Starting phenix.real_space_refine on Wed Sep 25 05:40:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bsw_30169/09_2024/7bsw_30169_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bsw_30169/09_2024/7bsw_30169.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bsw_30169/09_2024/7bsw_30169.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bsw_30169/09_2024/7bsw_30169.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bsw_30169/09_2024/7bsw_30169_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bsw_30169/09_2024/7bsw_30169_trim.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.008 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 Al 1 5.89 5 P 1 5.49 5 S 45 5.16 5 C 6078 2.51 5 N 1504 2.21 5 O 1696 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 9329 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 815, 6596 Classifications: {'peptide': 815} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 792} Chain breaks: 3 Chain: "C" Number of atoms: 2613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2613 Classifications: {'peptide': 324} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 298} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "A" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ALF': 1, 'PEE': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "C" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 66 Unusual residues: {'MAN': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 5.70, per 1000 atoms: 0.61 Number of scatterers: 9329 At special positions: 0 Unit cell: (97.2, 105.3, 141.75, 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) S 45 16.00 P 1 15.00 Al 1 13.00 F 4 9.00 O 1696 8.00 N 1504 7.00 C 6078 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS C 91 " - pdb=" SG CYS C 104 " distance=2.03 Simple disulfide: pdb=" SG CYS C 94 " - pdb=" SG CYS C 102 " distance=2.02 Simple disulfide: pdb=" SG CYS C 157 " - pdb=" SG CYS C 171 " 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 Atom "HETATM 9314 O5 NAG C 404 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9314 O5 NAG C 404 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-4 " NAG C 402 " - " MAN C 403 " BETA1-4 " NAG C 401 " - " NAG C 402 " NAG-ASN " NAG C 401 " - " ASN C 180 " " NAG C 404 " - " ASN C 294 " " NAG C 405 " - " ASN C 107 " Time building additional restraints: 2.97 Conformation dependent library (CDL) restraints added in 1.0 seconds 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2156 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 11 sheets defined 44.2% alpha, 8.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'A' and resid 54 through 64 removed outlier: 4.197A pdb=" N PHE A 61 " --> pdb=" O PRO A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 82 removed outlier: 3.915A pdb=" N LEU A 73 " --> pdb=" O ASN A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 93 Processing helix chain 'A' and resid 93 through 119 removed outlier: 3.686A pdb=" N ILE A 99 " --> pdb=" O LEU A 95 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR A 102 " --> pdb=" O VAL A 98 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ARG A 113 " --> pdb=" O GLU A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 141 No H-bonds generated for 'chain 'A' and resid 139 through 141' Processing helix chain 'A' and resid 286 through 314 removed outlier: 3.752A pdb=" N PHE A 297 " --> pdb=" O ILE A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 334 Processing helix chain 'A' and resid 335 through 351 removed outlier: 3.503A pdb=" N LYS A 339 " --> pdb=" O LEU A 335 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N PHE A 341 " --> pdb=" O VAL A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 355 Processing helix chain 'A' and resid 360 through 371 removed outlier: 4.097A pdb=" N MET A 365 " --> pdb=" O VAL A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 377 removed outlier: 3.763A pdb=" N SER A 375 " --> pdb=" O SER A 371 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASP A 377 " --> pdb=" O PHE A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 400 Processing helix chain 'A' and resid 657 through 666 Processing helix chain 'A' and resid 679 through 688 removed outlier: 4.005A pdb=" N SER A 683 " --> pdb=" O GLU A 679 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N CYS A 685 " --> pdb=" O ALA A 681 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 720 Processing helix chain 'A' and resid 754 through 762 removed outlier: 3.821A pdb=" N LEU A 758 " --> pdb=" O SER A 754 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 782 Processing helix chain 'A' and resid 791 through 802 removed outlier: 3.657A pdb=" N LYS A 795 " --> pdb=" O ALA A 791 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ALA A 796 " --> pdb=" O PRO A 792 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 827 Processing helix chain 'A' and resid 853 through 862 removed outlier: 4.583A pdb=" N LYS A 857 " --> pdb=" O LYS A 853 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU A 859 " --> pdb=" O LEU A 855 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 886 removed outlier: 4.246A pdb=" N ASN A 881 " --> pdb=" O PHE A 877 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N PHE A 884 " --> pdb=" O LYS A 880 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 891 Processing helix chain 'A' and resid 892 through 894 No H-bonds generated for 'chain 'A' and resid 892 through 894' Processing helix chain 'A' and resid 906 through 911 Processing helix chain 'A' and resid 918 through 926 Processing helix chain 'A' and resid 931 through 936 Processing helix chain 'A' and resid 938 through 945 removed outlier: 3.600A pdb=" N TYR A 942 " --> pdb=" O PRO A 939 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILE A 945 " --> pdb=" O TYR A 942 " (cutoff:3.500A) Processing helix chain 'A' and resid 948 through 951 Processing helix chain 'A' and resid 952 through 976 removed outlier: 3.715A pdb=" N ALA A 964 " --> pdb=" O THR A 960 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N PHE A 965 " --> pdb=" O PHE A 961 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N THR A 968 " --> pdb=" O ALA A 964 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N PHE A 971 " --> pdb=" O GLY A 967 " (cutoff:3.500A) Processing helix chain 'A' and resid 977 through 979 No H-bonds generated for 'chain 'A' and resid 977 through 979' Processing helix chain 'A' and resid 992 through 1015 removed outlier: 3.762A pdb=" N GLY A 996 " --> pdb=" O ASN A 992 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N LEU A1011 " --> pdb=" O VAL A1007 " (cutoff:3.500A) Processing helix chain 'A' and resid 1019 through 1041 removed outlier: 3.717A pdb=" N HIS A1023 " --> pdb=" O THR A1019 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE A1024 " --> pdb=" O TRP A1020 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLY A1041 " --> pdb=" O SER A1037 " (cutoff:3.500A) Processing helix chain 'A' and resid 1055 through 1062 removed outlier: 3.676A pdb=" N GLN A1059 " --> pdb=" O PHE A1055 " (cutoff:3.500A) Processing helix chain 'A' and resid 1064 through 1077 removed outlier: 3.648A pdb=" N LEU A1068 " --> pdb=" O VAL A1064 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N PHE A1075 " --> pdb=" O ILE A1071 " (cutoff:3.500A) Processing helix chain 'A' and resid 1078 through 1088 Processing helix chain 'C' and resid 46 through 51 Processing helix chain 'C' and resid 52 through 71 removed outlier: 4.060A pdb=" N GLY C 58 " --> pdb=" O PHE C 54 " (cutoff:3.500A) Proline residue: C 63 - end of helix Processing helix chain 'C' and resid 91 through 95 Processing helix chain 'C' and resid 131 through 136 removed outlier: 3.596A pdb=" N LYS C 136 " --> pdb=" O ARG C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 144 Processing helix chain 'C' and resid 148 through 152 Processing helix chain 'C' and resid 172 through 177 removed outlier: 3.547A pdb=" N SER C 177 " --> pdb=" O ALA C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 212 Processing helix chain 'C' and resid 239 through 243 removed outlier: 3.681A pdb=" N LEU C 243 " --> pdb=" O VAL C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 262 Processing helix chain 'C' and resid 323 through 350 removed outlier: 3.618A pdb=" N LEU C 339 " --> pdb=" O ILE C 335 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 22 Processing sheet with id=AA2, first strand: chain 'A' and resid 124 through 128 Processing sheet with id=AA3, first strand: chain 'A' and resid 146 through 150 removed outlier: 4.123A pdb=" N VAL A 149 " --> pdb=" O ILE A 257 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N TYR A 258 " --> pdb=" O SER A 163 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER A 163 " --> pdb=" O TYR A 258 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 159 through 160 removed outlier: 3.515A pdb=" N LEU A 245 " --> pdb=" O LEU A 159 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 187 through 188 removed outlier: 3.814A pdb=" N TYR A 172 " --> pdb=" O LYS A 252 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR A 250 " --> pdb=" O THR A 174 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 223 through 224 removed outlier: 3.855A pdb=" N GLY A 223 " --> pdb=" O LEU A 239 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 390 through 391 Processing sheet with id=AA8, first strand: chain 'A' and resid 405 through 408 removed outlier: 5.987A pdb=" N VAL A 406 " --> pdb=" O TRP A 671 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N LEU A 673 " --> pdb=" O VAL A 406 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N THR A 408 " --> pdb=" O LEU A 673 " (cutoff:3.500A) removed outlier: 8.965A pdb=" N LEU A 786 " --> pdb=" O TYR A 747 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LEU A 749 " --> pdb=" O LEU A 786 " (cutoff:3.500A) removed outlier: 8.349A pdb=" N CYS A 788 " --> pdb=" O LEU A 749 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ILE A 751 " --> pdb=" O CYS A 788 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLY A 748 " --> pdb=" O GLU A 696 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 812 through 815 removed outlier: 5.650A pdb=" N SER A 813 " --> pdb=" O ILE A 831 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 77 through 81 removed outlier: 3.517A pdb=" N ARG C 309 " --> pdb=" O GLY C 123 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N TYR C 122 " --> pdb=" O LEU C 272 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N LEU C 272 " --> pdb=" O TYR C 122 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 108 through 110 removed outlier: 3.588A pdb=" N PHE C 108 " --> pdb=" O TYR C 291 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N ARG C 290 " --> pdb=" O ILE C 188 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE C 188 " --> pdb=" O ARG C 290 " (cutoff:3.500A) 331 hydrogen bonds defined for protein. 936 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: 3.59 Time building geometry restraints manager: 3.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1518 1.32 - 1.45: 2643 1.45 - 1.57: 5325 1.57 - 1.69: 2 1.69 - 1.81: 71 Bond restraints: 9559 Sorted by residual: bond pdb=" F1 ALF A1101 " pdb="AL ALF A1101 " ideal model delta sigma weight residual 1.684 1.799 -0.115 2.00e-02 2.50e+03 3.29e+01 bond pdb=" F3 ALF A1101 " pdb="AL ALF A1101 " ideal model delta sigma weight residual 1.685 1.799 -0.114 2.00e-02 2.50e+03 3.23e+01 bond pdb=" F4 ALF A1101 " pdb="AL ALF A1101 " ideal model delta sigma weight residual 1.686 1.800 -0.114 2.00e-02 2.50e+03 3.23e+01 bond pdb=" F2 ALF A1101 " pdb="AL ALF A1101 " ideal model delta sigma weight residual 1.685 1.797 -0.112 2.00e-02 2.50e+03 3.13e+01 bond pdb=" N THR C 100 " pdb=" CA THR C 100 " ideal model delta sigma weight residual 1.455 1.487 -0.032 9.60e-03 1.09e+04 1.13e+01 ... (remaining 9554 not shown) Histogram of bond angle deviations from ideal: 0.00 - 14.11: 12955 14.11 - 28.22: 4 28.22 - 42.32: 0 42.32 - 56.43: 0 56.43 - 70.54: 2 Bond angle restraints: 12961 Sorted by residual: angle pdb=" F1 ALF A1101 " pdb="AL ALF A1101 " pdb=" F2 ALF A1101 " ideal model delta sigma weight residual 108.68 179.22 -70.54 3.00e+00 1.11e-01 5.53e+02 angle pdb=" F3 ALF A1101 " pdb="AL ALF A1101 " pdb=" F4 ALF A1101 " ideal model delta sigma weight residual 109.63 179.69 -70.06 3.00e+00 1.11e-01 5.45e+02 angle pdb=" N LYS A1088 " pdb=" CA LYS A1088 " pdb=" C LYS A1088 " ideal model delta sigma weight residual 112.93 103.39 9.54 1.12e+00 7.97e-01 7.26e+01 angle pdb=" F2 ALF A1101 " pdb="AL ALF A1101 " pdb=" F4 ALF A1101 " ideal model delta sigma weight residual 110.21 90.20 20.01 3.00e+00 1.11e-01 4.45e+01 angle pdb=" F2 ALF A1101 " pdb="AL ALF A1101 " pdb=" F3 ALF A1101 " ideal model delta sigma weight residual 109.59 89.68 19.91 3.00e+00 1.11e-01 4.41e+01 ... (remaining 12956 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.09: 5428 26.09 - 52.18: 245 52.18 - 78.27: 23 78.27 - 104.35: 17 104.35 - 130.44: 13 Dihedral angle restraints: 5726 sinusoidal: 2383 harmonic: 3343 Sorted by residual: dihedral pdb=" C3 PEE A1102 " pdb=" C1 PEE A1102 " pdb=" C2 PEE A1102 " pdb=" O3P PEE A1102 " ideal model delta sinusoidal sigma weight residual 62.73 -67.71 130.44 1 3.00e+01 1.11e-03 1.76e+01 dihedral pdb=" O2 PEE A1102 " pdb=" C1 PEE A1102 " pdb=" C2 PEE A1102 " pdb=" O3P PEE A1102 " ideal model delta sinusoidal sigma weight residual 300.04 170.89 129.15 1 3.00e+01 1.11e-03 1.74e+01 dihedral pdb=" N PEE A1102 " pdb=" C4 PEE A1102 " pdb=" C5 PEE A1102 " pdb=" O4P PEE A1102 " ideal model delta sinusoidal sigma weight residual -56.97 -178.16 121.19 1 3.00e+01 1.11e-03 1.62e+01 ... (remaining 5723 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.091: 1462 1.091 - 2.182: 0 2.182 - 3.272: 1 3.272 - 4.363: 0 4.363 - 5.454: 2 Chirality restraints: 1465 Sorted by residual: chirality pdb=" C1 NAG C 402 " pdb=" O4 NAG C 401 " pdb=" C2 NAG C 402 " pdb=" O5 NAG C 402 " both_signs ideal model delta sigma weight residual False -2.40 3.05 -5.45 2.00e-02 2.50e+03 7.44e+04 chirality pdb=" C1 MAN C 403 " pdb=" O4 NAG C 402 " pdb=" C2 MAN C 403 " pdb=" O5 MAN C 403 " both_signs ideal model delta sigma weight residual False 2.40 -2.42 4.82 2.00e-02 2.50e+03 5.81e+04 chirality pdb=" C1 NAG C 404 " pdb=" ND2 ASN C 294 " pdb=" C2 NAG C 404 " pdb=" O5 NAG C 404 " both_signs ideal model delta sigma weight residual False -2.40 -0.17 -2.23 2.00e-01 2.50e+01 1.25e+02 ... (remaining 1462 not shown) Planarity restraints: 1614 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 294 " 0.271 2.00e-02 2.50e+03 4.91e-01 3.01e+03 pdb=" CG ASN C 294 " -0.164 2.00e-02 2.50e+03 pdb=" OD1 ASN C 294 " 0.086 2.00e-02 2.50e+03 pdb=" ND2 ASN C 294 " -0.831 2.00e-02 2.50e+03 pdb=" C1 NAG C 404 " 0.639 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 402 " 0.275 2.00e-02 2.50e+03 2.27e-01 6.46e+02 pdb=" C7 NAG C 402 " -0.075 2.00e-02 2.50e+03 pdb=" C8 NAG C 402 " 0.187 2.00e-02 2.50e+03 pdb=" N2 NAG C 402 " -0.377 2.00e-02 2.50e+03 pdb=" O7 NAG C 402 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 401 " 0.130 2.00e-02 2.50e+03 1.10e-01 1.50e+02 pdb=" C7 NAG C 401 " -0.027 2.00e-02 2.50e+03 pdb=" C8 NAG C 401 " -0.032 2.00e-02 2.50e+03 pdb=" N2 NAG C 401 " -0.175 2.00e-02 2.50e+03 pdb=" O7 NAG C 401 " 0.104 2.00e-02 2.50e+03 ... (remaining 1611 not shown) Histogram of nonbonded interaction distances: 1.72 - 2.36: 56 2.36 - 2.99: 5632 2.99 - 3.63: 12950 3.63 - 4.26: 20676 4.26 - 4.90: 34904 Nonbonded interactions: 74218 Sorted by model distance: nonbonded pdb=" CD2 TYR A 876 " pdb=" CD1 ILE A 920 " model vdw 1.719 3.760 nonbonded pdb=" OE2 GLU A 181 " pdb=" OD2 ASP A 676 " model vdw 1.869 3.040 nonbonded pdb=" CG ASN C 294 " pdb=" O5 NAG C 404 " model vdw 1.919 2.616 nonbonded pdb=" OH TYR A 876 " pdb=" O VAL A1007 " model vdw 1.932 3.040 nonbonded pdb=" OD1 ASN C 294 " pdb=" O5 NAG C 404 " model vdw 1.962 3.040 ... (remaining 74213 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 24.980 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.050 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: 0.010 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 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 : 0.005 0.115 9559 Z= 0.314 Angle : 1.225 70.538 12961 Z= 0.602 Chirality : 0.206 5.454 1465 Planarity : 0.008 0.227 1611 Dihedral : 16.587 130.443 3561 Min Nonbonded Distance : 1.719 Molprobity Statistics. All-atom Clashscore : 37.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 0.69 % Allowed : 3.74 % Favored : 95.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.22 (0.19), residues: 1129 helix: -2.91 (0.19), residues: 474 sheet: -3.89 (0.33), residues: 151 loop : -3.83 (0.22), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 323 HIS 0.005 0.001 HIS C 348 PHE 0.012 0.001 PHE A 884 TYR 0.015 0.001 TYR C 350 ARG 0.005 0.000 ARG A 723 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 226 time to evaluate : 1.079 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 352 ASN cc_start: 0.7848 (t0) cc_final: 0.7585 (t0) REVERT: A 381 TYR cc_start: 0.7636 (t80) cc_final: 0.7287 (t80) REVERT: A 399 GLU cc_start: 0.8819 (tt0) cc_final: 0.8579 (mt-10) REVERT: A 826 GLU cc_start: 0.8349 (tp30) cc_final: 0.7988 (tp30) REVERT: A 914 CYS cc_start: 0.8052 (m) cc_final: 0.7751 (m) REVERT: A 1050 GLN cc_start: 0.8516 (pp30) cc_final: 0.8128 (pp30) REVERT: C 106 ILE cc_start: 0.8564 (mm) cc_final: 0.8300 (mm) REVERT: C 122 TYR cc_start: 0.8611 (p90) cc_final: 0.8410 (p90) REVERT: C 310 MET cc_start: 0.8525 (ttp) cc_final: 0.7885 (tmm) outliers start: 7 outliers final: 2 residues processed: 231 average time/residue: 0.2476 time to fit residues: 76.5397 Evaluate side-chains 145 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 143 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 PHE Chi-restraints excluded: chain A residue 275 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 0.3980 chunk 85 optimal weight: 6.9990 chunk 47 optimal weight: 9.9990 chunk 29 optimal weight: 7.9990 chunk 57 optimal weight: 5.9990 chunk 45 optimal weight: 9.9990 chunk 88 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 53 optimal weight: 0.4980 chunk 65 optimal weight: 4.9990 chunk 102 optimal weight: 5.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 GLN A 243 ASN A 314 GLN A 352 ASN A 392 ASN A 402 GLN A 653 GLN A 716 HIS A 744 HIS A 828 HIS A 862 HIS A 864 HIS A1089 ASN C 36 GLN C 129 GLN C 347 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 9559 Z= 0.338 Angle : 0.722 8.185 12961 Z= 0.365 Chirality : 0.049 0.194 1465 Planarity : 0.004 0.031 1611 Dihedral : 12.730 103.102 1381 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 2.56 % Allowed : 12.78 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.91 (0.22), residues: 1129 helix: -1.90 (0.21), residues: 477 sheet: -3.80 (0.31), residues: 158 loop : -2.77 (0.25), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 323 HIS 0.009 0.002 HIS C 302 PHE 0.021 0.002 PHE A1075 TYR 0.016 0.002 TYR A 879 ARG 0.004 0.001 ARG C 215 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 170 time to evaluate : 1.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 LYS cc_start: 0.8016 (mtpp) cc_final: 0.7617 (mmmt) REVERT: A 654 ASP cc_start: 0.7811 (m-30) cc_final: 0.7608 (m-30) REVERT: A 747 TYR cc_start: 0.6954 (m-80) cc_final: 0.6561 (m-80) REVERT: A 826 GLU cc_start: 0.8463 (tp30) cc_final: 0.8110 (tp30) REVERT: A 877 PHE cc_start: 0.8879 (OUTLIER) cc_final: 0.8092 (t80) REVERT: A 914 CYS cc_start: 0.8426 (m) cc_final: 0.8176 (m) REVERT: A 975 TYR cc_start: 0.9182 (t80) cc_final: 0.8849 (t80) REVERT: A 1014 ASP cc_start: 0.8574 (m-30) cc_final: 0.8350 (t0) REVERT: A 1050 GLN cc_start: 0.8841 (pp30) cc_final: 0.8304 (pp30) REVERT: C 310 MET cc_start: 0.8686 (ttp) cc_final: 0.8239 (tmm) outliers start: 26 outliers final: 18 residues processed: 184 average time/residue: 0.2150 time to fit residues: 56.3490 Evaluate side-chains 179 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 160 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 184 CYS Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 788 CYS Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 877 PHE Chi-restraints excluded: chain C residue 29 ASP Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain C residue 336 SER Chi-restraints excluded: chain C residue 341 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 57 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 85 optimal weight: 7.9990 chunk 69 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 chunk 102 optimal weight: 4.9990 chunk 111 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 101 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 82 optimal weight: 5.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 ASN A 397 ASN A 828 HIS C 347 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9559 Z= 0.206 Angle : 0.620 7.524 12961 Z= 0.311 Chirality : 0.045 0.179 1465 Planarity : 0.004 0.034 1611 Dihedral : 9.924 85.002 1376 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 3.34 % Allowed : 15.24 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.06 (0.23), residues: 1129 helix: -1.20 (0.23), residues: 479 sheet: -3.20 (0.33), residues: 158 loop : -2.36 (0.26), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 323 HIS 0.007 0.001 HIS C 302 PHE 0.016 0.001 PHE A1039 TYR 0.016 0.001 TYR A 108 ARG 0.004 0.000 ARG C 161 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 169 time to evaluate : 0.945 Fit side-chains revert: symmetry clash REVERT: A 142 LYS cc_start: 0.8025 (mtpp) cc_final: 0.7590 (mmmt) REVERT: A 183 ASN cc_start: 0.8945 (p0) cc_final: 0.8717 (p0) REVERT: A 366 GLN cc_start: 0.8380 (tm-30) cc_final: 0.8163 (tm-30) REVERT: A 780 MET cc_start: 0.7010 (ppp) cc_final: 0.6695 (ppp) REVERT: A 826 GLU cc_start: 0.8472 (tp30) cc_final: 0.8164 (tp30) REVERT: A 851 LYS cc_start: 0.7696 (mmtm) cc_final: 0.7082 (tppt) REVERT: A 877 PHE cc_start: 0.8867 (OUTLIER) cc_final: 0.8147 (t80) REVERT: A 910 MET cc_start: 0.8548 (mmm) cc_final: 0.8304 (mmm) REVERT: A 1014 ASP cc_start: 0.8592 (m-30) cc_final: 0.8369 (t0) REVERT: A 1050 GLN cc_start: 0.8897 (pp30) cc_final: 0.8455 (pp30) REVERT: C 310 MET cc_start: 0.8610 (ttp) cc_final: 0.8256 (tmm) outliers start: 34 outliers final: 19 residues processed: 187 average time/residue: 0.1983 time to fit residues: 53.2860 Evaluate side-chains 169 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 149 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 PHE Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 184 CYS Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 788 CYS Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 877 PHE Chi-restraints excluded: chain A residue 1019 THR Chi-restraints excluded: chain C residue 29 ASP Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain C residue 336 SER Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 345 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 3.9990 chunk 77 optimal weight: 0.4980 chunk 53 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 49 optimal weight: 8.9990 chunk 69 optimal weight: 0.9980 chunk 103 optimal weight: 6.9990 chunk 109 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 29 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 347 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.2949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9559 Z= 0.211 Angle : 0.608 10.200 12961 Z= 0.302 Chirality : 0.044 0.188 1465 Planarity : 0.004 0.030 1611 Dihedral : 8.938 84.458 1376 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 3.93 % Allowed : 16.32 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.54 (0.24), residues: 1129 helix: -0.77 (0.23), residues: 471 sheet: -2.80 (0.35), residues: 158 loop : -2.13 (0.26), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 323 HIS 0.006 0.001 HIS C 302 PHE 0.016 0.001 PHE A1039 TYR 0.016 0.001 TYR C 350 ARG 0.002 0.000 ARG A 113 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 152 time to evaluate : 1.078 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 ASP cc_start: 0.7742 (p0) cc_final: 0.7527 (p0) REVERT: A 152 ASP cc_start: 0.7991 (m-30) cc_final: 0.7781 (m-30) REVERT: A 174 THR cc_start: 0.9572 (OUTLIER) cc_final: 0.9288 (p) REVERT: A 183 ASN cc_start: 0.8971 (p0) cc_final: 0.8769 (p0) REVERT: A 851 LYS cc_start: 0.7809 (mmtm) cc_final: 0.7442 (mmmm) REVERT: A 877 PHE cc_start: 0.8861 (OUTLIER) cc_final: 0.8196 (t80) REVERT: A 1014 ASP cc_start: 0.8619 (m-30) cc_final: 0.8386 (t0) REVERT: A 1050 GLN cc_start: 0.8923 (pp30) cc_final: 0.8581 (pp30) REVERT: C 310 MET cc_start: 0.8595 (ttp) cc_final: 0.8303 (tmm) REVERT: C 347 ASN cc_start: 0.7493 (OUTLIER) cc_final: 0.7229 (t0) outliers start: 40 outliers final: 27 residues processed: 176 average time/residue: 0.2028 time to fit residues: 50.4816 Evaluate side-chains 169 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 139 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 PHE Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 184 CYS Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 717 GLU Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 788 CYS Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 877 PHE Chi-restraints excluded: chain A residue 879 TYR Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 1019 THR Chi-restraints excluded: chain C residue 29 ASP Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 336 SER Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 347 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 62 optimal weight: 4.9990 chunk 1 optimal weight: 10.0000 chunk 81 optimal weight: 0.9980 chunk 45 optimal weight: 7.9990 chunk 93 optimal weight: 6.9990 chunk 75 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 55 optimal weight: 7.9990 chunk 98 optimal weight: 7.9990 chunk 27 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 ASN A 844 ASN A1089 ASN ** C 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 347 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.3168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 9559 Z= 0.435 Angle : 0.744 9.062 12961 Z= 0.370 Chirality : 0.049 0.184 1465 Planarity : 0.004 0.034 1611 Dihedral : 8.675 83.094 1376 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer: Outliers : 4.33 % Allowed : 18.09 % Favored : 77.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.78 (0.23), residues: 1129 helix: -1.03 (0.23), residues: 478 sheet: -2.78 (0.35), residues: 168 loop : -2.22 (0.27), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 323 HIS 0.007 0.002 HIS A1023 PHE 0.018 0.002 PHE C 179 TYR 0.014 0.002 TYR A 879 ARG 0.003 0.000 ARG A 869 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 150 time to evaluate : 0.991 Fit side-chains REVERT: A 366 GLN cc_start: 0.8327 (tm-30) cc_final: 0.8104 (tm-30) REVERT: A 399 GLU cc_start: 0.8810 (tt0) cc_final: 0.8337 (mt-10) REVERT: A 877 PHE cc_start: 0.9071 (OUTLIER) cc_final: 0.8225 (t80) REVERT: A 1014 ASP cc_start: 0.8671 (m-30) cc_final: 0.8413 (t0) REVERT: A 1050 GLN cc_start: 0.8981 (pp30) cc_final: 0.8555 (pp30) REVERT: C 347 ASN cc_start: 0.7778 (OUTLIER) cc_final: 0.7402 (t0) outliers start: 44 outliers final: 32 residues processed: 174 average time/residue: 0.2015 time to fit residues: 51.0122 Evaluate side-chains 173 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 139 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 PHE Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 184 CYS Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain A residue 306 CYS Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 717 GLU Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 788 CYS Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 877 PHE Chi-restraints excluded: chain A residue 936 THR Chi-restraints excluded: chain A residue 950 MET Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 1019 THR Chi-restraints excluded: chain C residue 29 ASP Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 336 SER Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 347 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 98 optimal weight: 6.9990 chunk 21 optimal weight: 0.0670 chunk 64 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 109 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 chunk 50 optimal weight: 9.9990 chunk 9 optimal weight: 7.9990 chunk 36 optimal weight: 6.9990 chunk 57 optimal weight: 0.7980 chunk 105 optimal weight: 0.7980 overall best weight: 0.7120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 ASN A 844 ASN ** C 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 347 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.3409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 9559 Z= 0.181 Angle : 0.588 9.078 12961 Z= 0.291 Chirality : 0.043 0.193 1465 Planarity : 0.003 0.032 1611 Dihedral : 7.716 82.715 1376 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 3.15 % Allowed : 19.57 % Favored : 77.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.15 (0.24), residues: 1129 helix: -0.48 (0.24), residues: 470 sheet: -2.38 (0.38), residues: 163 loop : -1.94 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 260 HIS 0.005 0.001 HIS C 302 PHE 0.015 0.001 PHE A 221 TYR 0.017 0.001 TYR A 722 ARG 0.004 0.000 ARG A 135 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 153 time to evaluate : 0.981 Fit side-chains revert: symmetry clash REVERT: A 145 ASP cc_start: 0.7966 (p0) cc_final: 0.7663 (p0) REVERT: A 183 ASN cc_start: 0.8779 (p0) cc_final: 0.8571 (p0) REVERT: A 877 PHE cc_start: 0.9053 (OUTLIER) cc_final: 0.8268 (t80) REVERT: A 1014 ASP cc_start: 0.8516 (m-30) cc_final: 0.8266 (t0) REVERT: A 1050 GLN cc_start: 0.8933 (pp30) cc_final: 0.8647 (pp30) REVERT: C 310 MET cc_start: 0.8751 (tmm) cc_final: 0.8368 (tmm) REVERT: C 322 ASN cc_start: 0.8074 (t0) cc_final: 0.6520 (p0) outliers start: 32 outliers final: 25 residues processed: 178 average time/residue: 0.1925 time to fit residues: 49.2524 Evaluate side-chains 168 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 142 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 PHE Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 184 CYS Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 717 GLU Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 788 CYS Chi-restraints excluded: chain A residue 822 SER Chi-restraints excluded: chain A residue 877 PHE Chi-restraints excluded: chain A residue 879 TYR Chi-restraints excluded: chain A residue 936 THR Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 1019 THR Chi-restraints excluded: chain A residue 1085 ILE Chi-restraints excluded: chain C residue 29 ASP Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 336 SER Chi-restraints excluded: chain C residue 345 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 12 optimal weight: 0.5980 chunk 62 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 92 optimal weight: 8.9990 chunk 108 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 50 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 ASN ** C 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.3527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 9559 Z= 0.233 Angle : 0.615 9.179 12961 Z= 0.304 Chirality : 0.044 0.179 1465 Planarity : 0.004 0.044 1611 Dihedral : 7.521 83.303 1376 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 3.83 % Allowed : 21.04 % Favored : 75.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.24), residues: 1129 helix: -0.44 (0.23), residues: 473 sheet: -2.06 (0.39), residues: 167 loop : -1.86 (0.28), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 323 HIS 0.005 0.001 HIS C 302 PHE 0.020 0.001 PHE A 155 TYR 0.020 0.001 TYR A 722 ARG 0.011 0.000 ARG A 206 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 147 time to evaluate : 1.022 Fit side-chains revert: symmetry clash REVERT: A 145 ASP cc_start: 0.7995 (p0) cc_final: 0.7665 (p0) REVERT: A 183 ASN cc_start: 0.8768 (p0) cc_final: 0.8539 (p0) REVERT: A 399 GLU cc_start: 0.8682 (tt0) cc_final: 0.8118 (mt-10) REVERT: A 877 PHE cc_start: 0.9065 (OUTLIER) cc_final: 0.8136 (t80) REVERT: A 950 MET cc_start: 0.8262 (OUTLIER) cc_final: 0.7910 (mtm) REVERT: A 1014 ASP cc_start: 0.8553 (m-30) cc_final: 0.8260 (t0) REVERT: A 1050 GLN cc_start: 0.9023 (pp30) cc_final: 0.8752 (pp30) REVERT: C 310 MET cc_start: 0.8841 (tmm) cc_final: 0.8479 (tmm) REVERT: C 343 LEU cc_start: 0.7568 (mp) cc_final: 0.7050 (mp) outliers start: 39 outliers final: 32 residues processed: 171 average time/residue: 0.1920 time to fit residues: 47.2988 Evaluate side-chains 174 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 140 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 PHE Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 184 CYS Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 717 GLU Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 788 CYS Chi-restraints excluded: chain A residue 822 SER Chi-restraints excluded: chain A residue 823 MET Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 877 PHE Chi-restraints excluded: chain A residue 879 TYR Chi-restraints excluded: chain A residue 936 THR Chi-restraints excluded: chain A residue 950 MET Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 1019 THR Chi-restraints excluded: chain A residue 1085 ILE Chi-restraints excluded: chain C residue 29 ASP Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 336 SER Chi-restraints excluded: chain C residue 345 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 65 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 21 optimal weight: 10.0000 chunk 69 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 chunk 53 optimal weight: 0.4980 chunk 10 optimal weight: 0.1980 chunk 85 optimal weight: 7.9990 chunk 99 optimal weight: 2.9990 chunk 104 optimal weight: 0.0670 chunk 95 optimal weight: 2.9990 overall best weight: 0.7120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 ASN A 888 GLN ** C 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.3635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 9559 Z= 0.182 Angle : 0.573 8.594 12961 Z= 0.286 Chirality : 0.043 0.282 1465 Planarity : 0.003 0.035 1611 Dihedral : 7.070 81.787 1376 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 3.24 % Allowed : 21.53 % Favored : 75.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.25), residues: 1129 helix: -0.21 (0.24), residues: 479 sheet: -1.88 (0.40), residues: 166 loop : -1.71 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 260 HIS 0.005 0.001 HIS C 302 PHE 0.016 0.001 PHE A1039 TYR 0.020 0.001 TYR A 722 ARG 0.007 0.000 ARG A 206 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 145 time to evaluate : 1.025 Fit side-chains revert: symmetry clash REVERT: A 145 ASP cc_start: 0.7921 (p0) cc_final: 0.7577 (p0) REVERT: A 183 ASN cc_start: 0.8581 (p0) cc_final: 0.8155 (p0) REVERT: A 399 GLU cc_start: 0.8685 (tt0) cc_final: 0.8103 (mt-10) REVERT: A 877 PHE cc_start: 0.9030 (OUTLIER) cc_final: 0.8118 (t80) REVERT: A 882 LEU cc_start: 0.8784 (tp) cc_final: 0.8440 (tt) REVERT: A 950 MET cc_start: 0.8038 (OUTLIER) cc_final: 0.7743 (mtm) REVERT: A 1014 ASP cc_start: 0.8512 (m-30) cc_final: 0.8188 (t0) REVERT: A 1050 GLN cc_start: 0.8944 (pp30) cc_final: 0.8669 (pp30) REVERT: C 310 MET cc_start: 0.8844 (tmm) cc_final: 0.8464 (tmm) REVERT: C 322 ASN cc_start: 0.8103 (t0) cc_final: 0.6594 (p0) REVERT: C 343 LEU cc_start: 0.7822 (mp) cc_final: 0.7442 (mp) outliers start: 33 outliers final: 29 residues processed: 169 average time/residue: 0.2092 time to fit residues: 50.4950 Evaluate side-chains 170 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 139 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 PHE Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 184 CYS Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 717 GLU Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 788 CYS Chi-restraints excluded: chain A residue 822 SER Chi-restraints excluded: chain A residue 877 PHE Chi-restraints excluded: chain A residue 879 TYR Chi-restraints excluded: chain A residue 936 THR Chi-restraints excluded: chain A residue 950 MET Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 1019 THR Chi-restraints excluded: chain A residue 1044 ILE Chi-restraints excluded: chain A residue 1085 ILE Chi-restraints excluded: chain C residue 29 ASP Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 336 SER Chi-restraints excluded: chain C residue 345 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 44 optimal weight: 10.0000 chunk 79 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 chunk 95 optimal weight: 0.5980 chunk 66 optimal weight: 0.9990 chunk 107 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.3672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 9559 Z= 0.231 Angle : 0.604 8.967 12961 Z= 0.298 Chirality : 0.044 0.181 1465 Planarity : 0.003 0.032 1611 Dihedral : 6.943 82.324 1376 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 3.54 % Allowed : 21.83 % Favored : 74.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.25), residues: 1129 helix: -0.19 (0.24), residues: 485 sheet: -1.80 (0.41), residues: 166 loop : -1.70 (0.29), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 376 HIS 0.005 0.001 HIS C 302 PHE 0.020 0.001 PHE A1039 TYR 0.013 0.001 TYR C 350 ARG 0.006 0.000 ARG A 206 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 145 time to evaluate : 1.042 Fit side-chains REVERT: A 145 ASP cc_start: 0.7942 (p0) cc_final: 0.7621 (p0) REVERT: A 183 ASN cc_start: 0.8616 (p0) cc_final: 0.8184 (p0) REVERT: A 399 GLU cc_start: 0.8706 (tt0) cc_final: 0.8113 (mt-10) REVERT: A 790 MET cc_start: 0.9001 (mmm) cc_final: 0.8219 (mmm) REVERT: A 851 LYS cc_start: 0.7694 (mmtm) cc_final: 0.7168 (mmmm) REVERT: A 877 PHE cc_start: 0.9049 (OUTLIER) cc_final: 0.8132 (t80) REVERT: A 910 MET cc_start: 0.8823 (mmm) cc_final: 0.8412 (tpt) REVERT: A 950 MET cc_start: 0.8083 (OUTLIER) cc_final: 0.7807 (mtm) REVERT: A 1014 ASP cc_start: 0.8525 (m-30) cc_final: 0.8240 (t0) REVERT: A 1050 GLN cc_start: 0.8984 (pp30) cc_final: 0.8679 (pp30) REVERT: C 310 MET cc_start: 0.8876 (tmm) cc_final: 0.8486 (tmm) REVERT: C 343 LEU cc_start: 0.7543 (mp) cc_final: 0.7044 (mp) outliers start: 36 outliers final: 32 residues processed: 169 average time/residue: 0.1963 time to fit residues: 47.6910 Evaluate side-chains 176 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 142 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 PHE Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 184 CYS Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain A residue 306 CYS Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 717 GLU Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 788 CYS Chi-restraints excluded: chain A residue 822 SER Chi-restraints excluded: chain A residue 823 MET Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 877 PHE Chi-restraints excluded: chain A residue 879 TYR Chi-restraints excluded: chain A residue 936 THR Chi-restraints excluded: chain A residue 950 MET Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 1019 THR Chi-restraints excluded: chain A residue 1044 ILE Chi-restraints excluded: chain A residue 1085 ILE Chi-restraints excluded: chain C residue 29 ASP Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 336 SER Chi-restraints excluded: chain C residue 345 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 50 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 112 optimal weight: 8.9990 chunk 103 optimal weight: 10.0000 chunk 89 optimal weight: 7.9990 chunk 9 optimal weight: 0.9990 chunk 69 optimal weight: 0.7980 chunk 54 optimal weight: 4.9990 chunk 71 optimal weight: 0.7980 chunk 95 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 872 HIS ** C 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.3840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 9559 Z= 0.187 Angle : 0.573 8.557 12961 Z= 0.283 Chirality : 0.042 0.185 1465 Planarity : 0.003 0.044 1611 Dihedral : 6.620 80.363 1376 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 2.95 % Allowed : 22.42 % Favored : 74.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.25), residues: 1129 helix: 0.08 (0.24), residues: 479 sheet: -1.58 (0.41), residues: 166 loop : -1.64 (0.29), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 260 HIS 0.004 0.001 HIS C 302 PHE 0.021 0.001 PHE A1039 TYR 0.013 0.001 TYR C 350 ARG 0.007 0.000 ARG A 206 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 148 time to evaluate : 1.064 Fit side-chains REVERT: A 145 ASP cc_start: 0.7912 (p0) cc_final: 0.7591 (p0) REVERT: A 399 GLU cc_start: 0.8650 (tt0) cc_final: 0.7974 (mt-10) REVERT: A 680 THR cc_start: 0.8500 (OUTLIER) cc_final: 0.8255 (m) REVERT: A 790 MET cc_start: 0.8922 (mmm) cc_final: 0.8264 (mmm) REVERT: A 851 LYS cc_start: 0.7675 (mmtm) cc_final: 0.7224 (mmmm) REVERT: A 877 PHE cc_start: 0.9047 (OUTLIER) cc_final: 0.8082 (t80) REVERT: A 882 LEU cc_start: 0.8748 (tp) cc_final: 0.8335 (tt) REVERT: A 950 MET cc_start: 0.8047 (OUTLIER) cc_final: 0.7797 (mtm) REVERT: A 1050 GLN cc_start: 0.8968 (pp30) cc_final: 0.8696 (pp30) REVERT: C 310 MET cc_start: 0.8850 (tmm) cc_final: 0.8457 (tmm) REVERT: C 322 ASN cc_start: 0.7998 (t0) cc_final: 0.6639 (p0) REVERT: C 343 LEU cc_start: 0.7809 (mp) cc_final: 0.7422 (mp) outliers start: 30 outliers final: 26 residues processed: 170 average time/residue: 0.2046 time to fit residues: 49.5909 Evaluate side-chains 169 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 140 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 PHE Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 184 CYS Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 717 GLU Chi-restraints excluded: chain A residue 788 CYS Chi-restraints excluded: chain A residue 822 SER Chi-restraints excluded: chain A residue 823 MET Chi-restraints excluded: chain A residue 877 PHE Chi-restraints excluded: chain A residue 879 TYR Chi-restraints excluded: chain A residue 936 THR Chi-restraints excluded: chain A residue 950 MET Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 1019 THR Chi-restraints excluded: chain A residue 1044 ILE Chi-restraints excluded: chain A residue 1085 ILE Chi-restraints excluded: chain C residue 29 ASP Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 336 SER Chi-restraints excluded: chain C residue 345 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 82 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 24 optimal weight: 7.9990 chunk 89 optimal weight: 7.9990 chunk 37 optimal weight: 2.9990 chunk 92 optimal weight: 7.9990 chunk 11 optimal weight: 0.9990 chunk 16 optimal weight: 9.9990 chunk 78 optimal weight: 2.9990 chunk 5 optimal weight: 0.1980 chunk 64 optimal weight: 1.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 777 GLN ** C 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.167054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.157534 restraints weight = 10573.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 66)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.155566 restraints weight = 16086.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.154425 restraints weight = 18836.109| |-----------------------------------------------------------------------------| r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.3911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 9559 Z= 0.194 Angle : 0.585 8.394 12961 Z= 0.289 Chirality : 0.043 0.180 1465 Planarity : 0.004 0.049 1611 Dihedral : 6.538 80.218 1376 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 3.34 % Allowed : 22.71 % Favored : 73.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.26), residues: 1129 helix: 0.10 (0.24), residues: 485 sheet: -1.45 (0.42), residues: 166 loop : -1.56 (0.29), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 260 HIS 0.005 0.001 HIS C 302 PHE 0.021 0.001 PHE A1039 TYR 0.016 0.001 TYR C 122 ARG 0.007 0.000 ARG A 206 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1938.65 seconds wall clock time: 35 minutes 39.37 seconds (2139.37 seconds total)