Starting phenix.real_space_refine on Sun Sep 13 05:31:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9rog_54118/09_2026/9rog_54118_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9rog_54118/09_2026/9rog_54118.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9rog_54118/09_2026/9rog_54118.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9rog_54118/09_2026/9rog_54118.map" model { file = "/net/cci-nas-00/data/ceres_data/9rog_54118/09_2026/9rog_54118_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9rog_54118/09_2026/9rog_54118_trim.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.023 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: 8 Type Number sf(0) Gaussians P 3 5.49 5 Mg 1 5.21 5 S 60 5.16 5 Na 1 4.78 5 C 6511 2.51 5 N 1678 2.21 5 O 1902 1.98 5 H 10016 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 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: 20172 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 15034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 969, 15034 Classifications: {'peptide': 969} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 41, 'TRANS': 927} Chain breaks: 2 Chain: "B" Number of atoms: 4436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 4436 Classifications: {'peptide': 274} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 253} Chain breaks: 1 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {' MG': 1, ' NA': 1, 'ADP': 1, 'CLR': 1, 'PO3': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} 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 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.39, per 1000 atoms: 0.17 Number of scatterers: 20172 At special positions: 0 Unit cell: (91.9228, 84.4696, 171.424, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 60 16.00 P 3 15.00 Mg 1 11.99 Na 1 11.00 O 1902 8.00 N 1678 7.00 C 6511 6.00 H 10016 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 B1102 " - " ASN B 158 " " NAG B1103 " - " ASN B 193 " " NAG B1104 " - " ASN B 265 " Time building additional restraints: 4.64 Conformation dependent library (CDL) restraints added in 641.5 milliseconds 2530 Ramachandran restraints generated. 1265 Oldfield, 0 Emsley, 1265 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2354 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 12 sheets defined 50.9% alpha, 15.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 37 through 45 removed outlier: 3.717A 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 77 through 87 Processing helix chain 'A' and resid 90 through 109 Processing helix chain 'A' and resid 117 through 152 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 251 through 254 Processing helix chain 'A' and resid 255 through 260 removed outlier: 3.549A pdb=" N ILE A 260 " --> pdb=" O VAL A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 304 Processing helix chain 'A' and resid 306 through 321 Processing helix chain 'A' and resid 325 through 344 Processing helix chain 'A' and resid 352 through 359 removed outlier: 3.773A pdb=" N THR A 356 " --> pdb=" O GLU A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 419 removed outlier: 3.801A pdb=" N ASN A 419 " --> pdb=" O ALA A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 454 Processing helix chain 'A' and resid 456 through 464 removed outlier: 3.823A 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 removed outlier: 3.946A 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: 3.519A pdb=" N ASP A 662 " --> pdb=" O THR A 658 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 674 Processing helix chain 'A' and resid 684 through 698 removed outlier: 3.546A 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 746 through 771 removed outlier: 3.641A pdb=" N THR A 750 " --> pdb=" O ALA A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 772 through 786 removed outlier: 3.599A pdb=" N GLU A 776 " --> pdb=" O SER A 772 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE A 777 " --> pdb=" O ASN A 773 " (cutoff:3.500A) Proline residue: A 779 - end of helix Processing helix chain 'A' and resid 793 through 805 Processing helix chain 'A' and resid 806 through 812 removed outlier: 3.567A 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 820 through 824 removed outlier: 3.933A pdb=" N ARG A 824 " --> pdb=" O ILE A 821 " (cutoff:3.500A) Processing helix chain 'A' and resid 836 through 845 Processing helix chain 'A' and resid 846 through 867 removed outlier: 3.575A 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 882 Processing helix chain 'A' and resid 897 through 928 removed outlier: 3.857A 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 974 through 980 Processing helix chain 'A' and resid 981 through 1002 Processing helix chain 'A' and resid 1007 through 1012 Processing helix chain 'B' and resid 28 through 61 Processing helix chain 'B' and resid 94 through 97 Processing helix chain 'B' and resid 98 through 110 Processing helix chain 'B' and resid 111 through 118 removed outlier: 6.292A pdb=" N ASP B 114 " --> pdb=" O LYS B 111 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N SER B 115 " --> pdb=" O TYR B 112 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ARG B 118 " --> pdb=" O SER B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 160 removed outlier: 6.715A pdb=" N ASN B 158 " --> pdb=" O TRP B 155 " (cutoff:3.500A) 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: 4.300A pdb=" N LEU B 250 " --> pdb=" O TYR B 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 56 Processing sheet with id=AA1, first strand: chain 'A' and resid 158 through 163 Processing sheet with id=AA2, first strand: chain 'A' and resid 178 through 183 removed outlier: 6.102A pdb=" N ASP A 179 " --> pdb=" O VAL A 248 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N VAL A 248 " --> pdb=" O ASP A 179 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N LYS A 202 " --> pdb=" O VAL A 240 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLY A 242 " --> pdb=" O GLY A 200 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N GLY A 200 " --> pdb=" O GLY A 242 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ALA A 244 " --> pdb=" O ALA A 198 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ALA A 198 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N GLY A 246 " --> pdb=" O ILE A 196 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N ILE A 196 " --> pdb=" O GLY A 246 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N VAL A 248 " --> pdb=" O ARG A 194 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ARG A 194 " --> pdb=" O VAL A 248 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 187 through 188 removed outlier: 6.885A pdb=" N LYS A 202 " --> pdb=" O VAL A 240 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLY A 242 " --> pdb=" O GLY A 200 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N GLY A 200 " --> pdb=" O GLY A 242 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ALA A 244 " --> pdb=" O ALA A 198 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ALA A 198 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N GLY A 246 " --> pdb=" O ILE A 196 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N ILE A 196 " --> pdb=" O GLY A 246 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N VAL A 248 " --> pdb=" O ARG A 194 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ARG A 194 " --> pdb=" O VAL A 248 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 347 through 348 removed outlier: 6.329A pdb=" N GLY A 721 " --> pdb=" O MET A 738 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N LEU A 740 " --> pdb=" O GLY A 721 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N ALA A 723 " --> pdb=" O LEU A 740 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N VAL A 704 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N MET A 724 " --> pdb=" O VAL A 704 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N GLY A 706 " --> pdb=" O MET A 724 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 362 through 365 removed outlier: 7.027A pdb=" N VAL A 603 " --> pdb=" O ILE A 678 " (cutoff:3.500A) removed outlier: 8.418A pdb=" N PHE A 680 " --> pdb=" O VAL A 603 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N MET A 605 " --> pdb=" O PHE A 680 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 386 through 389 removed outlier: 6.134A pdb=" N VAL A 378 " --> pdb=" O ILE A 582 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N ILE A 582 " --> pdb=" O VAL A 378 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N PHE A 545 " --> pdb=" O VAL A 576 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N LEU A 578 " --> pdb=" O LEU A 543 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LEU A 543 " --> pdb=" O LEU A 578 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N SER A 580 " --> pdb=" O ARG A 541 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ARG A 541 " --> pdb=" O SER A 580 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 386 through 389 removed outlier: 6.134A pdb=" N VAL A 378 " --> pdb=" O ILE A 582 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N ILE A 582 " --> pdb=" O VAL A 378 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N CYS A 508 " --> pdb=" O LEU A 573 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N PHE A 575 " --> pdb=" O CYS A 508 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N THR A 510 " --> pdb=" O PHE A 575 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N GLY A 577 " --> pdb=" O THR A 510 " (cutoff:3.500A) removed outlier: 9.268A pdb=" N LEU A 512 " --> pdb=" O GLY A 577 " (cutoff:3.500A) removed outlier: 12.312A pdb=" N MET A 579 " --> pdb=" O LEU A 512 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 422 through 423 Processing sheet with id=AA9, first strand: chain 'A' and resid 888 through 889 Processing sheet with id=AB1, first strand: chain 'B' and resid 77 through 79 Processing sheet with id=AB2, first strand: chain 'B' and resid 87 through 90 removed outlier: 6.364A pdb=" N ILE B 88 " --> pdb=" O GLU B 300 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 123 through 124 534 hydrogen bonds defined for protein. 1494 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: 5.11 Time building geometry restraints manager: 2.96 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: 9990 1.03 - 1.23: 55 1.23 - 1.43: 4180 1.43 - 1.62: 6071 1.62 - 1.82: 88 Bond restraints: 20384 Sorted by residual: bond pdb=" O2 PO3 A1103 " pdb=" P PO3 A1103 " ideal model delta sigma weight residual 1.604 1.501 0.103 2.00e-02 2.50e+03 2.67e+01 bond pdb=" O1 PO3 A1103 " pdb=" P PO3 A1103 " ideal model delta sigma weight residual 1.604 1.501 0.103 2.00e-02 2.50e+03 2.64e+01 bond pdb=" O3 PO3 A1103 " pdb=" P PO3 A1103 " ideal model delta sigma weight residual 1.601 1.501 0.100 2.00e-02 2.50e+03 2.51e+01 bond pdb=" C1 NAG B1103 " pdb=" O5 NAG B1103 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.63e+00 bond pdb=" C5 NAG B1104 " pdb=" O5 NAG B1104 " ideal model delta sigma weight residual 1.413 1.438 -0.025 2.00e-02 2.50e+03 1.60e+00 ... (remaining 20379 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.12: 36663 2.12 - 4.23: 204 4.23 - 6.35: 17 6.35 - 8.47: 1 8.47 - 10.58: 1 Bond angle restraints: 36886 Sorted by residual: angle pdb=" CB MET B 121 " pdb=" CG MET B 121 " pdb=" SD MET B 121 " ideal model delta sigma weight residual 112.70 123.28 -10.58 3.00e+00 1.11e-01 1.24e+01 angle pdb=" C1' ADP A1102 " pdb=" C2' ADP A1102 " pdb=" C3' ADP A1102 " ideal model delta sigma weight residual 111.00 103.93 7.07 3.00e+00 1.11e-01 5.56e+00 angle pdb=" CA GLU A 141 " pdb=" CB GLU A 141 " pdb=" CG GLU A 141 " ideal model delta sigma weight residual 114.10 118.53 -4.43 2.00e+00 2.50e-01 4.91e+00 angle pdb=" CA GLU A 462 " pdb=" CB GLU A 462 " pdb=" CG GLU A 462 " ideal model delta sigma weight residual 114.10 118.40 -4.30 2.00e+00 2.50e-01 4.62e+00 angle pdb=" C SER B 89 " pdb=" N PHE B 90 " pdb=" CA PHE B 90 " ideal model delta sigma weight residual 121.62 117.77 3.85 1.83e+00 2.99e-01 4.43e+00 ... (remaining 36881 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.08: 9106 24.08 - 48.16: 486 48.16 - 72.24: 143 72.24 - 96.32: 27 96.32 - 120.40: 6 Dihedral angle restraints: 9768 sinusoidal: 5487 harmonic: 4281 Sorted by residual: dihedral pdb=" O1B ADP A1102 " pdb=" O3A ADP A1102 " pdb=" PB ADP A1102 " pdb=" PA ADP A1102 " ideal model delta sinusoidal sigma weight residual -60.00 11.14 -71.14 1 2.00e+01 2.50e-03 1.62e+01 dihedral pdb=" C1 CLR B1101 " pdb=" C2 CLR B1101 " pdb=" C3 CLR B1101 " pdb=" C4 CLR B1101 " ideal model delta sinusoidal sigma weight residual 57.41 -62.99 120.40 1 3.00e+01 1.11e-03 1.61e+01 dihedral pdb=" C1 CLR B1101 " pdb=" C2 CLR B1101 " pdb=" C3 CLR B1101 " pdb=" O1 CLR B1101 " ideal model delta sinusoidal sigma weight residual 180.04 60.37 119.67 1 3.00e+01 1.11e-03 1.59e+01 ... (remaining 9765 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1452 0.069 - 0.137: 151 0.137 - 0.206: 3 0.206 - 0.275: 0 0.275 - 0.343: 1 Chirality restraints: 1607 Sorted by residual: 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 -2.06 -0.34 2.00e-01 2.50e+01 2.95e+00 chirality pdb=" CA ILE B 88 " pdb=" N ILE B 88 " pdb=" C ILE B 88 " pdb=" CB ILE B 88 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.71e-01 chirality pdb=" CA ILE A 470 " pdb=" N ILE A 470 " pdb=" C ILE A 470 " pdb=" CB ILE A 470 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.92e-01 ... (remaining 1604 not shown) Planarity restraints: 3000 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A 35 " 0.008 2.00e-02 2.50e+03 1.72e-02 2.96e+00 pdb=" C LYS A 35 " -0.030 2.00e-02 2.50e+03 pdb=" O LYS A 35 " 0.011 2.00e-02 2.50e+03 pdb=" N MET A 36 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 462 " -0.008 2.00e-02 2.50e+03 1.69e-02 2.85e+00 pdb=" CD GLU A 462 " 0.029 2.00e-02 2.50e+03 pdb=" OE1 GLU A 462 " -0.011 2.00e-02 2.50e+03 pdb=" OE2 GLU A 462 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 141 " 0.007 2.00e-02 2.50e+03 1.39e-02 1.92e+00 pdb=" CD GLU A 141 " -0.024 2.00e-02 2.50e+03 pdb=" OE1 GLU A 141 " 0.009 2.00e-02 2.50e+03 pdb=" OE2 GLU A 141 " 0.009 2.00e-02 2.50e+03 ... (remaining 2997 not shown) Histogram of nonbonded interaction distances: 1.43 - 2.06: 286 2.06 - 2.70: 32445 2.70 - 3.33: 60745 3.33 - 3.97: 77890 3.97 - 4.60: 121073 Nonbonded interactions: 292439 Sorted by model distance: nonbonded pdb=" OE1 GLN A 686 " pdb=" H GLN A 686 " model vdw 1.427 2.450 nonbonded pdb=" OE1 GLU A 173 " pdb=" H GLU A 173 " model vdw 1.580 2.450 nonbonded pdb=" O ASP B 94 " pdb=" HG SER B 97 " model vdw 1.587 2.450 nonbonded pdb=" OE1 GLU B 63 " pdb=" H GLU B 63 " model vdw 1.605 2.450 nonbonded pdb=" OD1 ASP A 192 " pdb=" H PHE A 235 " model vdw 1.608 2.450 ... (remaining 292434 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: 0.980 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: 0.130 Extract box with map and model: 0.230 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 20.210 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 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 0.103 10374 Z= 0.154 Angle : 0.570 10.584 14086 Z= 0.284 Chirality : 0.042 0.343 1607 Planarity : 0.003 0.042 1788 Dihedral : 16.420 120.402 4050 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.55 % Allowed : 12.32 % Favored : 86.13 % 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: 1.30 (0.25), residues: 1265 helix: 1.87 (0.22), residues: 594 sheet: -0.74 (0.44), residues: 133 loop : 0.25 (0.29), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 830 TYR 0.016 0.001 TYR A 859 PHE 0.011 0.001 PHE A 90 TRP 0.005 0.001 TRP A 382 HIS 0.002 0.001 HIS A 547 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.15 (10368) covalent geometry : angle 0.56841 / 0.28 (14071) SS BOND : bond 0.00133 / 0.06 ( 3) SS BOND : angle 0.88204 / 0.51 ( 6) hydrogen bonds : bond 0.05910 / 3.52 ( 521) hydrogen bonds : angle 4.78274 / 3.35 ( 1494) link_NAG-ASN : bond 0.00562 / 0.28 ( 3) link_NAG-ASN : angle 1.76549 / 0.82 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2530 Ramachandran restraints generated. 1265 Oldfield, 0 Emsley, 1265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2530 Ramachandran restraints generated. 1265 Oldfield, 0 Emsley, 1265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 72 time to evaluate : 0.556 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: A 36 MET cc_start: 0.7885 (pmm) cc_final: 0.7652 (pmm) outliers start: 17 outliers final: 14 residues processed: 87 average time/residue: 0.9894 time to fit residues: 94.8506 Evaluate side-chains 84 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 70 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 GLN Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 135 CYS Chi-restraints excluded: chain A residue 225 ASN Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 711 ASP Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 193 ASN Chi-restraints excluded: chain B residue 199 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 108 optimal weight: 0.7980 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.0270 chunk 33 optimal weight: 0.6980 chunk 123 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 9.9990 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.099317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.070741 restraints weight = 57916.139| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 2.63 r_work: 0.2855 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2741 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.0423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10374 Z= 0.109 Angle : 0.548 8.184 14086 Z= 0.267 Chirality : 0.042 0.235 1607 Planarity : 0.003 0.029 1788 Dihedral : 9.492 70.812 1666 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.37 % Allowed : 12.32 % Favored : 86.31 % 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: 1.32 (0.25), residues: 1265 helix: 1.93 (0.22), residues: 600 sheet: -0.88 (0.44), residues: 133 loop : 0.24 (0.29), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 830 TYR 0.014 0.001 TYR A 859 PHE 0.009 0.001 PHE A 297 TRP 0.005 0.001 TRP A 408 HIS 0.003 0.001 HIS A 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 (10368) covalent geometry : angle 0.54579 / 0.27 (14071) SS BOND : bond 0.00101 / 0.05 ( 3) SS BOND : angle 0.98696 / 0.57 ( 6) hydrogen bonds : bond 0.03784 / 2.51 ( 521) hydrogen bonds : angle 4.52698 / 3.16 ( 1494) link_NAG-ASN : bond 0.00347 / 0.17 ( 3) link_NAG-ASN : angle 1.75440 / 0.96 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2530 Ramachandran restraints generated. 1265 Oldfield, 0 Emsley, 1265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2530 Ramachandran restraints generated. 1265 Oldfield, 0 Emsley, 1265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 75 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: A 36 MET cc_start: 0.8229 (pmm) cc_final: 0.7479 (pmm) REVERT: A 436 ASP cc_start: 0.8883 (p0) cc_final: 0.8633 (p0) REVERT: B 121 MET cc_start: 0.8450 (tmm) cc_final: 0.8231 (tmm) outliers start: 15 outliers final: 6 residues processed: 88 average time/residue: 1.0752 time to fit residues: 103.7221 Evaluate side-chains 73 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 67 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 CYS Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 193 ASN Chi-restraints excluded: chain B residue 199 TYR Chi-restraints excluded: chain C residue 55 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 30 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 89 optimal weight: 0.6980 chunk 76 optimal weight: 2.9990 chunk 113 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 47 optimal weight: 5.9990 chunk 13 optimal weight: 4.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.096784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.068144 restraints weight = 58692.089| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 2.63 r_work: 0.2807 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2691 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.0616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 10374 Z= 0.239 Angle : 0.575 6.859 14086 Z= 0.288 Chirality : 0.044 0.316 1607 Planarity : 0.003 0.033 1788 Dihedral : 7.421 58.777 1650 Min Nonbonded Distance : 1.713 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.73 % Allowed : 12.04 % Favored : 86.22 % 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: 1.15 (0.25), residues: 1265 helix: 1.80 (0.22), residues: 601 sheet: -1.01 (0.44), residues: 133 loop : 0.16 (0.29), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 71 TYR 0.019 0.001 TYR A 859 PHE 0.014 0.001 PHE A 297 TRP 0.006 0.001 TRP A 408 HIS 0.003 0.001 HIS A 547 Details of bonding type rmsd/Z covalent geometry : bond 0.00541 / 0.24 (10368) covalent geometry : angle 0.57276 / 0.29 (14071) SS BOND : bond 0.00162 / 0.08 ( 3) SS BOND : angle 1.11456 / 0.63 ( 6) hydrogen bonds : bond 0.03921 / 2.61 ( 521) hydrogen bonds : angle 4.54605 / 3.20 ( 1494) link_NAG-ASN : bond 0.00264 / 0.13 ( 3) link_NAG-ASN : angle 2.13927 / 1.12 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2530 Ramachandran restraints generated. 1265 Oldfield, 0 Emsley, 1265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2530 Ramachandran restraints generated. 1265 Oldfield, 0 Emsley, 1265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 69 time to evaluate : 0.568 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: A 381 MET cc_start: 0.9322 (mtm) cc_final: 0.9107 (mtt) REVERT: A 436 ASP cc_start: 0.8904 (p0) cc_final: 0.8650 (p0) REVERT: B 121 MET cc_start: 0.8492 (tmm) cc_final: 0.8257 (tmm) outliers start: 19 outliers final: 16 residues processed: 83 average time/residue: 1.1791 time to fit residues: 106.8028 Evaluate side-chains 82 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 66 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 135 CYS Chi-restraints excluded: chain A residue 225 ASN Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 143 ARG Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 193 ASN Chi-restraints excluded: chain B residue 199 TYR Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain C residue 55 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 107 optimal weight: 4.9990 chunk 103 optimal weight: 0.7980 chunk 49 optimal weight: 4.9990 chunk 79 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 5 optimal weight: 0.0040 chunk 28 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 117 optimal weight: 2.9990 overall best weight: 0.8994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 687 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.099222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.070472 restraints weight = 57841.874| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 2.66 r_work: 0.2859 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2742 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.0704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10374 Z= 0.117 Angle : 0.526 6.081 14086 Z= 0.260 Chirality : 0.042 0.324 1607 Planarity : 0.003 0.029 1788 Dihedral : 6.785 59.349 1648 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.73 % Allowed : 12.14 % Favored : 86.13 % 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: 1.28 (0.25), residues: 1265 helix: 1.92 (0.22), residues: 600 sheet: -1.04 (0.44), residues: 133 loop : 0.23 (0.29), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 830 TYR 0.014 0.001 TYR A 859 PHE 0.011 0.001 PHE A 297 TRP 0.005 0.001 TRP A 408 HIS 0.003 0.001 HIS A 547 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (10368) covalent geometry : angle 0.52361 / 0.26 (14071) SS BOND : bond 0.00067 / 0.03 ( 3) SS BOND : angle 0.84628 / 0.48 ( 6) hydrogen bonds : bond 0.03484 / 2.33 ( 521) hydrogen bonds : angle 4.32891 / 3.03 ( 1494) link_NAG-ASN : bond 0.00389 / 0.19 ( 3) link_NAG-ASN : angle 1.99487 / 1.02 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2530 Ramachandran restraints generated. 1265 Oldfield, 0 Emsley, 1265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2530 Ramachandran restraints generated. 1265 Oldfield, 0 Emsley, 1265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 74 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: A 436 ASP cc_start: 0.8901 (p0) cc_final: 0.8643 (p0) REVERT: A 528 PHE cc_start: 0.9446 (OUTLIER) cc_final: 0.9218 (t80) REVERT: B 121 MET cc_start: 0.8438 (tmm) cc_final: 0.8193 (tmm) outliers start: 19 outliers final: 13 residues processed: 87 average time/residue: 1.1676 time to fit residues: 110.8895 Evaluate side-chains 85 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 71 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 225 ASN Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 528 PHE Chi-restraints excluded: chain A residue 841 SER Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 143 ARG Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 193 ASN Chi-restraints excluded: chain B residue 199 TYR Chi-restraints excluded: chain C residue 55 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 119 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 59 optimal weight: 0.8980 chunk 107 optimal weight: 5.9990 chunk 16 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 2 optimal weight: 5.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.098287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.069470 restraints weight = 57821.902| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 2.64 r_work: 0.2844 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2728 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.0792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10374 Z= 0.174 Angle : 0.536 5.849 14086 Z= 0.268 Chirality : 0.042 0.290 1607 Planarity : 0.003 0.030 1788 Dihedral : 6.678 56.888 1647 Min Nonbonded Distance : 1.780 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.73 % Allowed : 12.32 % Favored : 85.95 % 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: 1.23 (0.25), residues: 1265 helix: 1.91 (0.22), residues: 600 sheet: -1.07 (0.43), residues: 133 loop : 0.17 (0.29), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 830 TYR 0.017 0.001 TYR A 859 PHE 0.012 0.001 PHE A 297 TRP 0.005 0.001 TRP A 408 HIS 0.003 0.001 HIS A 547 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.17 (10368) covalent geometry : angle 0.53440 / 0.27 (14071) SS BOND : bond 0.00117 / 0.06 ( 3) SS BOND : angle 1.02182 / 0.58 ( 6) hydrogen bonds : bond 0.03567 / 2.39 ( 521) hydrogen bonds : angle 4.33391 / 3.05 ( 1494) link_NAG-ASN : bond 0.00349 / 0.17 ( 3) link_NAG-ASN : angle 1.71232 / 0.83 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2530 Ramachandran restraints generated. 1265 Oldfield, 0 Emsley, 1265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2530 Ramachandran restraints generated. 1265 Oldfield, 0 Emsley, 1265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 74 time to evaluate : 0.560 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: A 36 MET cc_start: 0.8229 (pmm) cc_final: 0.7940 (pmm) REVERT: A 436 ASP cc_start: 0.8903 (p0) cc_final: 0.8638 (p0) REVERT: A 528 PHE cc_start: 0.9452 (OUTLIER) cc_final: 0.9231 (t80) REVERT: B 121 MET cc_start: 0.8447 (tmm) cc_final: 0.8228 (tmm) outliers start: 19 outliers final: 13 residues processed: 87 average time/residue: 1.0964 time to fit residues: 104.5799 Evaluate side-chains 85 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 71 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 225 ASN Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 528 PHE Chi-restraints excluded: chain A residue 841 SER Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 143 ARG Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 193 ASN Chi-restraints excluded: chain B residue 199 TYR Chi-restraints excluded: chain C residue 55 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 60 optimal weight: 5.9990 chunk 46 optimal weight: 5.9990 chunk 113 optimal weight: 5.9990 chunk 110 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 109 optimal weight: 4.9990 chunk 121 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.098258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.069417 restraints weight = 57569.857| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 2.65 r_work: 0.2841 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2724 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.0883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 10374 Z= 0.173 Angle : 0.533 5.722 14086 Z= 0.267 Chirality : 0.042 0.274 1607 Planarity : 0.003 0.034 1788 Dihedral : 6.633 55.831 1647 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.92 % Allowed : 12.32 % Favored : 85.77 % 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: 1.23 (0.25), residues: 1265 helix: 1.92 (0.22), residues: 600 sheet: -1.10 (0.43), residues: 133 loop : 0.17 (0.28), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 830 TYR 0.016 0.001 TYR A 859 PHE 0.013 0.001 PHE A 297 TRP 0.005 0.001 TRP A 408 HIS 0.003 0.001 HIS A 547 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.17 (10368) covalent geometry : angle 0.53104 / 0.27 (14071) SS BOND : bond 0.00084 / 0.04 ( 3) SS BOND : angle 1.00672 / 0.57 ( 6) hydrogen bonds : bond 0.03569 / 2.38 ( 521) hydrogen bonds : angle 4.30360 / 3.03 ( 1494) link_NAG-ASN : bond 0.00328 / 0.16 ( 3) link_NAG-ASN : angle 1.51287 / 0.71 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2530 Ramachandran restraints generated. 1265 Oldfield, 0 Emsley, 1265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2530 Ramachandran restraints generated. 1265 Oldfield, 0 Emsley, 1265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 74 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: A 36 MET cc_start: 0.8321 (pmm) cc_final: 0.8010 (pmm) REVERT: A 436 ASP cc_start: 0.8897 (p0) cc_final: 0.8631 (p0) REVERT: A 528 PHE cc_start: 0.9457 (OUTLIER) cc_final: 0.9236 (t80) REVERT: B 202 MET cc_start: 0.5338 (OUTLIER) cc_final: 0.5133 (ppp) outliers start: 21 outliers final: 15 residues processed: 88 average time/residue: 1.1570 time to fit residues: 111.5422 Evaluate side-chains 90 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 73 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 CYS Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 225 ASN Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 528 PHE Chi-restraints excluded: chain A residue 841 SER Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 143 ARG Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 193 ASN Chi-restraints excluded: chain B residue 199 TYR Chi-restraints excluded: chain B residue 202 MET Chi-restraints excluded: chain C residue 55 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 90 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 96 optimal weight: 0.9980 chunk 23 optimal weight: 0.3980 chunk 102 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.098632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.069915 restraints weight = 57821.374| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 2.65 r_work: 0.2850 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2732 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.0911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 10374 Z= 0.138 Angle : 0.524 7.083 14086 Z= 0.261 Chirality : 0.042 0.262 1607 Planarity : 0.003 0.036 1788 Dihedral : 6.528 55.416 1647 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.92 % Allowed : 12.77 % Favored : 85.31 % 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: 1.29 (0.25), residues: 1265 helix: 1.96 (0.22), residues: 600 sheet: -1.12 (0.43), residues: 133 loop : 0.21 (0.29), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 830 TYR 0.015 0.001 TYR A 859 PHE 0.012 0.001 PHE A 297 TRP 0.005 0.001 TRP A 408 HIS 0.003 0.001 HIS A 547 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (10368) covalent geometry : angle 0.52297 / 0.26 (14071) SS BOND : bond 0.00085 / 0.04 ( 3) SS BOND : angle 0.92265 / 0.53 ( 6) hydrogen bonds : bond 0.03445 / 2.30 ( 521) hydrogen bonds : angle 4.23768 / 2.98 ( 1494) link_NAG-ASN : bond 0.00348 / 0.17 ( 3) link_NAG-ASN : angle 1.36319 / 0.63 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2530 Ramachandran restraints generated. 1265 Oldfield, 0 Emsley, 1265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2530 Ramachandran restraints generated. 1265 Oldfield, 0 Emsley, 1265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 76 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: A 36 MET cc_start: 0.8371 (pmm) cc_final: 0.8001 (pmm) REVERT: A 436 ASP cc_start: 0.8905 (p0) cc_final: 0.8632 (p0) REVERT: A 528 PHE cc_start: 0.9455 (OUTLIER) cc_final: 0.9201 (t80) REVERT: B 202 MET cc_start: 0.5375 (OUTLIER) cc_final: 0.5160 (ppp) outliers start: 21 outliers final: 15 residues processed: 91 average time/residue: 1.1364 time to fit residues: 113.1639 Evaluate side-chains 90 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 73 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 225 ASN Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 528 PHE Chi-restraints excluded: chain A residue 841 SER Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 143 ARG Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 193 ASN Chi-restraints excluded: chain B residue 199 TYR Chi-restraints excluded: chain B residue 202 MET Chi-restraints excluded: chain C residue 55 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 95 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 chunk 48 optimal weight: 4.9990 chunk 121 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 chunk 115 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.098838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.070033 restraints weight = 57730.901| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 2.65 r_work: 0.2849 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2730 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.1006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10374 Z= 0.142 Angle : 0.522 8.725 14086 Z= 0.259 Chirality : 0.042 0.252 1607 Planarity : 0.003 0.039 1788 Dihedral : 6.463 55.516 1647 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.01 % Allowed : 12.50 % Favored : 85.49 % 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: 1.31 (0.25), residues: 1265 helix: 2.01 (0.22), residues: 600 sheet: -1.13 (0.43), residues: 133 loop : 0.19 (0.28), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 830 TYR 0.016 0.001 TYR A 859 PHE 0.012 0.001 PHE A 297 TRP 0.005 0.001 TRP A 408 HIS 0.003 0.001 HIS A 547 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (10368) covalent geometry : angle 0.52051 / 0.26 (14071) SS BOND : bond 0.00080 / 0.04 ( 3) SS BOND : angle 0.94553 / 0.54 ( 6) hydrogen bonds : bond 0.03433 / 2.29 ( 521) hydrogen bonds : angle 4.21806 / 2.97 ( 1494) link_NAG-ASN : bond 0.00331 / 0.16 ( 3) link_NAG-ASN : angle 1.28433 / 0.58 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2530 Ramachandran restraints generated. 1265 Oldfield, 0 Emsley, 1265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2530 Ramachandran restraints generated. 1265 Oldfield, 0 Emsley, 1265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 77 time to evaluate : 0.569 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: A 36 MET cc_start: 0.8459 (pmm) cc_final: 0.8096 (pmm) REVERT: A 436 ASP cc_start: 0.8913 (p0) cc_final: 0.8633 (p0) REVERT: A 528 PHE cc_start: 0.9454 (OUTLIER) cc_final: 0.9206 (t80) outliers start: 22 outliers final: 16 residues processed: 92 average time/residue: 1.0826 time to fit residues: 109.3102 Evaluate side-chains 90 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 73 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 135 CYS Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 225 ASN Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 528 PHE Chi-restraints excluded: chain A residue 841 SER Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 143 ARG Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 193 ASN Chi-restraints excluded: chain B residue 199 TYR Chi-restraints excluded: chain C residue 55 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 41 optimal weight: 0.6980 chunk 1 optimal weight: 10.0000 chunk 40 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 chunk 107 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.100119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.071063 restraints weight = 57717.391| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 2.65 r_work: 0.2836 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2718 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.1045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10374 Z= 0.172 Angle : 0.535 10.236 14086 Z= 0.267 Chirality : 0.042 0.246 1607 Planarity : 0.003 0.041 1788 Dihedral : 6.460 55.761 1647 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.82 % Allowed : 12.86 % Favored : 85.31 % 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: 1.27 (0.25), residues: 1265 helix: 2.00 (0.22), residues: 600 sheet: -1.18 (0.43), residues: 133 loop : 0.15 (0.28), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 830 TYR 0.017 0.001 TYR A 859 PHE 0.013 0.001 PHE A 297 TRP 0.006 0.001 TRP A 408 HIS 0.003 0.001 HIS A 547 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.17 (10368) covalent geometry : angle 0.53405 / 0.27 (14071) SS BOND : bond 0.00086 / 0.04 ( 3) SS BOND : angle 1.01302 / 0.58 ( 6) hydrogen bonds : bond 0.03506 / 2.34 ( 521) hydrogen bonds : angle 4.24157 / 3.00 ( 1494) link_NAG-ASN : bond 0.00310 / 0.15 ( 3) link_NAG-ASN : angle 1.25248 / 0.56 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2530 Ramachandran restraints generated. 1265 Oldfield, 0 Emsley, 1265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2530 Ramachandran restraints generated. 1265 Oldfield, 0 Emsley, 1265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 74 time to evaluate : 0.573 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: A 436 ASP cc_start: 0.8919 (p0) cc_final: 0.8632 (p0) REVERT: A 528 PHE cc_start: 0.9456 (OUTLIER) cc_final: 0.9212 (t80) REVERT: B 199 TYR cc_start: 0.7735 (OUTLIER) cc_final: 0.7471 (m-80) outliers start: 20 outliers final: 14 residues processed: 89 average time/residue: 1.0942 time to fit residues: 107.1873 Evaluate side-chains 88 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 72 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 CYS Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 225 ASN Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 528 PHE Chi-restraints excluded: chain A residue 841 SER Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 143 ARG Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 193 ASN Chi-restraints excluded: chain B residue 199 TYR Chi-restraints excluded: chain C residue 55 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 20 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 45 optimal weight: 4.9990 chunk 48 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 60 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 122 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 75 optimal weight: 0.7980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.100785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.071653 restraints weight = 58063.329| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 2.66 r_work: 0.2862 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2745 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.1092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10374 Z= 0.128 Angle : 0.529 9.996 14086 Z= 0.262 Chirality : 0.042 0.238 1607 Planarity : 0.003 0.042 1788 Dihedral : 6.400 55.710 1647 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.64 % Allowed : 12.96 % Favored : 85.40 % 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: 1.35 (0.25), residues: 1265 helix: 2.07 (0.22), residues: 597 sheet: -1.17 (0.43), residues: 133 loop : 0.21 (0.28), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 830 TYR 0.015 0.001 TYR A 859 PHE 0.011 0.001 PHE A 297 TRP 0.005 0.001 TRP A 79 HIS 0.003 0.001 HIS A 547 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (10368) covalent geometry : angle 0.52854 / 0.26 (14071) SS BOND : bond 0.00070 / 0.03 ( 3) SS BOND : angle 0.89744 / 0.51 ( 6) hydrogen bonds : bond 0.03388 / 2.26 ( 521) hydrogen bonds : angle 4.17204 / 2.94 ( 1494) link_NAG-ASN : bond 0.00328 / 0.16 ( 3) link_NAG-ASN : angle 1.16428 / 0.52 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2530 Ramachandran restraints generated. 1265 Oldfield, 0 Emsley, 1265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2530 Ramachandran restraints generated. 1265 Oldfield, 0 Emsley, 1265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 75 time to evaluate : 0.606 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: A 436 ASP cc_start: 0.8905 (p0) cc_final: 0.8638 (p0) REVERT: A 528 PHE cc_start: 0.9461 (OUTLIER) cc_final: 0.9221 (t80) REVERT: B 199 TYR cc_start: 0.7746 (OUTLIER) cc_final: 0.7533 (m-80) outliers start: 18 outliers final: 13 residues processed: 88 average time/residue: 1.1257 time to fit residues: 108.6482 Evaluate side-chains 88 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 73 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 CYS Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 225 ASN Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 528 PHE Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 143 ARG Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 193 ASN Chi-restraints excluded: chain B residue 199 TYR Chi-restraints excluded: chain C residue 55 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 3 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 74 optimal weight: 0.5980 chunk 5 optimal weight: 0.9980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.100745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.071743 restraints weight = 57803.626| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 2.63 r_work: 0.2862 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2745 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.1124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10374 Z= 0.127 Angle : 0.527 10.508 14086 Z= 0.260 Chirality : 0.042 0.230 1607 Planarity : 0.003 0.041 1788 Dihedral : 6.303 55.620 1646 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.55 % Allowed : 13.32 % Favored : 85.13 % 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: 1.43 (0.25), residues: 1265 helix: 2.09 (0.22), residues: 597 sheet: -1.16 (0.43), residues: 133 loop : 0.32 (0.28), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 830 TYR 0.016 0.001 TYR A 859 PHE 0.011 0.001 PHE A 297 TRP 0.005 0.001 TRP A 79 HIS 0.003 0.001 HIS A 547 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (10368) covalent geometry : angle 0.52597 / 0.26 (14071) SS BOND : bond 0.00074 / 0.04 ( 3) SS BOND : angle 0.87972 / 0.50 ( 6) hydrogen bonds : bond 0.03343 / 2.23 ( 521) hydrogen bonds : angle 4.13995 / 2.92 ( 1494) link_NAG-ASN : bond 0.00322 / 0.16 ( 3) link_NAG-ASN : angle 1.11359 / 0.49 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5937.82 seconds wall clock time: 101 minutes 36.83 seconds (6096.83 seconds total)