Starting phenix.real_space_refine on Sun Sep 13 06:49:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9roi_54120/09_2026/9roi_54120_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9roi_54120/09_2026/9roi_54120.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9roi_54120/09_2026/9roi_54120.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9roi_54120/09_2026/9roi_54120.map" model { file = "/net/cci-nas-00/data/ceres_data/9roi_54120/09_2026/9roi_54120_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9roi_54120/09_2026/9roi_54120_trim.cif" } resolution = 2.94 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.020 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: 7 Type Number sf(0) Gaussians K 2 8.98 5 P 1 5.49 5 S 61 5.16 5 C 6636 2.51 5 N 1711 2.21 5 O 1942 1.98 5 H 10241 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 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: 20594 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 15371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 992, 15371 Classifications: {'peptide': 992} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 41, 'TRANS': 950} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PHD:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 4491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 4491 Classifications: {'peptide': 277} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 256} Chain: "C" Number of atoms: 604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 604 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 1, 'TRANS': 35} Chain: "A" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 86 Unusual residues: {' K': 2, 'CLR': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 3.46, per 1000 atoms: 0.17 Number of scatterers: 20594 At special positions: 0 Unit cell: (93.165, 84.4696, 176.392, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) K 2 19.00 S 61 16.00 P 1 15.00 O 1942 8.00 N 1711 7.00 C 6636 6.00 H 10241 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 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 B 401 " - " ASN B 158 " " NAG B 402 " - " ASN B 193 " " NAG B 403 " - " ASN B 265 " Time building additional restraints: 2.02 Conformation dependent library (CDL) restraints added in 592.2 milliseconds 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2410 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 10 sheets defined 52.5% alpha, 15.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 37 through 45 removed outlier: 3.998A pdb=" N VAL A 41 " --> pdb=" O SER A 37 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N CYS A 42 " --> pdb=" O VAL A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 66 Processing helix chain 'A' and resid 77 through 86 Processing helix chain 'A' and resid 89 through 112 Processing helix chain 'A' and resid 117 through 141 Processing helix chain 'A' and resid 147 through 154 removed outlier: 3.671A pdb=" N MET A 154 " --> pdb=" O SER A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 175 Processing helix chain 'A' and resid 251 through 254 Processing helix chain 'A' and resid 255 through 266 Processing helix chain 'A' and resid 272 through 303 Processing helix chain 'A' and resid 306 through 322 Processing helix chain 'A' and resid 325 through 344 Processing helix chain 'A' and resid 350 through 357 removed outlier: 4.158A pdb=" N VAL A 354 " --> pdb=" O ASN A 350 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N GLU A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 360 No H-bonds generated for 'chain 'A' and resid 358 through 360' Processing helix chain 'A' and resid 405 through 418 removed outlier: 3.680A pdb=" N VAL A 409 " --> pdb=" O SER A 405 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N CYS A 418 " --> pdb=" O ILE A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 455 Processing helix chain 'A' and resid 456 through 464 removed outlier: 3.821A pdb=" N MET A 460 " --> pdb=" O SER A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 507 Processing helix chain 'A' and resid 521 through 538 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 662 removed outlier: 3.860A 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: 3.595A pdb=" N GLN A 698 " --> pdb=" O GLY A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 710 No H-bonds generated for 'chain 'A' and resid 708 through 710' Processing helix chain 'A' and resid 711 through 718 Processing helix chain 'A' and resid 729 through 736 Processing helix chain 'A' and resid 745 through 772 removed outlier: 4.263A pdb=" N VAL A 749 " --> pdb=" O PHE A 745 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR A 750 " --> pdb=" O ALA A 746 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE A 759 " --> pdb=" O GLY A 755 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TYR A 768 " --> pdb=" O LYS A 764 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER A 772 " --> pdb=" O TYR A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 772 through 786 removed outlier: 3.507A pdb=" N GLU A 776 " --> pdb=" O SER A 772 " (cutoff:3.500A) Proline residue: A 779 - end of helix Processing helix chain 'A' and resid 793 through 802 Processing helix chain 'A' and resid 805 through 812 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 820 through 824 Processing helix chain 'A' and resid 836 through 846 Processing helix chain 'A' and resid 846 through 867 removed outlier: 3.512A pdb=" N ILE A 850 " --> pdb=" O GLN A 846 " (cutoff:3.500A) Processing helix chain 'A' and resid 869 through 873 Processing helix chain 'A' and resid 876 through 881 Processing helix chain 'A' and resid 897 through 928 removed outlier: 3.873A 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 980 Processing helix chain 'A' and resid 981 through 1002 Processing helix chain 'A' and resid 1005 through 1012 Processing helix chain 'B' and resid 30 through 60 removed outlier: 4.042A pdb=" N LYS B 34 " --> pdb=" O GLY B 30 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLY B 44 " --> pdb=" O VAL B 40 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N THR B 60 " --> pdb=" O VAL B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 73 removed outlier: 3.586A pdb=" N ALA B 73 " --> pdb=" O ASP B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 110 removed outlier: 4.064A pdb=" N TYR B 98 " --> pdb=" O ASP B 94 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ALA B 100 " --> pdb=" O LYS B 96 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N TYR B 101 " --> pdb=" O SER B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 118 removed outlier: 6.351A pdb=" N ASP B 114 " --> pdb=" O LYS B 111 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N SER B 115 " --> pdb=" O TYR B 112 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ARG B 118 " --> pdb=" O SER B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 157 Processing helix chain 'B' and resid 160 through 166 Processing helix chain 'B' and resid 215 through 219 Processing helix chain 'B' and resid 241 through 243 No H-bonds generated for 'chain 'B' and resid 241 through 243' Processing helix chain 'B' and resid 246 through 251 removed outlier: 4.007A pdb=" N LEU B 250 " --> pdb=" O TYR B 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 30 Processing helix chain 'C' and resid 32 through 57 Processing sheet with id=AA1, first strand: chain 'A' and resid 166 through 170 removed outlier: 4.777A pdb=" N LEU A 160 " --> pdb=" O GLU A 182 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N LEU A 180 " --> pdb=" O ILE A 162 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N CYS A 239 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N LYS A 202 " --> pdb=" O CYS A 239 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N GLU A 241 " --> pdb=" O GLY A 200 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N GLY A 200 " --> pdb=" O GLU A 241 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N THR A 243 " --> pdb=" O ALA A 198 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N ALA A 198 " --> pdb=" O THR A 243 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ARG A 245 " --> pdb=" O ILE A 196 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ASP A 192 " --> pdb=" O VAL A 249 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ASN A 205 " --> pdb=" O GLU A 213 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N GLU A 213 " --> pdb=" O ASN A 205 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 166 through 170 removed outlier: 4.777A pdb=" N LEU A 160 " --> pdb=" O GLU A 182 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N LEU A 180 " --> pdb=" O ILE A 162 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N CYS A 239 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N LYS A 202 " --> pdb=" O CYS A 239 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N GLU A 241 " --> pdb=" O GLY A 200 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N GLY A 200 " --> pdb=" O GLU A 241 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N THR A 243 " --> pdb=" O ALA A 198 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N ALA A 198 " --> pdb=" O THR A 243 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ARG A 245 " --> pdb=" O ILE A 196 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ASP A 192 " --> pdb=" O VAL A 249 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 346 through 347 removed outlier: 6.792A pdb=" N VAL A 702 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 8.207A pdb=" N VAL A 722 " --> pdb=" O VAL A 702 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N VAL A 704 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N MET A 724 " --> pdb=" O VAL A 704 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N GLY A 706 " --> pdb=" O MET A 724 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N THR A 362 " --> pdb=" O ALA A 703 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N THR A 705 " --> pdb=" O THR A 362 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N CYS A 364 " --> pdb=" O THR A 705 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N VAL A 603 " --> pdb=" O ILE A 678 " (cutoff:3.500A) removed outlier: 8.682A pdb=" N PHE A 680 " --> pdb=" O VAL A 603 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N MET A 605 " --> pdb=" O PHE A 680 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N ILE A 655 " --> pdb=" O ALA A 681 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 386 through 389 removed outlier: 5.218A pdb=" N VAL A 378 " --> pdb=" O ILE A 582 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N ILE A 582 " --> pdb=" O VAL A 378 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N HIS A 380 " --> pdb=" O SER A 580 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N PHE A 545 " --> pdb=" O VAL A 576 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N TYR A 493 " --> pdb=" O LEU A 550 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N LEU A 480 " --> pdb=" O GLU A 469 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N GLU A 469 " --> pdb=" O LEU A 480 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ILE A 482 " --> pdb=" O VAL A 467 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 386 through 389 removed outlier: 5.218A pdb=" N VAL A 378 " --> pdb=" O ILE A 582 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N ILE A 582 " --> pdb=" O VAL A 378 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N HIS A 380 " --> pdb=" O SER A 580 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N CYS A 508 " --> pdb=" O LEU A 573 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N PHE A 575 " --> pdb=" O CYS A 508 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N THR A 510 " --> pdb=" O PHE A 575 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N GLY A 577 " --> pdb=" O THR A 510 " (cutoff:3.500A) removed outlier: 9.161A pdb=" N LEU A 512 " --> pdb=" O GLY A 577 " (cutoff:3.500A) removed outlier: 11.999A pdb=" N MET A 579 " --> pdb=" O LEU A 512 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 422 through 423 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 90 Processing sheet with id=AB1, first strand: chain 'B' and resid 123 through 124 546 hydrogen bonds defined for protein. 1524 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: 5.12 Time building geometry restraints manager: 2.62 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: 10215 1.03 - 1.23: 32 1.23 - 1.42: 4276 1.42 - 1.62: 6196 1.62 - 1.81: 91 Bond restraints: 20810 Sorted by residual: bond pdb=" OD1 PHD A 366 " pdb=" P PHD A 366 " ideal model delta sigma weight residual 1.816 1.781 0.035 2.00e-02 2.50e+03 2.98e+00 bond pdb=" N LYS A 367 " pdb=" CA LYS A 367 " ideal model delta sigma weight residual 1.458 1.487 -0.029 1.90e-02 2.77e+03 2.37e+00 bond pdb=" CG PHD A 366 " pdb=" OD2 PHD A 366 " ideal model delta sigma weight residual 1.218 1.249 -0.031 2.00e-02 2.50e+03 2.34e+00 bond pdb=" CG1 ILE A 504 " pdb=" CD1 ILE A 504 " ideal model delta sigma weight residual 1.513 1.455 0.058 3.90e-02 6.57e+02 2.20e+00 bond pdb=" C PHD A 366 " pdb=" O PHD A 366 " ideal model delta sigma weight residual 1.231 1.258 -0.027 2.00e-02 2.50e+03 1.85e+00 ... (remaining 20805 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.03: 37666 7.03 - 14.05: 5 14.05 - 21.08: 0 21.08 - 28.11: 0 28.11 - 35.13: 3 Bond angle restraints: 37674 Sorted by residual: angle pdb=" CB MET B 121 " pdb=" CA MET B 121 " pdb=" HA MET B 121 " ideal model delta sigma weight residual 109.00 73.87 35.13 3.00e+00 1.11e-01 1.37e+02 angle pdb=" C MET B 121 " pdb=" CA MET B 121 " pdb=" HA MET B 121 " ideal model delta sigma weight residual 110.00 75.46 34.54 3.00e+00 1.11e-01 1.33e+02 angle pdb=" N MET B 121 " pdb=" CA MET B 121 " pdb=" HA MET B 121 " ideal model delta sigma weight residual 110.00 75.51 34.49 3.00e+00 1.11e-01 1.32e+02 angle pdb=" CG PHD A 366 " pdb=" OD1 PHD A 366 " pdb=" P PHD A 366 " ideal model delta sigma weight residual 125.58 116.20 9.38 3.00e+00 1.11e-01 9.77e+00 angle pdb=" OD1 PHD A 366 " pdb=" CG PHD A 366 " pdb=" OD2 PHD A 366 " ideal model delta sigma weight residual 126.03 117.36 8.67 3.00e+00 1.11e-01 8.36e+00 ... (remaining 37669 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 8856 17.75 - 35.50: 773 35.50 - 53.25: 256 53.25 - 71.00: 76 71.00 - 88.76: 14 Dihedral angle restraints: 9975 sinusoidal: 5603 harmonic: 4372 Sorted by residual: dihedral pdb=" CA PHE B 295 " pdb=" C PHE B 295 " pdb=" N ASP B 296 " pdb=" CA ASP B 296 " ideal model delta harmonic sigma weight residual 180.00 157.58 22.42 0 5.00e+00 4.00e-02 2.01e+01 dihedral pdb=" CA ASP B 222 " pdb=" C ASP B 222 " pdb=" N LYS B 223 " pdb=" CA LYS B 223 " ideal model delta harmonic sigma weight residual 180.00 157.70 22.30 0 5.00e+00 4.00e-02 1.99e+01 dihedral pdb=" CA ASN B 205 " pdb=" C ASN B 205 " pdb=" N PRO B 206 " pdb=" CA PRO B 206 " ideal model delta harmonic sigma weight residual 180.00 -157.89 -22.11 0 5.00e+00 4.00e-02 1.96e+01 ... (remaining 9972 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 1509 0.074 - 0.149: 128 0.149 - 0.223: 1 0.223 - 0.297: 0 0.297 - 0.372: 1 Chirality restraints: 1639 Sorted by residual: chirality pdb=" CA MET B 121 " pdb=" N MET B 121 " pdb=" C MET B 121 " pdb=" CB MET B 121 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.45e+00 chirality pdb=" CA PRO B 206 " pdb=" N PRO B 206 " pdb=" C PRO B 206 " pdb=" CB PRO B 206 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.53e-01 chirality pdb=" C1 NAG B 401 " pdb=" ND2 ASN B 158 " pdb=" C2 NAG B 401 " pdb=" O5 NAG B 401 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-01 2.50e+01 5.25e-01 ... (remaining 1636 not shown) Planarity restraints: 3072 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHD A 366 " 0.025 2.00e-02 2.50e+03 5.00e-02 2.50e+01 pdb=" C PHD A 366 " -0.087 2.00e-02 2.50e+03 pdb=" O PHD A 366 " 0.032 2.00e-02 2.50e+03 pdb=" N LYS A 367 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHD A 366 " 0.009 2.00e-02 2.50e+03 1.71e-02 2.91e+00 pdb=" N LYS A 367 " -0.029 2.00e-02 2.50e+03 pdb=" CA LYS A 367 " 0.007 2.00e-02 2.50e+03 pdb=" H LYS A 367 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 54 " 0.008 2.00e-02 2.50e+03 1.66e-02 2.76e+00 pdb=" C ILE C 54 " -0.029 2.00e-02 2.50e+03 pdb=" O ILE C 54 " 0.011 2.00e-02 2.50e+03 pdb=" N VAL C 55 " 0.010 2.00e-02 2.50e+03 ... (remaining 3069 not shown) Histogram of nonbonded interaction distances: 1.45 - 2.19: 1295 2.19 - 2.93: 55780 2.93 - 3.67: 76266 3.67 - 4.40: 120176 4.40 - 5.14: 189328 Nonbonded interactions: 442845 Sorted by model distance: nonbonded pdb=" OE1 GLN A 686 " pdb=" H GLN A 686 " model vdw 1.454 2.450 nonbonded pdb=" OE1 GLU A 352 " pdb=" H GLU A 352 " model vdw 1.496 2.450 nonbonded pdb=" O LEU B 153 " pdb=" HG SER B 160 " model vdw 1.581 2.450 nonbonded pdb=" OE2 GLU A 815 " pdb=" HZ3 LYS A 928 " model vdw 1.593 2.450 nonbonded pdb=" H SER A 684 " pdb=" OE1 GLN A 687 " model vdw 1.597 2.450 ... (remaining 442840 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.560 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: 0.140 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 20.430 Find NCS groups from input model: 0.070 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:6.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 10575 Z= 0.130 Angle : 0.578 9.379 14357 Z= 0.289 Chirality : 0.041 0.372 1639 Planarity : 0.003 0.050 1829 Dihedral : 15.433 88.756 4132 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 1.52 % Allowed : 15.43 % Favored : 83.05 % 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: -0.56 (0.23), residues: 1297 helix: 0.04 (0.21), residues: 595 sheet: -0.90 (0.48), residues: 117 loop : -0.54 (0.26), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 290 TYR 0.015 0.001 TYR A 859 PHE 0.020 0.001 PHE A 313 TRP 0.013 0.001 TRP A 408 HIS 0.001 0.000 HIS A 483 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (10569) covalent geometry : angle 0.57741 / 0.29 (14342) SS BOND : bond 0.00067 / 0.03 ( 3) SS BOND : angle 0.82857 / 0.47 ( 6) hydrogen bonds : bond 0.14371 / 9.40 ( 523) hydrogen bonds : angle 7.21092 / 5.12 ( 1524) link_NAG-ASN : bond 0.00090 / 0.04 ( 3) link_NAG-ASN : angle 1.14303 / 0.59 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 67 time to evaluate : 0.589 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 94 ASP cc_start: 0.8969 (t0) cc_final: 0.8604 (t0) outliers start: 17 outliers final: 15 residues processed: 82 average time/residue: 0.8600 time to fit residues: 79.0139 Evaluate side-chains 75 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 60 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 CYS Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 476 ASN Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 732 SER Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 858 SER Chi-restraints excluded: chain B residue 158 ASN Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 214 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 98 optimal weight: 0.0270 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 55 optimal weight: 50.0000 chunk 35 optimal weight: 7.9990 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 491 ASN A 518 GLN B 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.150555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.092023 restraints weight = 55685.717| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 3.22 r_work: 0.3152 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.0581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10575 Z= 0.120 Angle : 0.545 7.564 14357 Z= 0.282 Chirality : 0.042 0.348 1639 Planarity : 0.004 0.056 1829 Dihedral : 6.772 55.775 1689 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.87 % Allowed : 15.34 % Favored : 82.78 % 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 (0.23), residues: 1297 helix: 0.69 (0.21), residues: 589 sheet: -1.05 (0.51), residues: 107 loop : -0.64 (0.25), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 136 TYR 0.015 0.001 TYR A 859 PHE 0.015 0.001 PHE B 38 TRP 0.008 0.001 TRP A 880 HIS 0.002 0.001 HIS A 675 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (10569) covalent geometry : angle 0.54352 / 0.28 (14342) SS BOND : bond 0.00102 / 0.05 ( 3) SS BOND : angle 0.92524 / 0.53 ( 6) hydrogen bonds : bond 0.04447 / 3.01 ( 523) hydrogen bonds : angle 5.24874 / 3.72 ( 1524) link_NAG-ASN : bond 0.00118 / 0.06 ( 3) link_NAG-ASN : angle 1.38585 / 0.69 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 68 time to evaluate : 0.562 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 94 ASP cc_start: 0.8916 (t0) cc_final: 0.8639 (t0) outliers start: 21 outliers final: 15 residues processed: 86 average time/residue: 0.7764 time to fit residues: 75.8138 Evaluate side-chains 79 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 64 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 388 HIS Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 476 ASN Chi-restraints excluded: chain A residue 518 GLN Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 139 PHE Chi-restraints excluded: chain B residue 158 ASN Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 214 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 31 optimal weight: 1.9990 chunk 92 optimal weight: 0.5980 chunk 116 optimal weight: 1.9990 chunk 3 optimal weight: 9.9990 chunk 19 optimal weight: 8.9990 chunk 109 optimal weight: 1.9990 chunk 43 optimal weight: 20.0000 chunk 85 optimal weight: 2.9990 chunk 117 optimal weight: 0.6980 chunk 122 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 374 ASN A 491 ASN B 82 GLN B 163 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.151584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.092881 restraints weight = 55649.391| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 3.22 r_work: 0.3139 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.0807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10575 Z= 0.141 Angle : 0.544 6.992 14357 Z= 0.281 Chirality : 0.042 0.355 1639 Planarity : 0.004 0.045 1829 Dihedral : 6.553 57.931 1683 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.14 % Allowed : 15.34 % Favored : 82.52 % 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: -0.06 (0.23), residues: 1297 helix: 0.82 (0.21), residues: 590 sheet: -1.07 (0.51), residues: 107 loop : -0.62 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 136 TYR 0.016 0.001 TYR A 859 PHE 0.094 0.002 PHE B 139 TRP 0.006 0.001 TRP A 977 HIS 0.003 0.000 HIS A 483 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (10569) covalent geometry : angle 0.54235 / 0.28 (14342) SS BOND : bond 0.00092 / 0.04 ( 3) SS BOND : angle 1.00057 / 0.58 ( 6) hydrogen bonds : bond 0.04026 / 2.75 ( 523) hydrogen bonds : angle 4.99579 / 3.55 ( 1524) link_NAG-ASN : bond 0.00047 / 0.02 ( 3) link_NAG-ASN : angle 1.37753 / 0.67 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 68 time to evaluate : 0.550 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: B 94 ASP cc_start: 0.8930 (t0) cc_final: 0.8658 (t0) outliers start: 24 outliers final: 15 residues processed: 85 average time/residue: 0.7846 time to fit residues: 75.7603 Evaluate side-chains 78 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 63 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 476 ASN Chi-restraints excluded: chain A residue 518 GLN Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 139 PHE Chi-restraints excluded: chain B residue 158 ASN Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 214 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 118 optimal weight: 6.9990 chunk 37 optimal weight: 30.0000 chunk 9 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 35 optimal weight: 6.9990 chunk 14 optimal weight: 20.0000 chunk 50 optimal weight: 30.0000 chunk 48 optimal weight: 8.9990 chunk 51 optimal weight: 20.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 491 ASN A 518 GLN B 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.147206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.087695 restraints weight = 56561.644| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 3.22 r_work: 0.3070 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.1116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 10575 Z= 0.315 Angle : 0.617 6.230 14357 Z= 0.324 Chirality : 0.046 0.366 1639 Planarity : 0.004 0.047 1829 Dihedral : 6.881 59.395 1683 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 2.41 % Allowed : 16.50 % Favored : 81.09 % 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: -0.38 (0.23), residues: 1297 helix: 0.55 (0.21), residues: 591 sheet: -1.08 (0.51), residues: 107 loop : -0.83 (0.25), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 901 TYR 0.023 0.002 TYR A 859 PHE 0.072 0.002 PHE B 139 TRP 0.010 0.001 TRP A 977 HIS 0.004 0.001 HIS A 675 Details of bonding type rmsd/Z covalent geometry : bond 0.00712 / 0.32 (10569) covalent geometry : angle 0.61563 / 0.32 (14342) SS BOND : bond 0.00223 / 0.11 ( 3) SS BOND : angle 1.21917 / 0.71 ( 6) hydrogen bonds : bond 0.04182 / 2.87 ( 523) hydrogen bonds : angle 5.08019 / 3.63 ( 1524) link_NAG-ASN : bond 0.00292 / 0.15 ( 3) link_NAG-ASN : angle 1.28635 / 0.63 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 63 time to evaluate : 0.525 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: B 94 ASP cc_start: 0.9029 (t0) cc_final: 0.8738 (t0) outliers start: 27 outliers final: 17 residues processed: 82 average time/residue: 0.7287 time to fit residues: 68.2526 Evaluate side-chains 76 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 59 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 CYS Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 476 ASN Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 711 ASP Chi-restraints excluded: chain A residue 748 ILE Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 158 ASN Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain C residue 49 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 72 optimal weight: 0.6980 chunk 59 optimal weight: 5.9990 chunk 52 optimal weight: 50.0000 chunk 85 optimal weight: 0.6980 chunk 86 optimal weight: 0.6980 chunk 47 optimal weight: 30.0000 chunk 2 optimal weight: 7.9990 chunk 106 optimal weight: 2.9990 chunk 4 optimal weight: 7.9990 chunk 113 optimal weight: 0.9990 chunk 17 optimal weight: 30.0000 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 491 ASN B 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.149305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.090443 restraints weight = 55423.637| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 3.21 r_work: 0.3126 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.1163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 10575 Z= 0.129 Angle : 0.537 6.286 14357 Z= 0.276 Chirality : 0.042 0.354 1639 Planarity : 0.003 0.031 1829 Dihedral : 6.502 59.557 1681 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.78 % Allowed : 16.86 % Favored : 81.36 % 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 (0.23), residues: 1297 helix: 0.76 (0.21), residues: 593 sheet: -1.11 (0.51), residues: 107 loop : -0.73 (0.25), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 901 TYR 0.015 0.001 TYR A 859 PHE 0.020 0.001 PHE B 139 TRP 0.007 0.001 TRP A 880 HIS 0.004 0.001 HIS A 483 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (10569) covalent geometry : angle 0.53584 / 0.28 (14342) SS BOND : bond 0.00061 / 0.03 ( 3) SS BOND : angle 0.96123 / 0.55 ( 6) hydrogen bonds : bond 0.03734 / 2.57 ( 523) hydrogen bonds : angle 4.76802 / 3.40 ( 1524) link_NAG-ASN : bond 0.00092 / 0.05 ( 3) link_NAG-ASN : angle 1.32432 / 0.61 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 64 time to evaluate : 0.547 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 57 MET cc_start: 0.8663 (ttp) cc_final: 0.8326 (ttp) REVERT: B 94 ASP cc_start: 0.9006 (t0) cc_final: 0.8721 (t0) outliers start: 20 outliers final: 14 residues processed: 79 average time/residue: 0.8355 time to fit residues: 74.5048 Evaluate side-chains 73 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 59 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 TYR Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 476 ASN Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 139 PHE Chi-restraints excluded: chain B residue 158 ASN Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 288 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 86 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 29 optimal weight: 0.6980 chunk 48 optimal weight: 7.9990 chunk 71 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 491 ASN B 82 GLN B 140 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.149714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.090314 restraints weight = 55756.163| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 3.22 r_work: 0.3095 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.1302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 10575 Z= 0.202 Angle : 0.554 6.820 14357 Z= 0.287 Chirality : 0.043 0.361 1639 Planarity : 0.003 0.033 1829 Dihedral : 6.491 58.612 1679 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 2.32 % Allowed : 16.86 % Favored : 80.82 % 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 (0.23), residues: 1297 helix: 0.77 (0.21), residues: 595 sheet: -1.08 (0.52), residues: 107 loop : -0.75 (0.25), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 901 TYR 0.019 0.001 TYR A 859 PHE 0.016 0.001 PHE A 913 TRP 0.008 0.001 TRP A 408 HIS 0.003 0.001 HIS A 483 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.20 (10569) covalent geometry : angle 0.55333 / 0.29 (14342) SS BOND : bond 0.00101 / 0.05 ( 3) SS BOND : angle 1.06979 / 0.62 ( 6) hydrogen bonds : bond 0.03734 / 2.57 ( 523) hydrogen bonds : angle 4.77356 / 3.42 ( 1524) link_NAG-ASN : bond 0.00131 / 0.07 ( 3) link_NAG-ASN : angle 1.14158 / 0.57 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 59 time to evaluate : 0.355 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 497 MET cc_start: 0.4759 (tmt) cc_final: 0.4456 (tpt) outliers start: 26 outliers final: 18 residues processed: 79 average time/residue: 0.6646 time to fit residues: 60.5027 Evaluate side-chains 77 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 59 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 TYR Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 476 ASN Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 711 ASP Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 139 PHE Chi-restraints excluded: chain B residue 141 HIS Chi-restraints excluded: chain B residue 158 ASN Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain C residue 49 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 43 optimal weight: 40.0000 chunk 71 optimal weight: 3.9990 chunk 19 optimal weight: 20.0000 chunk 55 optimal weight: 10.0000 chunk 82 optimal weight: 0.9990 chunk 51 optimal weight: 20.0000 chunk 50 optimal weight: 6.9990 chunk 102 optimal weight: 0.9990 chunk 12 optimal weight: 10.0000 chunk 8 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 491 ASN B 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.148776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.089429 restraints weight = 55797.630| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 3.23 r_work: 0.3088 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.1394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 10575 Z= 0.209 Angle : 0.559 6.744 14357 Z= 0.290 Chirality : 0.043 0.358 1639 Planarity : 0.003 0.033 1829 Dihedral : 6.510 57.966 1679 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.14 % Allowed : 17.22 % Favored : 80.64 % 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: -0.17 (0.23), residues: 1297 helix: 0.75 (0.21), residues: 595 sheet: -1.09 (0.52), residues: 107 loop : -0.75 (0.25), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 901 TYR 0.019 0.001 TYR A 859 PHE 0.017 0.001 PHE A 913 TRP 0.009 0.001 TRP A 408 HIS 0.003 0.001 HIS A 483 Details of bonding type rmsd/Z covalent geometry : bond 0.00475 / 0.21 (10569) covalent geometry : angle 0.55844 / 0.29 (14342) SS BOND : bond 0.00106 / 0.05 ( 3) SS BOND : angle 1.08542 / 0.62 ( 6) hydrogen bonds : bond 0.03713 / 2.56 ( 523) hydrogen bonds : angle 4.74754 / 3.41 ( 1524) link_NAG-ASN : bond 0.00135 / 0.07 ( 3) link_NAG-ASN : angle 1.11171 / 0.54 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 58 time to evaluate : 0.566 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 outliers start: 24 outliers final: 19 residues processed: 75 average time/residue: 0.7057 time to fit residues: 60.8747 Evaluate side-chains 77 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 58 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 TYR Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 476 ASN Chi-restraints excluded: chain A residue 491 ASN Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 748 ILE Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 139 PHE Chi-restraints excluded: chain B residue 158 ASN Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain C residue 49 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 91 optimal weight: 3.9990 chunk 115 optimal weight: 0.0970 chunk 63 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 98 optimal weight: 0.8980 chunk 43 optimal weight: 30.0000 chunk 127 optimal weight: 1.9990 chunk 39 optimal weight: 40.0000 chunk 27 optimal weight: 1.9990 chunk 46 optimal weight: 30.0000 chunk 117 optimal weight: 1.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 491 ASN B 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.149964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.090845 restraints weight = 55601.970| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 3.23 r_work: 0.3105 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.1433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10575 Z= 0.148 Angle : 0.540 6.804 14357 Z= 0.279 Chirality : 0.042 0.358 1639 Planarity : 0.003 0.032 1829 Dihedral : 6.410 57.096 1679 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.05 % Allowed : 17.22 % Favored : 80.73 % 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: -0.11 (0.23), residues: 1297 helix: 0.83 (0.21), residues: 595 sheet: -1.07 (0.52), residues: 107 loop : -0.74 (0.25), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 492 TYR 0.016 0.001 TYR A 859 PHE 0.019 0.001 PHE A 313 TRP 0.009 0.001 TRP A 408 HIS 0.003 0.001 HIS A 483 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 (10569) covalent geometry : angle 0.53890 / 0.28 (14342) SS BOND : bond 0.00058 / 0.03 ( 3) SS BOND : angle 0.99483 / 0.57 ( 6) hydrogen bonds : bond 0.03610 / 2.49 ( 523) hydrogen bonds : angle 4.66887 / 3.35 ( 1524) link_NAG-ASN : bond 0.00093 / 0.05 ( 3) link_NAG-ASN : angle 1.10130 / 0.54 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 61 time to evaluate : 0.521 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 381 MET cc_start: 0.5755 (pmm) cc_final: 0.4516 (pmm) REVERT: A 497 MET cc_start: 0.4752 (tmt) cc_final: 0.4427 (tpt) outliers start: 23 outliers final: 15 residues processed: 77 average time/residue: 0.7418 time to fit residues: 65.4911 Evaluate side-chains 76 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 61 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 476 ASN Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 748 ILE Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 139 PHE Chi-restraints excluded: chain B residue 158 ASN Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain C residue 49 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 105 optimal weight: 1.9990 chunk 128 optimal weight: 1.9990 chunk 53 optimal weight: 20.0000 chunk 107 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 44 optimal weight: 40.0000 chunk 23 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 54 optimal weight: 10.0000 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 491 ASN B 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.149168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.089948 restraints weight = 55761.673| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 3.22 r_work: 0.3090 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 10575 Z= 0.199 Angle : 0.555 7.129 14357 Z= 0.288 Chirality : 0.042 0.360 1639 Planarity : 0.003 0.034 1829 Dihedral : 6.398 56.244 1678 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.47 % Favored : 95.45 % Rotamer: Outliers : 2.14 % Allowed : 17.31 % Favored : 80.55 % 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: -0.13 (0.23), residues: 1297 helix: 0.82 (0.21), residues: 594 sheet: -1.07 (0.51), residues: 107 loop : -0.78 (0.25), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 901 TYR 0.018 0.001 TYR A 859 PHE 0.016 0.001 PHE A 913 TRP 0.012 0.001 TRP A 408 HIS 0.004 0.001 HIS A 483 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.20 (10569) covalent geometry : angle 0.55398 / 0.29 (14342) SS BOND : bond 0.00108 / 0.05 ( 3) SS BOND : angle 1.41182 / 0.79 ( 6) hydrogen bonds : bond 0.03640 / 2.51 ( 523) hydrogen bonds : angle 4.70530 / 3.38 ( 1524) link_NAG-ASN : bond 0.00132 / 0.07 ( 3) link_NAG-ASN : angle 1.04150 / 0.52 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 59 time to evaluate : 0.670 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 36 MET cc_start: 0.5766 (tpp) cc_final: 0.5564 (tpp) REVERT: A 381 MET cc_start: 0.5759 (pmm) cc_final: 0.4552 (pmm) REVERT: A 497 MET cc_start: 0.4700 (tmt) cc_final: 0.4359 (tpt) outliers start: 24 outliers final: 21 residues processed: 76 average time/residue: 0.7419 time to fit residues: 64.8733 Evaluate side-chains 80 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 59 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 CYS Chi-restraints excluded: chain A residue 138 TYR Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 476 ASN Chi-restraints excluded: chain A residue 491 ASN Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 711 ASP Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 748 ILE Chi-restraints excluded: chain A residue 925 ILE Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 139 PHE Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain C residue 49 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 44 optimal weight: 0.0370 chunk 101 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 15 optimal weight: 9.9990 chunk 13 optimal weight: 10.0000 chunk 107 optimal weight: 2.9990 chunk 122 optimal weight: 0.5980 chunk 51 optimal weight: 20.0000 chunk 2 optimal weight: 4.9990 chunk 95 optimal weight: 0.8980 chunk 86 optimal weight: 0.8980 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.147852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.088660 restraints weight = 55879.668| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 3.22 r_work: 0.3090 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.1507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.221 10575 Z= 0.208 Angle : 0.853 59.190 14357 Z= 0.500 Chirality : 0.043 0.361 1639 Planarity : 0.004 0.060 1829 Dihedral : 6.229 54.383 1676 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.39 % Favored : 95.53 % Rotamer: Outliers : 1.78 % Allowed : 17.75 % Favored : 80.46 % Cbeta Deviations : 0.17 % 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: -0.13 (0.23), residues: 1297 helix: 0.84 (0.21), residues: 594 sheet: -1.08 (0.51), residues: 107 loop : -0.79 (0.25), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 995 TYR 0.018 0.001 TYR A 859 PHE 0.015 0.001 PHE A 913 TRP 0.011 0.001 TRP A 408 HIS 0.003 0.001 HIS A 483 Details of bonding type rmsd/Z covalent geometry : bond 0.00483 / 0.21 (10569) covalent geometry : angle 0.85308 / 0.50 (14342) SS BOND : bond 0.00052 / 0.03 ( 3) SS BOND : angle 1.18172 / 0.67 ( 6) hydrogen bonds : bond 0.03606 / 2.48 ( 523) hydrogen bonds : angle 4.69638 / 3.38 ( 1524) link_NAG-ASN : bond 0.00130 / 0.06 ( 3) link_NAG-ASN : angle 1.04894 / 0.52 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 60 time to evaluate : 0.547 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 36 MET cc_start: 0.5785 (tpp) cc_final: 0.5548 (tpp) REVERT: A 381 MET cc_start: 0.5747 (pmm) cc_final: 0.4738 (pmm) REVERT: A 497 MET cc_start: 0.4747 (tmt) cc_final: 0.4378 (tpt) outliers start: 20 outliers final: 18 residues processed: 73 average time/residue: 0.7110 time to fit residues: 59.5450 Evaluate side-chains 77 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 59 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 CYS Chi-restraints excluded: chain A residue 138 TYR Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 476 ASN Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 711 ASP Chi-restraints excluded: chain A residue 748 ILE Chi-restraints excluded: chain A residue 842 MET Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 139 PHE Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain C residue 49 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 77 optimal weight: 1.9990 chunk 35 optimal weight: 8.9990 chunk 86 optimal weight: 0.6980 chunk 5 optimal weight: 0.0570 chunk 113 optimal weight: 0.0980 chunk 54 optimal weight: 4.9990 chunk 120 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 102 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.149719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.090515 restraints weight = 55763.666| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 3.22 r_work: 0.3088 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.1510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.221 10575 Z= 0.208 Angle : 0.853 59.190 14357 Z= 0.500 Chirality : 0.043 0.361 1639 Planarity : 0.004 0.060 1829 Dihedral : 6.229 54.383 1676 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.39 % Favored : 95.53 % Rotamer: Outliers : 1.69 % Allowed : 17.75 % Favored : 80.55 % Cbeta Deviations : 0.17 % 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: -0.13 (0.23), residues: 1297 helix: 0.84 (0.21), residues: 594 sheet: -1.08 (0.51), residues: 107 loop : -0.79 (0.25), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 995 TYR 0.018 0.001 TYR A 859 PHE 0.015 0.001 PHE A 913 TRP 0.011 0.001 TRP A 408 HIS 0.003 0.001 HIS A 483 Details of bonding type rmsd/Z covalent geometry : bond 0.00483 / 0.21 (10569) covalent geometry : angle 0.85308 / 0.50 (14342) SS BOND : bond 0.00052 / 0.03 ( 3) SS BOND : angle 1.18172 / 0.67 ( 6) hydrogen bonds : bond 0.03606 / 2.48 ( 523) hydrogen bonds : angle 4.69638 / 3.38 ( 1524) link_NAG-ASN : bond 0.00130 / 0.06 ( 3) link_NAG-ASN : angle 1.04894 / 0.52 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5898.18 seconds wall clock time: 100 minutes 52.99 seconds (6052.99 seconds total)