Starting phenix.real_space_refine on Wed Feb 4 08:14:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vq2_65258/02_2026/9vq2_65258.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vq2_65258/02_2026/9vq2_65258.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9vq2_65258/02_2026/9vq2_65258.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vq2_65258/02_2026/9vq2_65258.map" model { file = "/net/cci-nas-00/data/ceres_data/9vq2_65258/02_2026/9vq2_65258.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vq2_65258/02_2026/9vq2_65258.cif" } resolution = 3.4 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= 0.013 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 Al 1 5.89 5 P 1 5.49 5 Mg 1 5.21 5 S 45 5.16 5 C 6079 2.51 5 N 1503 2.21 5 O 1698 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 62 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9332 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 6592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 815, 6592 Classifications: {'peptide': 815} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 792} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 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: "B" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'MAN': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 60 Unusual residues: {' MG': 1, 'ALF': 1} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3, 'water': 1} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 2.17, per 1000 atoms: 0.23 Number of scatterers: 9332 At special positions: 0 Unit cell: (145.888, 102.272, 78.208, 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 45 16.00 P 1 15.00 Al 1 13.00 Mg 1 11.99 F 4 9.00 O 1698 8.00 N 1503 7.00 C 6079 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=2.03 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 Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-4 " NAG B 1 " - " MAN B 2 " NAG-ASN " NAG C 401 " - " ASN C 180 " " NAG C 402 " - " ASN C 294 " " NAG C 403 " - " ASN C 107 " Time building additional restraints: 0.85 Conformation dependent library (CDL) restraints added in 409.7 milliseconds 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: 2158 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 7 sheets defined 49.5% alpha, 10.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 54 through 65 Processing helix chain 'A' and resid 66 through 82 Processing helix chain 'A' and resid 88 through 121 Proline residue: A 94 - end of helix removed outlier: 3.682A 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 190 through 194 removed outlier: 3.710A pdb=" N ILE A 194 " --> pdb=" O ARG A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 273 removed outlier: 3.903A pdb=" N ASN A 273 " --> pdb=" O LYS A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 314 Processing helix chain 'A' and resid 315 through 320 removed outlier: 6.167A pdb=" N TYR A 318 " --> pdb=" O SER A 315 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ASP A 320 " --> pdb=" O PRO A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 334 Processing helix chain 'A' and resid 335 through 351 removed outlier: 3.874A 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 356 through 371 removed outlier: 4.169A pdb=" N TYR A 360 " --> pdb=" O PRO A 356 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER A 371 " --> pdb=" O LYS A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 377 removed outlier: 4.032A pdb=" N SER A 375 " --> pdb=" O SER A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 403 removed outlier: 4.258A pdb=" N VAL A 403 " --> pdb=" O LEU A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 666 Processing helix chain 'A' and resid 677 through 688 removed outlier: 4.051A pdb=" N SER A 683 " --> pdb=" O GLU A 679 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N THR A 684 " --> pdb=" O THR A 680 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 721 removed outlier: 3.696A pdb=" N ASP A 713 " --> pdb=" O GLU A 709 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU A 721 " --> pdb=" O GLU A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 753 through 762 Processing helix chain 'A' and resid 770 through 781 removed outlier: 3.835A pdb=" N ILE A 778 " --> pdb=" O ILE A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 791 through 805 removed outlier: 3.605A pdb=" N LYS A 795 " --> pdb=" O ALA A 791 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ALA A 796 " --> pdb=" O PRO A 792 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASN A 804 " --> pdb=" O ARG A 800 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LEU A 805 " --> pdb=" O MET A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 819 No H-bonds generated for 'chain 'A' and resid 817 through 819' Processing helix chain 'A' and resid 820 through 825 Processing helix chain 'A' and resid 839 through 844 removed outlier: 3.835A pdb=" N ASN A 844 " --> pdb=" O GLN A 840 " (cutoff:3.500A) Processing helix chain 'A' and resid 853 through 861 removed outlier: 4.518A pdb=" N LYS A 857 " --> pdb=" O LYS A 853 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ALA A 861 " --> pdb=" O LYS A 857 " (cutoff:3.500A) Processing helix chain 'A' and resid 861 through 892 removed outlier: 3.572A pdb=" N ASN A 881 " --> pdb=" O PHE A 877 " (cutoff:3.500A) Proline residue: A 887 - end of helix removed outlier: 3.679A pdb=" N GLN A 892 " --> pdb=" O GLN A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 904 through 911 Processing helix chain 'A' and resid 916 through 926 removed outlier: 4.355A pdb=" N ILE A 920 " --> pdb=" O THR A 916 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU A 921 " --> pdb=" O SER A 917 " (cutoff:3.500A) Processing helix chain 'A' and resid 931 through 938 removed outlier: 3.664A pdb=" N SER A 937 " --> pdb=" O ASP A 933 " (cutoff:3.500A) Processing helix chain 'A' and resid 939 through 946 removed outlier: 3.718A 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 978 Processing helix chain 'A' and resid 991 through 1015 removed outlier: 3.761A pdb=" N PHE A 995 " --> pdb=" O GLY A 991 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU A1011 " --> pdb=" O VAL A1007 " (cutoff:3.500A) Processing helix chain 'A' and resid 1019 through 1041 removed outlier: 3.760A pdb=" N LEU A1030 " --> pdb=" O ILE A1026 " (cutoff:3.500A) Processing helix chain 'A' and resid 1055 through 1061 Processing helix chain 'A' and resid 1063 through 1077 removed outlier: 3.573A 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 72 Proline residue: C 52 - end of helix removed outlier: 3.787A pdb=" N PHE C 55 " --> pdb=" O LEU C 51 " (cutoff:3.500A) removed outlier: 3.672A 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 89 through 95 removed outlier: 4.182A pdb=" N LYS C 93 " --> pdb=" O PRO C 90 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU C 95 " --> pdb=" O ASN C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 136 removed outlier: 3.516A pdb=" N LYS C 136 " --> pdb=" O ARG C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 145 Processing helix chain 'C' and resid 146 through 152 removed outlier: 3.670A pdb=" N LEU C 151 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASN C 152 " --> pdb=" O SER C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 177 Processing helix chain 'C' and resid 206 through 212 Processing helix chain 'C' and resid 239 through 243 removed outlier: 4.161A pdb=" N LEU C 243 " --> pdb=" O VAL C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 250 removed outlier: 3.632A pdb=" N ASN C 250 " --> pdb=" O PRO C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 262 removed outlier: 3.605A pdb=" N ARG C 262 " --> pdb=" O ILE C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 305 removed outlier: 3.555A pdb=" N PHE C 304 " --> pdb=" O VAL C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 348 removed outlier: 3.547A pdb=" N HIS C 348 " --> pdb=" O LEU C 344 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 23 Processing sheet with id=AA2, first strand: chain 'A' and resid 133 through 137 removed outlier: 3.522A pdb=" N LYS A 136 " --> pdb=" O VAL A 125 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL A 125 " --> pdb=" O LYS A 136 " (cutoff:3.500A) removed outlier: 12.568A pdb=" N THR A 124 " --> pdb=" O GLN A 150 " (cutoff:3.500A) removed outlier: 8.571A pdb=" N GLN A 150 " --> pdb=" O THR A 124 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N TYR A 126 " --> pdb=" O GLU A 148 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE A 128 " --> pdb=" O VAL A 146 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N VAL A 146 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N VAL A 149 " --> pdb=" O ILE A 257 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE A 257 " --> pdb=" O VAL A 149 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N LYS A 256 " --> pdb=" O SER A 164 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N SER A 164 " --> pdb=" O LYS A 256 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N TYR A 258 " --> pdb=" O LEU A 162 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 185 through 188 removed outlier: 3.764A pdb=" N TYR A 172 " --> pdb=" O LYS A 252 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 390 through 391 removed outlier: 3.532A pdb=" N VAL A 849 " --> pdb=" O GLY A 832 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N THR A 811 " --> pdb=" O VAL A 829 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N ILE A 831 " --> pdb=" O THR A 811 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N SER A 813 " --> pdb=" O ILE A 831 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N ILE A 833 " --> pdb=" O SER A 813 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N GLY A 815 " --> pdb=" O ILE A 833 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N VAL A 406 " --> pdb=" O TRP A 671 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N LEU A 673 " --> pdb=" O VAL A 406 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N THR A 408 " --> pdb=" O LEU A 673 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N VAL A 785 " --> pdb=" O VAL A 670 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ASP A 752 " --> pdb=" O LEU A 700 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 81 removed outlier: 3.609A pdb=" N ARG C 307 " --> pdb=" O SER C 125 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N VAL C 118 " --> pdb=" O LEU C 275 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N LEU C 275 " --> pdb=" O VAL C 118 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N MET C 120 " --> pdb=" O TYR C 273 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 102 through 109 removed outlier: 4.528A pdb=" N CYS C 102 " --> pdb=" O TYR C 297 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N PHE C 108 " --> pdb=" O TYR C 291 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N ARG C 290 " --> pdb=" O ILE C 188 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE C 188 " --> pdb=" O ARG C 290 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N THR C 182 " --> pdb=" O THR C 296 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 162 through 163 401 hydrogen bonds defined for protein. 1125 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: 1.51 Time building geometry restraints manager: 1.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.35: 2871 1.35 - 1.50: 2753 1.50 - 1.65: 3865 1.65 - 1.80: 54 1.80 - 1.95: 17 Bond restraints: 9560 Sorted by residual: bond pdb=" F4 ALF A1101 " pdb="AL ALF A1101 " ideal model delta sigma weight residual 1.686 1.955 -0.269 2.00e-02 2.50e+03 1.80e+02 bond pdb=" F3 ALF A1101 " pdb="AL ALF A1101 " ideal model delta sigma weight residual 1.685 1.808 -0.123 2.00e-02 2.50e+03 3.81e+01 bond pdb=" F2 ALF A1101 " pdb="AL ALF A1101 " ideal model delta sigma weight residual 1.685 1.804 -0.119 2.00e-02 2.50e+03 3.51e+01 bond pdb=" F1 ALF A1101 " pdb="AL ALF A1101 " ideal model delta sigma weight residual 1.684 1.791 -0.107 2.00e-02 2.50e+03 2.89e+01 bond pdb=" N VAL A 363 " pdb=" CA VAL A 363 " ideal model delta sigma weight residual 1.461 1.496 -0.035 1.24e-02 6.50e+03 7.83e+00 ... (remaining 9555 not shown) Histogram of bond angle deviations from ideal: 0.00 - 13.44: 12957 13.44 - 26.88: 4 26.88 - 40.32: 0 40.32 - 53.77: 0 53.77 - 67.21: 2 Bond angle restraints: 12963 Sorted by residual: angle pdb=" F1 ALF A1101 " pdb="AL ALF A1101 " pdb=" F2 ALF A1101 " ideal model delta sigma weight residual 108.68 175.89 -67.21 3.00e+00 1.11e-01 5.02e+02 angle pdb=" F3 ALF A1101 " pdb="AL ALF A1101 " pdb=" F4 ALF A1101 " ideal model delta sigma weight residual 109.63 170.55 -60.92 3.00e+00 1.11e-01 4.12e+02 angle pdb=" F1 ALF A1101 " pdb="AL ALF A1101 " pdb=" F3 ALF A1101 " ideal model delta sigma weight residual 109.69 88.00 21.69 3.00e+00 1.11e-01 5.23e+01 angle pdb=" F2 ALF A1101 " pdb="AL ALF A1101 " pdb=" F4 ALF A1101 " ideal model delta sigma weight residual 110.21 88.96 21.25 3.00e+00 1.11e-01 5.02e+01 angle pdb=" F1 ALF A1101 " pdb="AL ALF A1101 " pdb=" F4 ALF A1101 " ideal model delta sigma weight residual 109.02 90.53 18.49 3.00e+00 1.11e-01 3.80e+01 ... (remaining 12958 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.61: 5501 35.61 - 71.21: 210 71.21 - 106.82: 19 106.82 - 142.43: 5 142.43 - 178.03: 5 Dihedral angle restraints: 5740 sinusoidal: 2395 harmonic: 3345 Sorted by residual: dihedral pdb=" CB CYS C 91 " pdb=" SG CYS C 91 " pdb=" SG CYS C 104 " pdb=" CB CYS C 104 " ideal model delta sinusoidal sigma weight residual 93.00 173.16 -80.16 1 1.00e+01 1.00e-02 7.96e+01 dihedral pdb=" C38 P5S A1103 " pdb=" C39 P5S A1103 " pdb=" C40 P5S A1103 " pdb=" C41 P5S A1103 " ideal model delta sinusoidal sigma weight residual 64.51 -117.46 -178.03 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C21 P5S A1103 " pdb=" C22 P5S A1103 " pdb=" C23 P5S A1103 " pdb=" C24 P5S A1103 " ideal model delta sinusoidal sigma weight residual -64.63 112.33 -176.96 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 5737 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1003 0.041 - 0.082: 337 0.082 - 0.123: 105 0.123 - 0.165: 16 0.165 - 0.206: 4 Chirality restraints: 1465 Sorted by residual: chirality pdb=" CG LEU A 52 " pdb=" CB LEU A 52 " pdb=" CD1 LEU A 52 " pdb=" CD2 LEU A 52 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" C1 NAG C 403 " pdb=" ND2 ASN C 107 " pdb=" C2 NAG C 403 " pdb=" O5 NAG C 403 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-01 2.50e+01 9.81e-01 chirality pdb=" CB VAL A 363 " pdb=" CA VAL A 363 " pdb=" CG1 VAL A 363 " pdb=" CG2 VAL A 363 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 8.43e-01 ... (remaining 1462 not shown) Planarity restraints: 1614 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 403 " -0.302 2.00e-02 2.50e+03 2.55e-01 8.14e+02 pdb=" C7 NAG C 403 " 0.078 2.00e-02 2.50e+03 pdb=" C8 NAG C 403 " -0.183 2.00e-02 2.50e+03 pdb=" N2 NAG C 403 " 0.440 2.00e-02 2.50e+03 pdb=" O7 NAG C 403 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 107 " -0.127 2.00e-02 2.50e+03 1.45e-01 2.62e+02 pdb=" CG ASN C 107 " 0.051 2.00e-02 2.50e+03 pdb=" OD1 ASN C 107 " 0.017 2.00e-02 2.50e+03 pdb=" ND2 ASN C 107 " 0.234 2.00e-02 2.50e+03 pdb=" C1 NAG C 403 " -0.176 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS C 238 " 0.060 5.00e-02 4.00e+02 8.83e-02 1.25e+01 pdb=" N PRO C 239 " -0.153 5.00e-02 4.00e+02 pdb=" CA PRO C 239 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO C 239 " 0.049 5.00e-02 4.00e+02 ... (remaining 1611 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.70: 240 2.70 - 3.25: 8950 3.25 - 3.80: 13965 3.80 - 4.35: 18157 4.35 - 4.90: 31130 Nonbonded interactions: 72442 Sorted by model distance: nonbonded pdb=" OD1 ASN A 992 " pdb=" OG1 THR C 263 " model vdw 2.145 3.040 nonbonded pdb=" OG1 THR A 51 " pdb=" OD1 ASN A 54 " model vdw 2.184 3.040 nonbonded pdb=" ND2 ASN C 216 " pdb=" O GLY C 251 " model vdw 2.228 3.120 nonbonded pdb=" N GLU A 398 " pdb=" OE1 GLU A 398 " model vdw 2.231 3.120 nonbonded pdb=" O SER A 182 " pdb=" OG SER A 182 " model vdw 2.240 3.040 ... (remaining 72437 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 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: 5.770 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: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 9.750 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 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 0.269 9567 Z= 0.285 Angle : 1.166 67.208 12981 Z= 0.552 Chirality : 0.045 0.206 1465 Planarity : 0.008 0.255 1611 Dihedral : 19.505 178.031 3573 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.05 % Favored : 94.86 % Rotamer: Outliers : 0.49 % Allowed : 27.46 % Favored : 72.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.25), residues: 1129 helix: 0.71 (0.24), residues: 487 sheet: -0.06 (0.46), residues: 139 loop : -2.01 (0.26), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 723 TYR 0.015 0.001 TYR A 324 PHE 0.027 0.001 PHE A 297 TRP 0.017 0.001 TRP A 323 HIS 0.005 0.001 HIS C 283 Details of bonding type rmsd covalent geometry : bond 0.00535 ( 9560) covalent geometry : angle 1.16534 (12963) SS BOND : bond 0.00289 ( 3) SS BOND : angle 0.55001 ( 6) hydrogen bonds : bond 0.18308 ( 401) hydrogen bonds : angle 6.30069 ( 1125) link_ALPHA1-4 : bond 0.00657 ( 1) link_ALPHA1-4 : angle 1.77806 ( 3) link_NAG-ASN : bond 0.00384 ( 3) link_NAG-ASN : angle 2.08772 ( 9) *********************** 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 149 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 144 time to evaluate : 0.301 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 ASP cc_start: 0.8025 (OUTLIER) cc_final: 0.7635 (m-30) REVERT: A 129 GLU cc_start: 0.6742 (tp30) cc_final: 0.6529 (tp30) outliers start: 5 outliers final: 2 residues processed: 148 average time/residue: 0.0870 time to fit residues: 18.3144 Evaluate side-chains 130 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 127 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 CYS Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 879 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 108 optimal weight: 0.4980 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.4980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 5.9990 chunk 106 optimal weight: 8.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.126364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.095253 restraints weight = 14717.795| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 2.66 r_work: 0.2988 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.1032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9567 Z= 0.138 Angle : 0.846 29.673 12981 Z= 0.365 Chirality : 0.043 0.189 1465 Planarity : 0.004 0.058 1611 Dihedral : 13.159 179.365 1396 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 2.76 % Allowed : 24.11 % Favored : 73.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.25), residues: 1129 helix: 1.08 (0.24), residues: 491 sheet: 0.26 (0.46), residues: 143 loop : -1.81 (0.27), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 714 TYR 0.012 0.001 TYR C 134 PHE 0.013 0.001 PHE A 995 TRP 0.015 0.001 TRP A 323 HIS 0.003 0.001 HIS A 114 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 9560) covalent geometry : angle 0.83902 (12963) SS BOND : bond 0.00297 ( 3) SS BOND : angle 0.47717 ( 6) hydrogen bonds : bond 0.04832 ( 401) hydrogen bonds : angle 4.57511 ( 1125) link_ALPHA1-4 : bond 0.01589 ( 1) link_ALPHA1-4 : angle 3.34180 ( 3) link_NAG-ASN : bond 0.00103 ( 3) link_NAG-ASN : angle 3.66151 ( 9) *********************** 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 158 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 130 time to evaluate : 0.225 Fit side-chains revert: symmetry clash REVERT: A 71 TYR cc_start: 0.8891 (t80) cc_final: 0.8661 (t80) REVERT: A 117 ASP cc_start: 0.8027 (m-30) cc_final: 0.7669 (m-30) REVERT: A 129 GLU cc_start: 0.7585 (tp30) cc_final: 0.7240 (tp30) REVERT: A 340 MET cc_start: 0.8552 (mpp) cc_final: 0.8299 (mpp) REVERT: A 707 GLU cc_start: 0.3204 (OUTLIER) cc_final: 0.2469 (tp30) REVERT: A 940 ARG cc_start: 0.8586 (ttm110) cc_final: 0.8263 (mtm-85) REVERT: A 946 SER cc_start: 0.8476 (t) cc_final: 0.8185 (p) outliers start: 28 outliers final: 15 residues processed: 151 average time/residue: 0.0929 time to fit residues: 19.9612 Evaluate side-chains 135 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 119 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 365 MET Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 707 GLU Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 802 VAL Chi-restraints excluded: chain A residue 879 TYR Chi-restraints excluded: chain A residue 1084 LEU Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 335 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 90 optimal weight: 1.9990 chunk 21 optimal weight: 6.9990 chunk 49 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 52 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 275 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.120914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.089294 restraints weight = 14969.022| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 2.66 r_work: 0.2880 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2739 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 9567 Z= 0.216 Angle : 0.885 29.999 12981 Z= 0.388 Chirality : 0.046 0.277 1465 Planarity : 0.005 0.054 1611 Dihedral : 11.010 172.332 1395 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 5.12 % Allowed : 22.44 % Favored : 72.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.25), residues: 1129 helix: 1.05 (0.24), residues: 485 sheet: 0.53 (0.46), residues: 139 loop : -1.79 (0.27), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 162 TYR 0.020 0.002 TYR C 122 PHE 0.018 0.002 PHE A 995 TRP 0.014 0.002 TRP A 323 HIS 0.003 0.001 HIS A1023 Details of bonding type rmsd covalent geometry : bond 0.00520 ( 9560) covalent geometry : angle 0.87728 (12963) SS BOND : bond 0.00412 ( 3) SS BOND : angle 0.76772 ( 6) hydrogen bonds : bond 0.06047 ( 401) hydrogen bonds : angle 4.34767 ( 1125) link_ALPHA1-4 : bond 0.01531 ( 1) link_ALPHA1-4 : angle 3.81359 ( 3) link_NAG-ASN : bond 0.00250 ( 3) link_NAG-ASN : angle 3.98562 ( 9) *********************** 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 173 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 121 time to evaluate : 0.345 Fit side-chains REVERT: A 71 TYR cc_start: 0.8975 (t80) cc_final: 0.8764 (t80) REVERT: A 83 ASP cc_start: 0.8157 (t70) cc_final: 0.7854 (t0) REVERT: A 129 GLU cc_start: 0.7850 (tp30) cc_final: 0.7481 (tp30) REVERT: A 196 LEU cc_start: 0.8272 (mt) cc_final: 0.7608 (tp) REVERT: A 387 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7403 (mt-10) REVERT: A 707 GLU cc_start: 0.3625 (OUTLIER) cc_final: 0.3168 (tp30) REVERT: A 751 ILE cc_start: 0.8788 (OUTLIER) cc_final: 0.8577 (tt) REVERT: A 786 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8705 (tp) REVERT: A 940 ARG cc_start: 0.8905 (ttm110) cc_final: 0.8514 (mtm110) REVERT: A 946 SER cc_start: 0.8657 (t) cc_final: 0.8424 (p) REVERT: C 244 ASP cc_start: 0.7918 (t0) cc_final: 0.7688 (t0) outliers start: 52 outliers final: 27 residues processed: 162 average time/residue: 0.0785 time to fit residues: 18.7042 Evaluate side-chains 145 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 114 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 275 GLN Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 707 GLU Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 802 VAL 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 885 ILE Chi-restraints excluded: chain A residue 978 PHE Chi-restraints excluded: chain A residue 1006 THR Chi-restraints excluded: chain A residue 1055 PHE Chi-restraints excluded: chain A residue 1065 SER Chi-restraints excluded: chain A residue 1084 LEU Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 129 GLN Chi-restraints excluded: chain C residue 238 LYS Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 335 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 109 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 101 optimal weight: 0.0060 chunk 40 optimal weight: 0.5980 chunk 13 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 85 optimal weight: 0.8980 chunk 11 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 83 optimal weight: 8.9990 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 275 GLN C 216 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.122477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.091214 restraints weight = 14825.693| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 2.66 r_work: 0.2923 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2782 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9567 Z= 0.131 Angle : 0.823 29.992 12981 Z= 0.350 Chirality : 0.042 0.155 1465 Planarity : 0.004 0.052 1611 Dihedral : 10.477 175.463 1395 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 3.84 % Allowed : 23.52 % Favored : 72.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.26), residues: 1129 helix: 1.17 (0.24), residues: 491 sheet: 0.64 (0.46), residues: 139 loop : -1.74 (0.27), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 162 TYR 0.016 0.001 TYR A 311 PHE 0.013 0.001 PHE A 995 TRP 0.015 0.001 TRP A 323 HIS 0.002 0.001 HIS C 283 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 9560) covalent geometry : angle 0.81580 (12963) SS BOND : bond 0.00315 ( 3) SS BOND : angle 0.72762 ( 6) hydrogen bonds : bond 0.04885 ( 401) hydrogen bonds : angle 4.12365 ( 1125) link_ALPHA1-4 : bond 0.01678 ( 1) link_ALPHA1-4 : angle 3.58136 ( 3) link_NAG-ASN : bond 0.00107 ( 3) link_NAG-ASN : angle 3.57277 ( 9) *********************** 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 167 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 128 time to evaluate : 0.312 Fit side-chains REVERT: A 71 TYR cc_start: 0.8936 (t80) cc_final: 0.8650 (t80) REVERT: A 83 ASP cc_start: 0.8133 (t70) cc_final: 0.7869 (t0) REVERT: A 87 SER cc_start: 0.8880 (OUTLIER) cc_final: 0.8492 (m) REVERT: A 122 LYS cc_start: 0.8761 (mttm) cc_final: 0.8369 (mtpp) REVERT: A 129 GLU cc_start: 0.7849 (tp30) cc_final: 0.7427 (tp30) REVERT: A 196 LEU cc_start: 0.8336 (mt) cc_final: 0.7645 (tp) REVERT: A 242 GLU cc_start: 0.8669 (pm20) cc_final: 0.8454 (pm20) REVERT: A 387 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7461 (mt-10) REVERT: A 707 GLU cc_start: 0.3612 (OUTLIER) cc_final: 0.3069 (tp30) REVERT: A 723 ARG cc_start: 0.7730 (mtp-110) cc_final: 0.7367 (ptm160) REVERT: A 786 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8692 (tp) REVERT: A 877 PHE cc_start: 0.8956 (OUTLIER) cc_final: 0.8429 (t80) REVERT: A 940 ARG cc_start: 0.8855 (ttm110) cc_final: 0.8554 (mtm-85) REVERT: A 1050 GLN cc_start: 0.8709 (OUTLIER) cc_final: 0.8208 (pp30) outliers start: 39 outliers final: 23 residues processed: 158 average time/residue: 0.0813 time to fit residues: 18.5071 Evaluate side-chains 146 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 117 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 275 GLN Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 707 GLU Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 802 VAL Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 877 PHE Chi-restraints excluded: chain A residue 879 TYR Chi-restraints excluded: chain A residue 978 PHE Chi-restraints excluded: chain A residue 982 SER Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1050 GLN Chi-restraints excluded: chain A residue 1055 PHE Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 129 GLN Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 335 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 39 optimal weight: 4.9990 chunk 4 optimal weight: 0.7980 chunk 95 optimal weight: 0.0470 chunk 73 optimal weight: 2.9990 chunk 86 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 53 optimal weight: 0.6980 chunk 94 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 overall best weight: 0.8680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 275 GLN C 216 ASN C 254 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.121782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.090590 restraints weight = 14888.734| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 2.66 r_work: 0.2918 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2775 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9567 Z= 0.146 Angle : 0.835 29.995 12981 Z= 0.354 Chirality : 0.042 0.152 1465 Planarity : 0.004 0.051 1611 Dihedral : 10.141 176.329 1395 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 4.33 % Allowed : 23.62 % Favored : 72.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.25), residues: 1129 helix: 1.21 (0.24), residues: 487 sheet: 0.88 (0.46), residues: 137 loop : -1.73 (0.27), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 162 TYR 0.016 0.001 TYR A1054 PHE 0.014 0.001 PHE A 995 TRP 0.015 0.001 TRP A 323 HIS 0.002 0.001 HIS A 114 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 9560) covalent geometry : angle 0.82960 (12963) SS BOND : bond 0.00274 ( 3) SS BOND : angle 0.74494 ( 6) hydrogen bonds : bond 0.04859 ( 401) hydrogen bonds : angle 4.07430 ( 1125) link_ALPHA1-4 : bond 0.01771 ( 1) link_ALPHA1-4 : angle 3.78419 ( 3) link_NAG-ASN : bond 0.00309 ( 3) link_NAG-ASN : angle 3.13625 ( 9) *********************** 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 167 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 123 time to evaluate : 0.392 Fit side-chains REVERT: A 43 ASN cc_start: 0.8990 (t0) cc_final: 0.8635 (t0) REVERT: A 71 TYR cc_start: 0.8950 (t80) cc_final: 0.8669 (t80) REVERT: A 83 ASP cc_start: 0.8161 (t70) cc_final: 0.7868 (t0) REVERT: A 87 SER cc_start: 0.8838 (OUTLIER) cc_final: 0.8463 (m) REVERT: A 122 LYS cc_start: 0.8714 (mttm) cc_final: 0.8202 (mtpp) REVERT: A 129 GLU cc_start: 0.7857 (tp30) cc_final: 0.7405 (tp30) REVERT: A 137 GLU cc_start: 0.8510 (mm-30) cc_final: 0.8278 (mm-30) REVERT: A 196 LEU cc_start: 0.8382 (mt) cc_final: 0.7699 (tp) REVERT: A 242 GLU cc_start: 0.8680 (pm20) cc_final: 0.8411 (pm20) REVERT: A 387 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.7441 (mt-10) REVERT: A 707 GLU cc_start: 0.3633 (OUTLIER) cc_final: 0.3043 (tp30) REVERT: A 723 ARG cc_start: 0.7738 (mtp-110) cc_final: 0.7455 (ptm160) REVERT: A 786 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8683 (tp) REVERT: A 877 PHE cc_start: 0.8954 (OUTLIER) cc_final: 0.8414 (t80) REVERT: A 940 ARG cc_start: 0.8885 (ttm110) cc_final: 0.8589 (mtm-85) REVERT: A 1050 GLN cc_start: 0.8721 (OUTLIER) cc_final: 0.8216 (pp30) outliers start: 44 outliers final: 31 residues processed: 158 average time/residue: 0.0803 time to fit residues: 18.5188 Evaluate side-chains 160 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 123 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 275 GLN Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 707 GLU Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 802 VAL Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 877 PHE Chi-restraints excluded: chain A residue 879 TYR Chi-restraints excluded: chain A residue 910 MET Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 978 PHE Chi-restraints excluded: chain A residue 982 SER Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1050 GLN Chi-restraints excluded: chain A residue 1055 PHE Chi-restraints excluded: chain A residue 1065 SER Chi-restraints excluded: chain A residue 1084 LEU Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 129 GLN Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 335 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 10 optimal weight: 3.9990 chunk 17 optimal weight: 7.9990 chunk 6 optimal weight: 0.0000 chunk 5 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 93 optimal weight: 0.0470 chunk 37 optimal weight: 0.8980 chunk 102 optimal weight: 1.9990 overall best weight: 0.5882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 275 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.122955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.091888 restraints weight = 14871.427| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 2.66 r_work: 0.2930 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2788 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9567 Z= 0.122 Angle : 0.818 29.968 12981 Z= 0.344 Chirality : 0.042 0.155 1465 Planarity : 0.004 0.050 1611 Dihedral : 9.832 177.625 1395 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 4.13 % Allowed : 23.62 % Favored : 72.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.26), residues: 1129 helix: 1.31 (0.24), residues: 487 sheet: 0.98 (0.46), residues: 137 loop : -1.67 (0.27), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 162 TYR 0.017 0.001 TYR A1054 PHE 0.014 0.001 PHE A1055 TRP 0.015 0.001 TRP A 323 HIS 0.002 0.001 HIS A 114 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 9560) covalent geometry : angle 0.81257 (12963) SS BOND : bond 0.00654 ( 3) SS BOND : angle 1.14334 ( 6) hydrogen bonds : bond 0.04455 ( 401) hydrogen bonds : angle 3.98541 ( 1125) link_ALPHA1-4 : bond 0.01851 ( 1) link_ALPHA1-4 : angle 3.80945 ( 3) link_NAG-ASN : bond 0.00030 ( 3) link_NAG-ASN : angle 2.99636 ( 9) *********************** 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 170 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 128 time to evaluate : 0.386 Fit side-chains REVERT: A 43 ASN cc_start: 0.8983 (t0) cc_final: 0.8663 (t0) REVERT: A 71 TYR cc_start: 0.8936 (t80) cc_final: 0.8602 (t80) REVERT: A 83 ASP cc_start: 0.8082 (t70) cc_final: 0.7852 (t0) REVERT: A 87 SER cc_start: 0.8819 (OUTLIER) cc_final: 0.8606 (m) REVERT: A 106 GLN cc_start: 0.8272 (OUTLIER) cc_final: 0.7986 (mt0) REVERT: A 122 LYS cc_start: 0.8712 (mttm) cc_final: 0.8169 (mtpp) REVERT: A 129 GLU cc_start: 0.7842 (tp30) cc_final: 0.7394 (tp30) REVERT: A 137 GLU cc_start: 0.8575 (mm-30) cc_final: 0.8278 (mm-30) REVERT: A 196 LEU cc_start: 0.8385 (mt) cc_final: 0.7725 (tp) REVERT: A 212 GLU cc_start: 0.8345 (tt0) cc_final: 0.7984 (tt0) REVERT: A 242 GLU cc_start: 0.8681 (pm20) cc_final: 0.8386 (pm20) REVERT: A 387 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.7441 (mt-10) REVERT: A 707 GLU cc_start: 0.3632 (OUTLIER) cc_final: 0.3063 (tp30) REVERT: A 877 PHE cc_start: 0.8918 (OUTLIER) cc_final: 0.8405 (t80) REVERT: A 940 ARG cc_start: 0.8867 (ttm110) cc_final: 0.8600 (mtm-85) REVERT: A 1050 GLN cc_start: 0.8709 (OUTLIER) cc_final: 0.8190 (pp30) outliers start: 42 outliers final: 31 residues processed: 160 average time/residue: 0.0844 time to fit residues: 19.6163 Evaluate side-chains 159 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 122 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 106 GLN Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 275 GLN Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 336 LYS Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 365 MET Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 707 GLU Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 802 VAL Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 877 PHE Chi-restraints excluded: chain A residue 879 TYR Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 910 MET Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 978 PHE Chi-restraints excluded: chain A residue 982 SER Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1050 GLN Chi-restraints excluded: chain A residue 1084 LEU Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 129 GLN Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 335 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 26 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 108 optimal weight: 0.4980 chunk 107 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 85 optimal weight: 0.6980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 275 GLN A 761 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.121407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.090359 restraints weight = 15020.856| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 2.67 r_work: 0.2917 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2773 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9567 Z= 0.156 Angle : 0.829 30.034 12981 Z= 0.353 Chirality : 0.042 0.149 1465 Planarity : 0.004 0.049 1611 Dihedral : 9.557 178.066 1395 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 4.23 % Allowed : 23.52 % Favored : 72.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.26), residues: 1129 helix: 1.27 (0.24), residues: 488 sheet: 1.00 (0.46), residues: 137 loop : -1.67 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 162 TYR 0.017 0.001 TYR A1054 PHE 0.015 0.001 PHE A1055 TRP 0.014 0.001 TRP A 323 HIS 0.002 0.001 HIS A 114 Details of bonding type rmsd covalent geometry : bond 0.00371 ( 9560) covalent geometry : angle 0.82343 (12963) SS BOND : bond 0.00290 ( 3) SS BOND : angle 1.02470 ( 6) hydrogen bonds : bond 0.04801 ( 401) hydrogen bonds : angle 3.98969 ( 1125) link_ALPHA1-4 : bond 0.02067 ( 1) link_ALPHA1-4 : angle 4.20996 ( 3) link_NAG-ASN : bond 0.00117 ( 3) link_NAG-ASN : angle 2.85488 ( 9) *********************** 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 167 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 124 time to evaluate : 0.372 Fit side-chains REVERT: A 43 ASN cc_start: 0.8993 (t0) cc_final: 0.8656 (t0) REVERT: A 71 TYR cc_start: 0.8958 (t80) cc_final: 0.8673 (t80) REVERT: A 83 ASP cc_start: 0.8135 (t70) cc_final: 0.7865 (t0) REVERT: A 87 SER cc_start: 0.8840 (OUTLIER) cc_final: 0.8484 (m) REVERT: A 106 GLN cc_start: 0.8286 (OUTLIER) cc_final: 0.7996 (mt0) REVERT: A 122 LYS cc_start: 0.8711 (mttm) cc_final: 0.8166 (mtpp) REVERT: A 137 GLU cc_start: 0.8628 (mm-30) cc_final: 0.8315 (mm-30) REVERT: A 196 LEU cc_start: 0.8481 (mt) cc_final: 0.7826 (tp) REVERT: A 212 GLU cc_start: 0.8315 (tt0) cc_final: 0.7970 (tt0) REVERT: A 242 GLU cc_start: 0.8697 (pm20) cc_final: 0.8383 (pm20) REVERT: A 387 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7511 (mt-10) REVERT: A 707 GLU cc_start: 0.3556 (OUTLIER) cc_final: 0.3020 (tp30) REVERT: A 724 LYS cc_start: 0.8237 (OUTLIER) cc_final: 0.7986 (pttm) REVERT: A 786 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8629 (tp) REVERT: A 877 PHE cc_start: 0.8956 (OUTLIER) cc_final: 0.8409 (t80) REVERT: A 940 ARG cc_start: 0.8895 (ttm110) cc_final: 0.8632 (mtm-85) REVERT: A 1050 GLN cc_start: 0.8718 (OUTLIER) cc_final: 0.8221 (pp30) outliers start: 43 outliers final: 30 residues processed: 158 average time/residue: 0.0926 time to fit residues: 20.7239 Evaluate side-chains 158 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 120 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 106 GLN Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 275 GLN Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 336 LYS Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 707 GLU Chi-restraints excluded: chain A residue 724 LYS Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 802 VAL Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 877 PHE Chi-restraints excluded: chain A residue 879 TYR Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 910 MET Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 978 PHE Chi-restraints excluded: chain A residue 982 SER Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1050 GLN Chi-restraints excluded: chain A residue 1084 LEU Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 129 GLN Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 335 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 46 optimal weight: 7.9990 chunk 53 optimal weight: 0.9980 chunk 24 optimal weight: 4.9990 chunk 73 optimal weight: 0.8980 chunk 82 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 84 optimal weight: 0.7980 chunk 104 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 275 GLN A 761 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.121668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.090711 restraints weight = 14857.076| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 2.66 r_work: 0.2912 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2771 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9567 Z= 0.142 Angle : 0.824 30.006 12981 Z= 0.350 Chirality : 0.042 0.157 1465 Planarity : 0.004 0.049 1611 Dihedral : 9.308 179.143 1395 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 4.13 % Allowed : 23.43 % Favored : 72.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.26), residues: 1129 helix: 1.30 (0.24), residues: 489 sheet: 1.06 (0.46), residues: 137 loop : -1.64 (0.27), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 44 TYR 0.017 0.001 TYR A1054 PHE 0.016 0.001 PHE A 221 TRP 0.014 0.001 TRP A 323 HIS 0.002 0.001 HIS A 114 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 9560) covalent geometry : angle 0.81837 (12963) SS BOND : bond 0.00341 ( 3) SS BOND : angle 0.96193 ( 6) hydrogen bonds : bond 0.04694 ( 401) hydrogen bonds : angle 3.95347 ( 1125) link_ALPHA1-4 : bond 0.02378 ( 1) link_ALPHA1-4 : angle 4.47900 ( 3) link_NAG-ASN : bond 0.00081 ( 3) link_NAG-ASN : angle 2.75261 ( 9) *********************** 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 167 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 125 time to evaluate : 0.359 Fit side-chains REVERT: A 43 ASN cc_start: 0.8971 (t0) cc_final: 0.8697 (t0) REVERT: A 71 TYR cc_start: 0.8943 (t80) cc_final: 0.8607 (t80) REVERT: A 87 SER cc_start: 0.8833 (OUTLIER) cc_final: 0.8621 (m) REVERT: A 106 GLN cc_start: 0.8279 (OUTLIER) cc_final: 0.7991 (mt0) REVERT: A 122 LYS cc_start: 0.8713 (mttm) cc_final: 0.8210 (mtpp) REVERT: A 137 GLU cc_start: 0.8615 (mm-30) cc_final: 0.8314 (mm-30) REVERT: A 196 LEU cc_start: 0.8502 (mt) cc_final: 0.7847 (tp) REVERT: A 212 GLU cc_start: 0.8341 (tt0) cc_final: 0.7990 (tt0) REVERT: A 242 GLU cc_start: 0.8710 (pm20) cc_final: 0.8385 (pm20) REVERT: A 387 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7464 (mt-10) REVERT: A 707 GLU cc_start: 0.3538 (OUTLIER) cc_final: 0.3159 (tp30) REVERT: A 724 LYS cc_start: 0.8299 (OUTLIER) cc_final: 0.7905 (pttm) REVERT: A 751 ILE cc_start: 0.8779 (OUTLIER) cc_final: 0.8518 (tt) REVERT: A 786 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8539 (tp) REVERT: A 877 PHE cc_start: 0.8949 (OUTLIER) cc_final: 0.8406 (t80) REVERT: A 940 ARG cc_start: 0.8887 (ttm110) cc_final: 0.8623 (mtm-85) REVERT: A 1050 GLN cc_start: 0.8694 (OUTLIER) cc_final: 0.8175 (pp30) outliers start: 42 outliers final: 30 residues processed: 158 average time/residue: 0.0829 time to fit residues: 18.7083 Evaluate side-chains 161 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 122 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 106 GLN Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 275 GLN Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 365 MET Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 707 GLU Chi-restraints excluded: chain A residue 724 LYS Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 802 VAL Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 877 PHE Chi-restraints excluded: chain A residue 879 TYR Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 910 MET Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 978 PHE Chi-restraints excluded: chain A residue 982 SER Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1050 GLN Chi-restraints excluded: chain A residue 1084 LEU Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 129 GLN Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 335 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 39 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 112 optimal weight: 0.3980 chunk 90 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 chunk 50 optimal weight: 0.0870 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 275 GLN ** A 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 761 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.122233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.091299 restraints weight = 14813.684| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 2.66 r_work: 0.2928 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2787 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9567 Z= 0.130 Angle : 0.825 29.975 12981 Z= 0.350 Chirality : 0.042 0.200 1465 Planarity : 0.004 0.049 1611 Dihedral : 8.972 179.888 1395 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 4.13 % Allowed : 23.62 % Favored : 72.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.26), residues: 1129 helix: 1.37 (0.24), residues: 489 sheet: 1.13 (0.46), residues: 137 loop : -1.63 (0.27), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 44 TYR 0.017 0.001 TYR A1054 PHE 0.016 0.001 PHE A 221 TRP 0.014 0.001 TRP A 323 HIS 0.002 0.001 HIS A 114 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 9560) covalent geometry : angle 0.81958 (12963) SS BOND : bond 0.00288 ( 3) SS BOND : angle 0.93349 ( 6) hydrogen bonds : bond 0.04522 ( 401) hydrogen bonds : angle 3.92268 ( 1125) link_ALPHA1-4 : bond 0.02445 ( 1) link_ALPHA1-4 : angle 4.62657 ( 3) link_NAG-ASN : bond 0.00058 ( 3) link_NAG-ASN : angle 2.62806 ( 9) *********************** 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 168 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 126 time to evaluate : 0.414 Fit side-chains REVERT: A 43 ASN cc_start: 0.8963 (t0) cc_final: 0.8701 (t0) REVERT: A 71 TYR cc_start: 0.8938 (t80) cc_final: 0.8606 (t80) REVERT: A 87 SER cc_start: 0.8836 (OUTLIER) cc_final: 0.8627 (m) REVERT: A 122 LYS cc_start: 0.8715 (mttm) cc_final: 0.8207 (mtpp) REVERT: A 137 GLU cc_start: 0.8615 (mm-30) cc_final: 0.8298 (mm-30) REVERT: A 196 LEU cc_start: 0.8507 (mt) cc_final: 0.7850 (tp) REVERT: A 212 GLU cc_start: 0.8341 (tt0) cc_final: 0.8002 (tt0) REVERT: A 387 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.7487 (mt-10) REVERT: A 707 GLU cc_start: 0.3506 (OUTLIER) cc_final: 0.2835 (tp30) REVERT: A 724 LYS cc_start: 0.8287 (OUTLIER) cc_final: 0.7854 (pttm) REVERT: A 751 ILE cc_start: 0.8787 (OUTLIER) cc_final: 0.8520 (tt) REVERT: A 786 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8528 (tp) REVERT: A 877 PHE cc_start: 0.8926 (OUTLIER) cc_final: 0.8394 (t80) REVERT: A 940 ARG cc_start: 0.8887 (ttm110) cc_final: 0.8629 (mtm-85) REVERT: A 1050 GLN cc_start: 0.8695 (OUTLIER) cc_final: 0.8197 (pp30) REVERT: C 146 ASP cc_start: 0.8705 (t0) cc_final: 0.8475 (t0) outliers start: 42 outliers final: 28 residues processed: 158 average time/residue: 0.0977 time to fit residues: 21.8149 Evaluate side-chains 156 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 120 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 336 LYS Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 365 MET Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 707 GLU Chi-restraints excluded: chain A residue 724 LYS Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 802 VAL Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 877 PHE Chi-restraints excluded: chain A residue 879 TYR Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 910 MET Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 978 PHE Chi-restraints excluded: chain A residue 982 SER Chi-restraints excluded: chain A residue 1050 GLN Chi-restraints excluded: chain A residue 1084 LEU Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 129 GLN Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 335 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 23 optimal weight: 4.9990 chunk 51 optimal weight: 0.6980 chunk 16 optimal weight: 4.9990 chunk 55 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 57 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 6 optimal weight: 0.0010 chunk 84 optimal weight: 0.0980 chunk 10 optimal weight: 0.6980 chunk 61 optimal weight: 0.7980 overall best weight: 0.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 761 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.123842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.093070 restraints weight = 14804.545| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 2.67 r_work: 0.2955 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9567 Z= 0.116 Angle : 0.824 29.961 12981 Z= 0.348 Chirality : 0.042 0.260 1465 Planarity : 0.004 0.049 1611 Dihedral : 8.463 179.601 1395 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 3.15 % Allowed : 24.61 % Favored : 72.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.26), residues: 1129 helix: 1.36 (0.24), residues: 493 sheet: 1.20 (0.46), residues: 137 loop : -1.60 (0.27), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 44 TYR 0.016 0.001 TYR A1054 PHE 0.015 0.001 PHE A 221 TRP 0.015 0.001 TRP A 323 HIS 0.002 0.001 HIS A 187 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 9560) covalent geometry : angle 0.81928 (12963) SS BOND : bond 0.00285 ( 3) SS BOND : angle 0.82512 ( 6) hydrogen bonds : bond 0.04114 ( 401) hydrogen bonds : angle 3.85766 ( 1125) link_ALPHA1-4 : bond 0.02412 ( 1) link_ALPHA1-4 : angle 4.69122 ( 3) link_NAG-ASN : bond 0.00012 ( 3) link_NAG-ASN : angle 2.30391 ( 9) ********************** 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 162 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 130 time to evaluate : 0.246 Fit side-chains REVERT: A 43 ASN cc_start: 0.8950 (t0) cc_final: 0.8699 (t0) REVERT: A 122 LYS cc_start: 0.8720 (mttm) cc_final: 0.8192 (mtpp) REVERT: A 137 GLU cc_start: 0.8610 (mm-30) cc_final: 0.8298 (mm-30) REVERT: A 196 LEU cc_start: 0.8502 (mt) cc_final: 0.7879 (tp) REVERT: A 212 GLU cc_start: 0.8348 (tt0) cc_final: 0.7997 (tt0) REVERT: A 387 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.7446 (mt-10) REVERT: A 707 GLU cc_start: 0.3386 (OUTLIER) cc_final: 0.2765 (tp30) REVERT: A 751 ILE cc_start: 0.8792 (OUTLIER) cc_final: 0.8452 (tt) REVERT: A 780 MET cc_start: 0.8604 (tpp) cc_final: 0.8232 (mmm) REVERT: A 786 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8483 (tp) REVERT: A 877 PHE cc_start: 0.8883 (OUTLIER) cc_final: 0.8389 (t80) REVERT: A 940 ARG cc_start: 0.8883 (ttm110) cc_final: 0.8613 (mtm-85) REVERT: A 1050 GLN cc_start: 0.8686 (OUTLIER) cc_final: 0.8177 (pp30) outliers start: 32 outliers final: 22 residues processed: 157 average time/residue: 0.0904 time to fit residues: 20.2989 Evaluate side-chains 153 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 125 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 336 LYS Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 707 GLU Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 802 VAL Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 877 PHE Chi-restraints excluded: chain A residue 879 TYR Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 910 MET Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 978 PHE Chi-restraints excluded: chain A residue 982 SER Chi-restraints excluded: chain A residue 1050 GLN Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 335 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 42 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 25 optimal weight: 0.1980 chunk 93 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 106 optimal weight: 0.9980 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.119375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.088518 restraints weight = 14965.163| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 2.65 r_work: 0.2885 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2744 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 9567 Z= 0.204 Angle : 0.866 30.029 12981 Z= 0.377 Chirality : 0.045 0.237 1465 Planarity : 0.004 0.049 1611 Dihedral : 8.584 179.323 1395 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 3.25 % Allowed : 24.61 % Favored : 72.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.26), residues: 1129 helix: 1.18 (0.24), residues: 502 sheet: 1.22 (0.46), residues: 137 loop : -1.67 (0.28), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 44 TYR 0.019 0.002 TYR C 122 PHE 0.017 0.002 PHE A 884 TRP 0.013 0.001 TRP A 323 HIS 0.004 0.001 HIS A 114 Details of bonding type rmsd covalent geometry : bond 0.00490 ( 9560) covalent geometry : angle 0.86039 (12963) SS BOND : bond 0.00320 ( 3) SS BOND : angle 1.01436 ( 6) hydrogen bonds : bond 0.05496 ( 401) hydrogen bonds : angle 4.03489 ( 1125) link_ALPHA1-4 : bond 0.02244 ( 1) link_ALPHA1-4 : angle 5.03583 ( 3) link_NAG-ASN : bond 0.00235 ( 3) link_NAG-ASN : angle 2.39783 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2255.40 seconds wall clock time: 39 minutes 22.94 seconds (2362.94 seconds total)