004 0.066 1815 Dihedral : 5.436 58.939 1656 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 2.07 % Allowed : 17.81 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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: 0.03 (0.24), residues: 1291 helix: 1.87 (0.22), residues: 560 sheet: -1.66 (0.40), residues: 152 loop : -1.40 (0.26), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 756 TYR 0.022 0.001 TYR A 859 PHE 0.008 0.001 PHE B 108 TRP 0.003 0.001 TRP A 408 HIS 0.002 0.001 HIS B 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.16 (10482) covalent geometry : angle 0.50930 / 0.26 (14226) SS BOND : bond 0.00387 / 0.13 ( 4) SS BOND : angle 0.37073 / 0.23 ( 8) hydrogen bonds : bond 0.03815 / 2.58 ( 493) hydrogen bonds : angle 4.41086 / 3.18 ( 1455) link_NAG-ASN : bond 0.00131 / 0.06 ( 3) link_NAG-ASN : angle 1.15546 / 0.56 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 87 time to evaluate : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 973 LEU cc_start: 0.9363 (OUTLIER) cc_final: 0.9116 (mp) REVERT: B 266 LEU cc_start: 0.8248 (OUTLIER) cc_final: 0.8013 (mp) outliers start: 23 outliers final: 21 residues processed: 105 average time/residue: 0.2452 time to fit residues: 35.8094 Evaluate side-chains 106 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 83 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 346 CYS Chi-restraints excluded: chain A residue 355 GLU Chi-restraints excluded: chain A residue 423 PHE Chi-restraints excluded: chain A residue 442 SER Chi-restraints excluded: chain A residue 443 GLU Chi-restraints excluded: chain A residue 528 PHE Chi-restraints excluded: chain A residue 596 CYS Chi-restraints excluded: chain A residue 766 ILE Chi-restraints excluded: chain A residue 794 THR Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 858 SER Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 193 ASN Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain C residue 46 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 47 optimal weight: 4.9990 chunk 124 optimal weight: 2.9990 chunk 79 optimal weight: 0.4980 chunk 44 optimal weight: 0.9990 chunk 96 optimal weight: 0.6980 chunk 61 optimal weight: 5.9990 chunk 13 optimal weight: 6.9990 chunk 7 optimal weight: 4.9990 chunk 76 optimal weight: 0.9990 chunk 34 optimal weight: 4.9990 chunk 122 optimal weight: 0.9980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 158 GLN A 851 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.106083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.075061 restraints weight = 82775.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.078650 restraints weight = 30481.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.080884 restraints weight = 17283.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.082194 restraints weight = 12533.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.082771 restraints weight = 10485.042| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.1322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 10489 Z= 0.110 Angle : 0.482 5.240 14243 Z= 0.248 Chirality : 0.040 0.141 1628 Planarity : 0.003 0.062 1815 Dihedral : 5.339 59.949 1656 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 1.98 % Allowed : 18.35 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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 (0.24), residues: 1291 helix: 2.05 (0.22), residues: 559 sheet: -1.63 (0.43), residues: 142 loop : -1.31 (0.26), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 756 TYR 0.019 0.001 TYR A 859 PHE 0.011 0.001 PHE A 234 TRP 0.004 0.001 TRP A1006 HIS 0.002 0.001 HIS A 388 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 (10482) covalent geometry : angle 0.48183 / 0.25 (14226) SS BOND : bond 0.00289 / 0.10 ( 4) SS BOND : angle 0.34836 / 0.22 ( 8) hydrogen bonds : bond 0.03604 / 2.44 ( 493) hydrogen bonds : angle 4.22997 / 3.04 ( 1455) link_NAG-ASN : bond 0.00159 / 0.07 ( 3) link_NAG-ASN : angle 0.93570 / 0.45 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 86 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 973 LEU cc_start: 0.9471 (OUTLIER) cc_final: 0.9219 (mp) REVERT: B 266 LEU cc_start: 0.8203 (OUTLIER) cc_final: 0.7962 (mp) outliers start: 22 outliers final: 19 residues processed: 104 average time/residue: 0.2421 time to fit residues: 35.3000 Evaluate side-chains 104 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 83 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 346 CYS Chi-restraints excluded: chain A residue 355 GLU Chi-restraints excluded: chain A residue 442 SER Chi-restraints excluded: chain A residue 443 GLU Chi-restraints excluded: chain A residue 528 PHE Chi-restraints excluded: chain A residue 596 CYS Chi-restraints excluded: chain A residue 766 ILE Chi-restraints excluded: chain A residue 794 THR Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 858 SER Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 193 ASN Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain C residue 46 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 93 optimal weight: 0.2980 chunk 19 optimal weight: 0.9990 chunk 83 optimal weight: 0.9980 chunk 54 optimal weight: 0.0970 chunk 47 optimal weight: 0.8980 chunk 90 optimal weight: 3.9990 chunk 110 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 21 optimal weight: 7.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 158 GLN A 851 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.106685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.075700 restraints weight = 82453.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.079294 restraints weight = 30778.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.081527 restraints weight = 17538.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.082851 restraints weight = 12765.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.083564 restraints weight = 10662.280| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.1396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 10489 Z= 0.100 Angle : 0.477 5.156 14243 Z= 0.244 Chirality : 0.040 0.140 1628 Planarity : 0.003 0.062 1815 Dihedral : 5.202 59.920 1656 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 1.80 % Allowed : 18.62 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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: 0.34 (0.24), residues: 1291 helix: 2.16 (0.22), residues: 559 sheet: -1.52 (0.43), residues: 142 loop : -1.27 (0.26), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 827 TYR 0.024 0.001 TYR A 859 PHE 0.010 0.001 PHE B 108 TRP 0.004 0.000 TRP A1006 HIS 0.009 0.001 HIS A 610 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.10 (10482) covalent geometry : angle 0.47634 / 0.24 (14226) SS BOND : bond 0.00230 / 0.08 ( 4) SS BOND : angle 0.36030 / 0.22 ( 8) hydrogen bonds : bond 0.03434 / 2.33 ( 493) hydrogen bonds : angle 4.13635 / 2.97 ( 1455) link_NAG-ASN : bond 0.00165 / 0.07 ( 3) link_NAG-ASN : angle 0.89490 / 0.43 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 89 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 497 MET cc_start: 0.7793 (mtp) cc_final: 0.7396 (mmm) REVERT: A 973 LEU cc_start: 0.9480 (OUTLIER) cc_final: 0.9228 (mp) REVERT: B 266 LEU cc_start: 0.8183 (OUTLIER) cc_final: 0.7934 (mp) outliers start: 20 outliers final: 15 residues processed: 104 average time/residue: 0.2548 time to fit residues: 37.0058 Evaluate side-chains 104 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 87 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 528 PHE Chi-restraints excluded: chain A residue 596 CYS Chi-restraints excluded: chain A residue 766 ILE Chi-restraints excluded: chain A residue 794 THR Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 858 SER Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 193 ASN Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain C residue 46 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 26 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 47 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 118 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 158 GLN A 419 ASN A 851 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.105757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.074599 restraints weight = 82793.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.078165 restraints weight = 30849.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.080391 restraints weight = 17586.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.081741 restraints weight = 12832.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.082450 restraints weight = 10701.228| |-----------------------------------------------------------------------------| r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.1442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 10489 Z= 0.144 Angle : 0.497 5.382 14243 Z= 0.256 Chirality : 0.040 0.144 1628 Planarity : 0.004 0.070 1815 Dihedral : 5.231 59.789 1656 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 1.62 % Allowed : 18.79 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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: 0.28 (0.24), residues: 1291 helix: 2.07 (0.22), residues: 559 sheet: -1.44 (0.44), residues: 136 loop : -1.31 (0.26), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 756 TYR 0.023 0.001 TYR A 859 PHE 0.008 0.001 PHE B 108 TRP 0.003 0.001 TRP A1006 HIS 0.002 0.001 HIS B 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 (10482) covalent geometry : angle 0.49617 / 0.26 (14226) SS BOND : bond 0.00356 / 0.12 ( 4) SS BOND : angle 0.36108 / 0.22 ( 8) hydrogen bonds : bond 0.03562 / 2.41 ( 493) hydrogen bonds : angle 4.20686 / 3.03 ( 1455) link_NAG-ASN : bond 0.00105 / 0.05 ( 3) link_NAG-ASN : angle 1.07081 / 0.52 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 84 time to evaluate : 0.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 973 LEU cc_start: 0.9461 (OUTLIER) cc_final: 0.9206 (mp) outliers start: 18 outliers final: 16 residues processed: 98 average time/residue: 0.2484 time to fit residues: 33.7876 Evaluate side-chains 101 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 84 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 528 PHE Chi-restraints excluded: chain A residue 596 CYS Chi-restraints excluded: chain A residue 766 ILE Chi-restraints excluded: chain A residue 794 THR Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 858 SER Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 193 ASN Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain C residue 46 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 42 optimal weight: 7.9990 chunk 15 optimal weight: 10.0000 chunk 50 optimal weight: 0.9980 chunk 54 optimal weight: 0.7980 chunk 111 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 158 GLN A 851 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.106231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.075133 restraints weight = 82971.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.078695 restraints weight = 30558.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.080948 restraints weight = 17459.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.082269 restraints weight = 12680.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.082930 restraints weight = 10615.260| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.1469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10489 Z= 0.115 Angle : 0.487 5.268 14243 Z= 0.250 Chirality : 0.040 0.144 1628 Planarity : 0.004 0.071 1815 Dihedral : 5.221 59.696 1656 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 1.71 % Allowed : 18.97 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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: 0.31 (0.24), residues: 1291 helix: 2.13 (0.22), residues: 559 sheet: -1.52 (0.43), residues: 142 loop : -1.29 (0.26), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 827 TYR 0.022 0.001 TYR A 859 PHE 0.009 0.001 PHE B 108 TRP 0.003 0.001 TRP A1006 HIS 0.011 0.001 HIS A 610 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.11 (10482) covalent geometry : angle 0.48636 / 0.25 (14226) SS BOND : bond 0.00287 / 0.10 ( 4) SS BOND : angle 0.34705 / 0.22 ( 8) hydrogen bonds : bond 0.03494 / 2.37 ( 493) hydrogen bonds : angle 4.14127 / 2.97 ( 1455) link_NAG-ASN : bond 0.00151 / 0.07 ( 3) link_NAG-ASN : angle 0.97508 / 0.48 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3412.80 seconds wall clock time: 58 minutes 56.21 seconds (3536.21 seconds total)