Starting phenix.real_space_refine on Fri Jul 3 07:11:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7a69_11667/07_2026/7a69_11667.cif Found real_map, /net/cci-nas-00/data/ceres_data/7a69_11667/07_2026/7a69_11667.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7a69_11667/07_2026/7a69_11667.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7a69_11667/07_2026/7a69_11667.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7a69_11667/07_2026/7a69_11667.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7a69_11667/07_2026/7a69_11667.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7a69_11667/07_2026/7a69_11667.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7a69_11667/07_2026/7a69_11667.cif" } resolution = 3.2 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= 0.001 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: 4 Type Number sf(0) Gaussians S 50 5.16 5 C 8175 2.51 5 N 2090 2.21 5 O 2322 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12637 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1164, 9050 Classifications: {'peptide': 1164} Link IDs: {'PTRANS': 27, 'TRANS': 1136} Chain breaks: 2 Chain: "B" Number of atoms: 1656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1656 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 203} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CYS%COO:oxt': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 1647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1647 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 205} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PRO%COO:oxt': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 284 Unusual residues: {'CLR': 8, 'R1Q': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Time building chain proxies: 2.66, per 1000 atoms: 0.21 Number of scatterers: 12637 At special positions: 0 Unit cell: (102.48, 208.32, 99.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 50 16.00 O 2322 8.00 N 2090 7.00 C 8175 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 93 " distance=2.04 Simple disulfide: pdb=" SG CYS B 139 " - pdb=" SG CYS B 199 " distance=2.04 Simple disulfide: pdb=" SG CYS B 220 " - pdb=" SG CYS C 133 " distance=2.03 Simple disulfide: pdb=" SG CYS C 21 " - pdb=" SG CYS C 95 " distance=2.05 Simple disulfide: pdb=" SG CYS C 145 " - pdb=" SG CYS C 200 " distance=2.04 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 Time building additional restraints: 1.14 Conformation dependent library (CDL) restraints added in 690.1 milliseconds 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2940 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 14 sheets defined 51.8% alpha, 16.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 44 through 81 removed outlier: 3.550A pdb=" N VAL A 52 " --> pdb=" O LYS A 48 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N LEU A 65 " --> pdb=" O HIS A 61 " (cutoff:3.500A) Proline residue: A 66 - end of helix removed outlier: 3.752A pdb=" N ASP A 77 " --> pdb=" O GLY A 73 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ILE A 78 " --> pdb=" O GLU A 74 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N PHE A 79 " --> pdb=" O MET A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 157 removed outlier: 4.000A pdb=" N ASP A 110 " --> pdb=" O ASN A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 166 Processing helix chain 'A' and resid 167 through 187 removed outlier: 3.957A pdb=" N THR A 176 " --> pdb=" O ASN A 172 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLY A 185 " --> pdb=" O LYS A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 211 removed outlier: 4.324A pdb=" N GLY A 191 " --> pdb=" O GLY A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 237 removed outlier: 3.509A pdb=" N THR A 215 " --> pdb=" O GLY A 211 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL A 217 " --> pdb=" O LYS A 213 " (cutoff:3.500A) Proline residue: A 223 - end of helix Processing helix chain 'A' and resid 240 through 258 removed outlier: 4.949A pdb=" N LYS A 249 " --> pdb=" O LEU A 245 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N ALA A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 268 Processing helix chain 'A' and resid 269 through 323 removed outlier: 4.143A pdb=" N GLU A 273 " --> pdb=" O GLY A 269 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR A 319 " --> pdb=" O TRP A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 347 removed outlier: 3.826A pdb=" N GLY A 346 " --> pdb=" O ALA A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 371 removed outlier: 4.108A pdb=" N ILE A 352 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU A 353 " --> pdb=" O SER A 349 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU A 364 " --> pdb=" O GLY A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 441 removed outlier: 3.651A pdb=" N GLN A 441 " --> pdb=" O VAL A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 461 removed outlier: 3.690A pdb=" N THR A 460 " --> pdb=" O ASP A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 469 removed outlier: 3.569A pdb=" N LEU A 466 " --> pdb=" O ASN A 462 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE A 469 " --> pdb=" O PHE A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 490 Processing helix chain 'A' and resid 496 through 507 Processing helix chain 'A' and resid 510 through 516 Processing helix chain 'A' and resid 525 through 529 Processing helix chain 'A' and resid 532 through 546 Processing helix chain 'A' and resid 562 through 574 Processing helix chain 'A' and resid 611 through 619 Processing helix chain 'A' and resid 620 through 630 Processing helix chain 'A' and resid 699 through 704 removed outlier: 3.588A pdb=" N LEU A 703 " --> pdb=" O ARG A 699 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ASN A 704 " --> pdb=" O ILE A 700 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 699 through 704' Processing helix chain 'A' and resid 707 through 737 removed outlier: 3.792A pdb=" N PHE A 711 " --> pdb=" O GLU A 707 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N GLN A 725 " --> pdb=" O ASN A 721 " (cutoff:3.500A) Proline residue: A 726 - end of helix Processing helix chain 'A' and resid 744 through 798 Processing helix chain 'A' and resid 800 through 805 removed outlier: 3.855A pdb=" N PHE A 804 " --> pdb=" O ASP A 800 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 854 removed outlier: 3.737A pdb=" N THR A 815 " --> pdb=" O THR A 811 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ALA A 823 " --> pdb=" O ALA A 819 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LYS A 826 " --> pdb=" O ALA A 822 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU A 833 " --> pdb=" O ILE A 829 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N THR A 837 " --> pdb=" O LEU A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 854 through 862 Processing helix chain 'A' and resid 864 through 881 Processing helix chain 'A' and resid 886 through 903 removed outlier: 4.473A pdb=" N ILE A 896 " --> pdb=" O GLY A 892 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA A 897 " --> pdb=" O ALA A 893 " (cutoff:3.500A) Processing helix chain 'A' and resid 903 through 911 removed outlier: 4.032A pdb=" N SER A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 966 removed outlier: 4.194A pdb=" N MET A 919 " --> pdb=" O LYS A 915 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N VAL A 926 " --> pdb=" O GLN A 922 " (cutoff:3.500A) Proline residue: A 927 - end of helix removed outlier: 3.804A pdb=" N ILE A 940 " --> pdb=" O HIS A 936 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N MET A 949 " --> pdb=" O THR A 945 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N TYR A 950 " --> pdb=" O GLN A 946 " (cutoff:3.500A) Processing helix chain 'A' and resid 970 through 982 Processing helix chain 'A' and resid 985 through 995 Processing helix chain 'A' and resid 998 through 1014 Processing helix chain 'A' and resid 1077 through 1084 Processing helix chain 'A' and resid 1105 through 1113 removed outlier: 3.828A pdb=" N LEU A1109 " --> pdb=" O ASN A1105 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ARG A1110 " --> pdb=" O VAL A1106 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU A1113 " --> pdb=" O LEU A1109 " (cutoff:3.500A) Processing helix chain 'A' and resid 1127 through 1132 Processing helix chain 'A' and resid 1141 through 1152 Processing helix chain 'A' and resid 1154 through 1160 Processing helix chain 'A' and resid 1170 through 1174 Processing helix chain 'A' and resid 1177 through 1191 removed outlier: 3.579A pdb=" N VAL A1191 " --> pdb=" O ALA A1187 " (cutoff:3.500A) Processing helix chain 'A' and resid 1207 through 1223 removed outlier: 3.823A pdb=" N LYS A1212 " --> pdb=" O THR A1208 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL A1213 " --> pdb=" O GLU A1209 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ALA A1217 " --> pdb=" O VAL A1213 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU A1218 " --> pdb=" O VAL A1214 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLU A1223 " --> pdb=" O ASP A1219 " (cutoff:3.500A) Processing helix chain 'A' and resid 1234 through 1239 removed outlier: 4.232A pdb=" N ASN A1239 " --> pdb=" O SER A1235 " (cutoff:3.500A) Processing helix chain 'A' and resid 1257 through 1263 removed outlier: 3.501A pdb=" N GLN A1263 " --> pdb=" O GLN A1259 " (cutoff:3.500A) Processing helix chain 'A' and resid 1265 through 1272 removed outlier: 3.780A pdb=" N SER A1269 " --> pdb=" O GLY A1265 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 132 removed outlier: 3.584A pdb=" N SER B 132 " --> pdb=" O GLU B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 193 Processing helix chain 'C' and resid 27 through 31 Processing helix chain 'C' and resid 86 through 90 Processing helix chain 'C' and resid 131 through 135 Processing helix chain 'C' and resid 161 through 163 No H-bonds generated for 'chain 'C' and resid 161 through 163' Processing helix chain 'C' and resid 205 through 208 Processing sheet with id=AA1, first strand: chain 'A' and resid 415 through 417 removed outlier: 3.897A pdb=" N ARG A 395 " --> pdb=" O MET A 450 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N MET A 450 " --> pdb=" O ARG A 395 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N VAL A 397 " --> pdb=" O GLU A 448 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N GLU A 448 " --> pdb=" O VAL A 397 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 470 through 473 removed outlier: 3.854A pdb=" N LEU A 425 " --> pdb=" O VAL A 584 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N GLY A 600 " --> pdb=" O VAL A 607 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1056 through 1060 removed outlier: 5.573A pdb=" N LEU A1056 " --> pdb=" O GLU A1039 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N VAL A1040 " --> pdb=" O ALA A1091 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N ALA A1091 " --> pdb=" O VAL A1040 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1114 through 1116 removed outlier: 3.690A pdb=" N LEU A1198 " --> pdb=" O GLY A1114 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL A1116 " --> pdb=" O LEU A1198 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ASP A1200 " --> pdb=" O VAL A1116 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N LEU A1197 " --> pdb=" O ILE A1228 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N ILE A1230 " --> pdb=" O LEU A1197 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N LEU A1199 " --> pdb=" O ILE A1230 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU A1068 " --> pdb=" O VAL A1229 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N ILE A1243 " --> pdb=" O HIS A1254 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N HIS A1254 " --> pdb=" O ILE A1243 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N VAL A1245 " --> pdb=" O LYS A1252 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 5 through 6 removed outlier: 3.980A pdb=" N PHE B 76 " --> pdb=" O CYS B 23 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 10 through 13 removed outlier: 6.441A pdb=" N LEU B 11 " --> pdb=" O GLU B 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 50 through 52 Processing sheet with id=AA8, first strand: chain 'B' and resid 119 through 123 Processing sheet with id=AA9, first strand: chain 'B' and resid 159 through 161 removed outlier: 4.343A pdb=" N TRP B 153 " --> pdb=" O GLN B 161 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 2 through 6 Processing sheet with id=AB2, first strand: chain 'C' and resid 10 through 11 removed outlier: 6.876A pdb=" N MET C 33 " --> pdb=" O THR C 49 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N THR C 49 " --> pdb=" O MET C 33 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N TRP C 35 " --> pdb=" O VAL C 47 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 10 through 11 removed outlier: 6.900A pdb=" N CYS C 95 " --> pdb=" O TRP C 108 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N TRP C 108 " --> pdb=" O CYS C 95 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ARG C 97 " --> pdb=" O ALA C 106 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N TYR C 99 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N TRP C 104 " --> pdb=" O TYR C 99 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 127 through 129 removed outlier: 3.513A pdb=" N LEU C 129 " --> pdb=" O GLY C 144 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N TYR C 180 " --> pdb=" O GLY C 149 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N LEU C 179 " --> pdb=" O LEU C 175 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N LEU C 175 " --> pdb=" O LEU C 179 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N THR C 181 " --> pdb=" O ALA C 173 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ALA C 173 " --> pdb=" O THR C 181 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N SER C 183 " --> pdb=" O PHE C 171 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 156 through 159 removed outlier: 4.369A pdb=" N ILE C 198 " --> pdb=" O ILE C 215 " (cutoff:3.500A) 719 hydrogen bonds defined for protein. 2037 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: 2.48 Time building geometry restraints manager: 1.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2018 1.31 - 1.44: 3412 1.44 - 1.57: 7369 1.57 - 1.70: 33 1.70 - 1.83: 83 Bond restraints: 12915 Sorted by residual: bond pdb=" C51 R1Q A1400 " pdb=" C52 R1Q A1400 " ideal model delta sigma weight residual 1.562 1.299 0.263 2.00e-02 2.50e+03 1.72e+02 bond pdb=" C23 R1Q A1400 " pdb=" N28 R1Q A1400 " ideal model delta sigma weight residual 1.414 1.608 -0.194 2.00e-02 2.50e+03 9.39e+01 bond pdb=" C32 R1Q A1400 " pdb=" C38 R1Q A1400 " ideal model delta sigma weight residual 1.543 1.359 0.184 2.00e-02 2.50e+03 8.45e+01 bond pdb=" C48 R1Q A1400 " pdb=" N49 R1Q A1400 " ideal model delta sigma weight residual 1.467 1.324 0.143 2.00e-02 2.50e+03 5.10e+01 bond pdb=" C05 R1Q A1400 " pdb=" C06 R1Q A1400 " ideal model delta sigma weight residual 1.501 1.638 -0.137 2.00e-02 2.50e+03 4.70e+01 ... (remaining 12910 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.79: 17482 5.79 - 11.59: 63 11.59 - 17.38: 2 17.38 - 23.18: 0 23.18 - 28.97: 1 Bond angle restraints: 17548 Sorted by residual: angle pdb=" C48 R1Q A1400 " pdb=" N49 R1Q A1400 " pdb=" C50 R1Q A1400 " ideal model delta sigma weight residual 110.62 81.65 28.97 3.00e+00 1.11e-01 9.33e+01 angle pdb=" N TYR B 54 " pdb=" CA TYR B 54 " pdb=" C TYR B 54 " ideal model delta sigma weight residual 113.15 119.98 -6.83 1.19e+00 7.06e-01 3.30e+01 angle pdb=" C15 R1Q A1400 " pdb=" C07 R1Q A1400 " pdb=" N08 R1Q A1400 " ideal model delta sigma weight residual 117.40 130.70 -13.30 3.00e+00 1.11e-01 1.97e+01 angle pdb=" C22 CLR A1404 " pdb=" C23 CLR A1404 " pdb=" C24 CLR A1404 " ideal model delta sigma weight residual 111.95 99.24 12.71 3.00e+00 1.11e-01 1.80e+01 angle pdb=" C LYS B 55 " pdb=" N ILE B 56 " pdb=" CA ILE B 56 " ideal model delta sigma weight residual 122.01 116.55 5.46 1.42e+00 4.96e-01 1.48e+01 ... (remaining 17543 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.60: 6866 16.60 - 33.20: 617 33.20 - 49.80: 165 49.80 - 66.40: 47 66.40 - 83.00: 10 Dihedral angle restraints: 7705 sinusoidal: 3119 harmonic: 4586 Sorted by residual: dihedral pdb=" CA ASN B 216 " pdb=" C ASN B 216 " pdb=" N ARG B 217 " pdb=" CA ARG B 217 " ideal model delta harmonic sigma weight residual 180.00 151.22 28.78 0 5.00e+00 4.00e-02 3.31e+01 dihedral pdb=" CA ALA B 99 " pdb=" C ALA B 99 " pdb=" N PRO B 100 " pdb=" CA PRO B 100 " ideal model delta harmonic sigma weight residual 180.00 156.52 23.48 0 5.00e+00 4.00e-02 2.21e+01 dihedral pdb=" CA HIS B 98 " pdb=" C HIS B 98 " pdb=" N ALA B 99 " pdb=" CA ALA B 99 " ideal model delta harmonic sigma weight residual -180.00 -156.70 -23.30 0 5.00e+00 4.00e-02 2.17e+01 ... (remaining 7702 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.129: 1964 0.129 - 0.258: 48 0.258 - 0.387: 16 0.387 - 0.516: 1 0.516 - 0.645: 2 Chirality restraints: 2031 Sorted by residual: chirality pdb=" C52 R1Q A1400 " pdb=" C22 R1Q A1400 " pdb=" C31 R1Q A1400 " pdb=" C51 R1Q A1400 " both_signs ideal model delta sigma weight residual False 3.01 2.37 0.65 2.00e-01 2.50e+01 1.04e+01 chirality pdb=" C38 R1Q A1400 " pdb=" C32 R1Q A1400 " pdb=" C43 R1Q A1400 " pdb=" O39 R1Q A1400 " both_signs ideal model delta sigma weight residual False -2.59 -1.95 -0.64 2.00e-01 2.50e+01 1.01e+01 chirality pdb=" C17 CLR A1404 " pdb=" C13 CLR A1404 " pdb=" C16 CLR A1404 " pdb=" C20 CLR A1404 " both_signs ideal model delta sigma weight residual False 2.55 2.99 -0.44 2.00e-01 2.50e+01 4.84e+00 ... (remaining 2028 not shown) Planarity restraints: 2162 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 744 " 0.043 5.00e-02 4.00e+02 6.41e-02 6.58e+00 pdb=" N PRO A 745 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO A 745 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 745 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 39 " 0.037 5.00e-02 4.00e+02 5.52e-02 4.88e+00 pdb=" N PRO C 40 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO C 40 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 40 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 94 " 0.020 2.00e-02 2.50e+03 1.48e-02 3.84e+00 pdb=" CG PHE B 94 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 PHE B 94 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE B 94 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE B 94 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE B 94 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE B 94 " 0.007 2.00e-02 2.50e+03 ... (remaining 2159 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 137 2.61 - 3.19: 11325 3.19 - 3.76: 18802 3.76 - 4.33: 25916 4.33 - 4.90: 43632 Nonbonded interactions: 99812 Sorted by model distance: nonbonded pdb=" OD1 ASP A 47 " pdb=" NH1 ARG A 142 " model vdw 2.042 3.120 nonbonded pdb=" NE1 TRP A 803 " pdb=" NZ LYS A1014 " model vdw 2.073 3.200 nonbonded pdb=" CD1 ILE B 53 " pdb=" O ASN B 58 " model vdw 2.128 3.460 nonbonded pdb=" O TYR A 490 " pdb=" NE2 GLN A 912 " model vdw 2.131 3.120 nonbonded pdb=" O GLY A 269 " pdb=" OH TYR A1133 " model vdw 2.171 3.040 ... (remaining 99807 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: 4.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 12.860 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 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 : 0.012 0.263 12920 Z= 0.536 Angle : 1.018 28.974 17558 Z= 0.496 Chirality : 0.064 0.645 2031 Planarity : 0.004 0.064 2162 Dihedral : 14.414 83.000 4750 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.73 % Favored : 95.20 % Rotamer: Outliers : 4.42 % Allowed : 12.58 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -2.83 (0.18), residues: 1584 helix: -1.46 (0.16), residues: 751 sheet: -1.19 (0.28), residues: 295 loop : -2.66 (0.22), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 113 TYR 0.026 0.003 TYR C 94 PHE 0.033 0.003 PHE B 94 TRP 0.013 0.002 TRP C 46 HIS 0.004 0.001 HIS A 918 Details of bonding type rmsd/Z covalent geometry : bond 0.01208 / 0.54 (12915) covalent geometry : angle 1.01683 / 0.50 (17548) SS BOND : bond 0.00898 / 0.52 ( 5) SS BOND : angle 2.26090 / 1.14 ( 10) hydrogen bonds : bond 0.16525 / 10.99 ( 714) hydrogen bonds : angle 6.80343 / 4.85 ( 2037) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 166 time to evaluate : 0.434 Fit side-chains revert: symmetry clash REVERT: A 232 TRP cc_start: 0.7404 (t60) cc_final: 0.7139 (t60) REVERT: A 520 PHE cc_start: 0.3302 (OUTLIER) cc_final: 0.2188 (m-80) REVERT: A 628 MET cc_start: 0.0608 (tpp) cc_final: 0.0328 (tpp) REVERT: A 983 PHE cc_start: 0.8527 (OUTLIER) cc_final: 0.8218 (m-10) REVERT: A 1019 ASP cc_start: 0.1067 (OUTLIER) cc_final: -0.0009 (t0) REVERT: A 1027 MET cc_start: 0.3161 (tpp) cc_final: 0.2457 (tpt) REVERT: A 1056 LEU cc_start: 0.4830 (OUTLIER) cc_final: 0.4557 (tp) REVERT: B 36 THR cc_start: 0.8838 (OUTLIER) cc_final: 0.8575 (t) REVERT: B 52 LEU cc_start: 0.7055 (OUTLIER) cc_final: 0.6814 (mp) REVERT: B 143 ASN cc_start: 0.7741 (m110) cc_final: 0.7493 (m-40) REVERT: B 148 ASP cc_start: 0.1997 (m-30) cc_final: 0.1643 (m-30) REVERT: C 110 GLN cc_start: 0.7289 (pt0) cc_final: 0.7010 (pt0) outliers start: 59 outliers final: 33 residues processed: 223 average time/residue: 0.1123 time to fit residues: 35.9505 Evaluate side-chains 149 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 110 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 48 LYS Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 137 CYS Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 387 ASN Chi-restraints excluded: chain A residue 520 PHE Chi-restraints excluded: chain A residue 733 SER Chi-restraints excluded: chain A residue 752 SER Chi-restraints excluded: chain A residue 756 SER Chi-restraints excluded: chain A residue 821 ASP Chi-restraints excluded: chain A residue 835 VAL Chi-restraints excluded: chain A residue 837 THR Chi-restraints excluded: chain A residue 983 PHE Chi-restraints excluded: chain A residue 993 SER Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1019 ASP Chi-restraints excluded: chain A residue 1056 LEU Chi-restraints excluded: chain A residue 1139 VAL Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 55 LYS Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain C residue 4 VAL Chi-restraints excluded: chain C residue 34 SER Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 83 SER Chi-restraints excluded: chain C residue 100 ARG Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 136 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 0.0020 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 6.9990 overall best weight: 0.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 398 HIS A 438 GLN A 537 GLN A 750 GLN ** A 799 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 912 GLN A 990 GLN A1054 GLN ** A1105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1130 ASN A1153 ASN A1182 GLN B 18 GLN B 58 ASN B 129 GLN C 56 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4539 r_free = 0.4539 target = 0.225508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.179178 restraints weight = 16368.197| |-----------------------------------------------------------------------------| r_work (start): 0.4089 rms_B_bonded: 2.53 r_work: 0.3493 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12920 Z= 0.139 Angle : 0.592 9.131 17558 Z= 0.301 Chirality : 0.042 0.256 2031 Planarity : 0.004 0.045 2162 Dihedral : 8.184 97.061 1976 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.84 % Favored : 97.10 % Rotamer: Outliers : 3.75 % Allowed : 15.58 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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 (0.20), residues: 1584 helix: 0.52 (0.18), residues: 772 sheet: -0.43 (0.30), residues: 285 loop : -2.18 (0.23), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 905 TYR 0.014 0.001 TYR C 94 PHE 0.014 0.001 PHE A 732 TRP 0.011 0.001 TRP C 46 HIS 0.005 0.001 HIS A 612 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.14 (12915) covalent geometry : angle 0.59157 / 0.30 (17548) SS BOND : bond 0.00437 / 0.22 ( 5) SS BOND : angle 0.85564 / 0.35 ( 10) hydrogen bonds : bond 0.05914 / 3.84 ( 714) hydrogen bonds : angle 4.88677 / 3.50 ( 2037) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 123 time to evaluate : 0.402 Fit side-chains revert: symmetry clash REVERT: A 111 MET cc_start: 0.8261 (mmp) cc_final: 0.7896 (mmt) REVERT: A 497 MET cc_start: 0.5508 (mmp) cc_final: 0.5167 (mtt) REVERT: A 520 PHE cc_start: 0.3402 (OUTLIER) cc_final: 0.2354 (m-80) REVERT: A 876 MET cc_start: 0.7096 (mmm) cc_final: 0.6719 (mmm) REVERT: A 930 ASN cc_start: 0.8044 (t0) cc_final: 0.7829 (m-40) REVERT: A 986 MET cc_start: 0.8977 (mtt) cc_final: 0.8625 (mtm) REVERT: A 1014 LYS cc_start: 0.8391 (tptt) cc_final: 0.8190 (tptt) REVERT: A 1019 ASP cc_start: 0.2410 (OUTLIER) cc_final: 0.0812 (t0) REVERT: A 1027 MET cc_start: 0.3502 (tpp) cc_final: 0.2817 (tpt) REVERT: B 143 ASN cc_start: 0.7803 (m110) cc_final: 0.7479 (m-40) REVERT: B 148 ASP cc_start: 0.2163 (m-30) cc_final: 0.1903 (m-30) REVERT: C 101 TYR cc_start: 0.8691 (m-80) cc_final: 0.8475 (m-80) outliers start: 50 outliers final: 23 residues processed: 169 average time/residue: 0.0960 time to fit residues: 24.5053 Evaluate side-chains 127 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 102 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 520 PHE Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 735 ILE Chi-restraints excluded: chain A residue 752 SER Chi-restraints excluded: chain A residue 756 SER Chi-restraints excluded: chain A residue 821 ASP Chi-restraints excluded: chain A residue 835 VAL Chi-restraints excluded: chain A residue 1015 THR Chi-restraints excluded: chain A residue 1019 ASP Chi-restraints excluded: chain A residue 1139 VAL Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 55 LYS Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 110 GLU Chi-restraints excluded: chain B residue 168 TRP Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 83 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 59 optimal weight: 0.9980 chunk 103 optimal weight: 7.9990 chunk 1 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 120 optimal weight: 0.1980 chunk 55 optimal weight: 0.2980 chunk 130 optimal weight: 3.9990 chunk 138 optimal weight: 0.6980 chunk 98 optimal weight: 8.9990 chunk 90 optimal weight: 8.9990 chunk 134 optimal weight: 7.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 143 GLN A 280 ASN A 799 GLN A1105 ASN A1130 ASN A1153 ASN A1232 HIS C 196 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4559 r_free = 0.4559 target = 0.227447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.182276 restraints weight = 16401.619| |-----------------------------------------------------------------------------| r_work (start): 0.4119 rms_B_bonded: 2.63 r_work: 0.3478 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.2637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12920 Z= 0.123 Angle : 0.539 9.979 17558 Z= 0.272 Chirality : 0.040 0.229 2031 Planarity : 0.003 0.030 2162 Dihedral : 6.648 101.566 1939 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.46 % Favored : 97.47 % Rotamer: Outliers : 2.70 % Allowed : 17.38 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.21), residues: 1584 helix: 1.31 (0.18), residues: 770 sheet: -0.04 (0.31), residues: 279 loop : -1.78 (0.24), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 160 TYR 0.016 0.001 TYR C 94 PHE 0.012 0.001 PHE A 957 TRP 0.009 0.001 TRP A 803 HIS 0.003 0.001 HIS A 966 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (12915) covalent geometry : angle 0.53814 / 0.27 (17548) SS BOND : bond 0.00352 / 0.18 ( 5) SS BOND : angle 1.08704 / 0.58 ( 10) hydrogen bonds : bond 0.05108 / 3.32 ( 714) hydrogen bonds : angle 4.40576 / 3.15 ( 2037) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 114 time to evaluate : 0.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 236 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.8122 (tp) REVERT: A 520 PHE cc_start: 0.3482 (OUTLIER) cc_final: 0.2787 (m-10) REVERT: A 840 ILE cc_start: 0.8731 (OUTLIER) cc_final: 0.8342 (mt) REVERT: A 876 MET cc_start: 0.7106 (mmm) cc_final: 0.6673 (mmm) REVERT: A 930 ASN cc_start: 0.8047 (t0) cc_final: 0.7781 (m-40) REVERT: A 986 MET cc_start: 0.8757 (mtt) cc_final: 0.8417 (mtm) REVERT: A 1014 LYS cc_start: 0.8452 (tptt) cc_final: 0.8149 (tptt) REVERT: A 1019 ASP cc_start: 0.1958 (OUTLIER) cc_final: 0.0666 (t0) REVERT: A 1027 MET cc_start: 0.3660 (tpp) cc_final: 0.3045 (tpt) REVERT: B 79 LYS cc_start: 0.8263 (mtmm) cc_final: 0.7912 (mtmt) REVERT: B 143 ASN cc_start: 0.7846 (m110) cc_final: 0.7519 (m-40) REVERT: B 168 TRP cc_start: 0.6654 (m-90) cc_final: 0.6413 (m-90) REVERT: B 175 ASP cc_start: 0.8621 (p0) cc_final: 0.8415 (p0) outliers start: 36 outliers final: 20 residues processed: 146 average time/residue: 0.0984 time to fit residues: 21.2665 Evaluate side-chains 119 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 95 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 520 PHE Chi-restraints excluded: chain A residue 735 ILE Chi-restraints excluded: chain A residue 752 SER Chi-restraints excluded: chain A residue 821 ASP Chi-restraints excluded: chain A residue 829 ILE Chi-restraints excluded: chain A residue 840 ILE Chi-restraints excluded: chain A residue 1015 THR Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1019 ASP Chi-restraints excluded: chain A residue 1023 THR Chi-restraints excluded: chain A residue 1139 VAL Chi-restraints excluded: chain A residue 1176 LEU Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain C residue 6 SER Chi-restraints excluded: chain C residue 110 GLN Chi-restraints excluded: chain C residue 196 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 75 optimal weight: 0.8980 chunk 108 optimal weight: 10.0000 chunk 52 optimal weight: 6.9990 chunk 89 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 44 optimal weight: 5.9990 chunk 96 optimal weight: 6.9990 chunk 103 optimal weight: 5.9990 chunk 128 optimal weight: 6.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 441 GLN A 487 ASN A1238 GLN B 6 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.219987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.177238 restraints weight = 16300.477| |-----------------------------------------------------------------------------| r_work (start): 0.4070 rms_B_bonded: 2.58 r_work: 0.3388 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 12920 Z= 0.203 Angle : 0.620 11.494 17558 Z= 0.316 Chirality : 0.043 0.255 2031 Planarity : 0.004 0.031 2162 Dihedral : 6.498 99.550 1924 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.79 % Favored : 96.15 % Rotamer: Outliers : 3.82 % Allowed : 18.20 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.21), residues: 1584 helix: 1.10 (0.18), residues: 768 sheet: 0.18 (0.32), residues: 279 loop : -1.65 (0.25), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 193 TYR 0.020 0.002 TYR C 94 PHE 0.019 0.002 PHE A 957 TRP 0.011 0.002 TRP C 104 HIS 0.005 0.001 HIS B 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00471 / 0.20 (12915) covalent geometry : angle 0.61844 / 0.32 (17548) SS BOND : bond 0.00895 / 0.45 ( 5) SS BOND : angle 1.95157 / 1.04 ( 10) hydrogen bonds : bond 0.06297 / 4.09 ( 714) hydrogen bonds : angle 4.68736 / 3.35 ( 2037) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 104 time to evaluate : 0.300 Fit side-chains revert: symmetry clash REVERT: A 111 MET cc_start: 0.8403 (mmp) cc_final: 0.8035 (mmp) REVERT: A 418 GLN cc_start: 0.6719 (tp40) cc_final: 0.6289 (tt0) REVERT: A 478 VAL cc_start: 0.6270 (OUTLIER) cc_final: 0.5825 (t) REVERT: A 520 PHE cc_start: 0.3537 (OUTLIER) cc_final: 0.2766 (m-10) REVERT: A 840 ILE cc_start: 0.8864 (OUTLIER) cc_final: 0.8609 (mt) REVERT: A 930 ASN cc_start: 0.8141 (t0) cc_final: 0.7939 (m-40) REVERT: A 1019 ASP cc_start: 0.2074 (OUTLIER) cc_final: 0.0771 (t0) REVERT: A 1027 MET cc_start: 0.3571 (tpp) cc_final: 0.3026 (tpt) REVERT: B 143 ASN cc_start: 0.8113 (m110) cc_final: 0.7908 (m-40) REVERT: B 168 TRP cc_start: 0.6885 (m-90) cc_final: 0.6149 (m-90) REVERT: B 175 ASP cc_start: 0.8682 (p0) cc_final: 0.8171 (p0) REVERT: B 180 MET cc_start: 0.7168 (ttt) cc_final: 0.6577 (ttt) outliers start: 51 outliers final: 31 residues processed: 152 average time/residue: 0.0860 time to fit residues: 20.0256 Evaluate side-chains 127 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 92 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 137 CYS Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 520 PHE Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 735 ILE Chi-restraints excluded: chain A residue 752 SER Chi-restraints excluded: chain A residue 821 ASP Chi-restraints excluded: chain A residue 829 ILE Chi-restraints excluded: chain A residue 840 ILE Chi-restraints excluded: chain A residue 1015 THR Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1019 ASP Chi-restraints excluded: chain A residue 1023 THR Chi-restraints excluded: chain A residue 1139 VAL Chi-restraints excluded: chain A residue 1176 LEU Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain C residue 4 VAL Chi-restraints excluded: chain C residue 6 SER Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 136 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 132 optimal weight: 0.1980 chunk 85 optimal weight: 0.8980 chunk 117 optimal weight: 5.9990 chunk 96 optimal weight: 5.9990 chunk 147 optimal weight: 0.6980 chunk 40 optimal weight: 20.0000 chunk 24 optimal weight: 0.9980 chunk 149 optimal weight: 7.9990 chunk 62 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 chunk 41 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1238 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4543 r_free = 0.4543 target = 0.225503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.184897 restraints weight = 16507.374| |-----------------------------------------------------------------------------| r_work (start): 0.4145 rms_B_bonded: 2.48 r_work: 0.3491 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.3321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12920 Z= 0.120 Angle : 0.527 8.897 17558 Z= 0.266 Chirality : 0.040 0.226 2031 Planarity : 0.003 0.030 2162 Dihedral : 5.991 102.301 1924 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.71 % Favored : 97.22 % Rotamer: Outliers : 3.00 % Allowed : 19.18 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.51 (0.21), residues: 1584 helix: 1.58 (0.19), residues: 760 sheet: 0.31 (0.33), residues: 273 loop : -1.44 (0.26), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 905 TYR 0.014 0.001 TYR C 94 PHE 0.029 0.001 PHE A 994 TRP 0.018 0.001 TRP A 232 HIS 0.002 0.000 HIS A 966 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.12 (12915) covalent geometry : angle 0.52674 / 0.27 (17548) SS BOND : bond 0.00471 / 0.24 ( 5) SS BOND : angle 0.98819 / 0.53 ( 10) hydrogen bonds : bond 0.04999 / 3.23 ( 714) hydrogen bonds : angle 4.34078 / 3.10 ( 2037) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 104 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 418 GLN cc_start: 0.6451 (tp40) cc_final: 0.6170 (tt0) REVERT: A 478 VAL cc_start: 0.6130 (OUTLIER) cc_final: 0.5703 (t) REVERT: A 520 PHE cc_start: 0.3247 (OUTLIER) cc_final: 0.2468 (m-10) REVERT: A 876 MET cc_start: 0.7187 (mmm) cc_final: 0.6678 (mmm) REVERT: A 986 MET cc_start: 0.8776 (mtt) cc_final: 0.8465 (mtm) REVERT: A 1019 ASP cc_start: 0.2489 (OUTLIER) cc_final: 0.0902 (t0) REVERT: A 1027 MET cc_start: 0.3496 (tpp) cc_final: 0.2909 (tpt) REVERT: B 36 THR cc_start: 0.8895 (OUTLIER) cc_final: 0.8411 (p) REVERT: B 143 ASN cc_start: 0.8207 (m110) cc_final: 0.7933 (m-40) REVERT: B 175 ASP cc_start: 0.8667 (p0) cc_final: 0.8110 (p0) outliers start: 40 outliers final: 24 residues processed: 141 average time/residue: 0.0977 time to fit residues: 20.7177 Evaluate side-chains 123 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 95 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 520 PHE Chi-restraints excluded: chain A residue 735 ILE Chi-restraints excluded: chain A residue 752 SER Chi-restraints excluded: chain A residue 821 ASP Chi-restraints excluded: chain A residue 829 ILE Chi-restraints excluded: chain A residue 1015 THR Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1019 ASP Chi-restraints excluded: chain A residue 1023 THR Chi-restraints excluded: chain A residue 1139 VAL Chi-restraints excluded: chain A residue 1176 LEU Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain C residue 6 SER Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 37 ARG Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 136 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 117 optimal weight: 6.9990 chunk 57 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 36 optimal weight: 7.9990 chunk 70 optimal weight: 1.9990 chunk 157 optimal weight: 10.0000 chunk 137 optimal weight: 0.0470 chunk 25 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 overall best weight: 1.3484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 296 ASN ** 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 = 0.4497 r_free = 0.4497 target = 0.220693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.176230 restraints weight = 16309.187| |-----------------------------------------------------------------------------| r_work (start): 0.4062 rms_B_bonded: 2.76 r_work: 0.3384 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.3479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12920 Z= 0.166 Angle : 0.589 10.343 17558 Z= 0.296 Chirality : 0.042 0.249 2031 Planarity : 0.003 0.029 2162 Dihedral : 6.239 101.758 1924 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.54 % Favored : 96.40 % Rotamer: Outliers : 3.37 % Allowed : 19.33 % Favored : 77.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.49 (0.21), residues: 1584 helix: 1.49 (0.19), residues: 762 sheet: 0.41 (0.33), residues: 273 loop : -1.38 (0.26), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 905 TYR 0.020 0.001 TYR C 94 PHE 0.022 0.002 PHE A 994 TRP 0.019 0.001 TRP A 232 HIS 0.003 0.001 HIS B 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.17 (12915) covalent geometry : angle 0.58801 / 0.30 (17548) SS BOND : bond 0.00641 / 0.32 ( 5) SS BOND : angle 1.43445 / 0.73 ( 10) hydrogen bonds : bond 0.05722 / 3.70 ( 714) hydrogen bonds : angle 4.44094 / 3.18 ( 2037) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 99 time to evaluate : 0.484 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 418 GLN cc_start: 0.6588 (tp40) cc_final: 0.6217 (tt0) REVERT: A 478 VAL cc_start: 0.6326 (OUTLIER) cc_final: 0.5899 (t) REVERT: A 520 PHE cc_start: 0.3395 (OUTLIER) cc_final: 0.2560 (m-10) REVERT: A 840 ILE cc_start: 0.8812 (OUTLIER) cc_final: 0.8475 (mt) REVERT: A 876 MET cc_start: 0.7266 (mmm) cc_final: 0.6847 (mmm) REVERT: A 1019 ASP cc_start: 0.2139 (OUTLIER) cc_final: 0.0831 (t0) REVERT: A 1027 MET cc_start: 0.3542 (tpp) cc_final: 0.2947 (tpt) REVERT: A 1171 ASP cc_start: 0.2644 (OUTLIER) cc_final: 0.1940 (p0) REVERT: B 168 TRP cc_start: 0.6967 (m-90) cc_final: 0.6098 (m-90) outliers start: 45 outliers final: 30 residues processed: 142 average time/residue: 0.0931 time to fit residues: 20.0575 Evaluate side-chains 127 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 92 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 137 CYS Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 520 PHE Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 735 ILE Chi-restraints excluded: chain A residue 821 ASP Chi-restraints excluded: chain A residue 829 ILE Chi-restraints excluded: chain A residue 837 THR Chi-restraints excluded: chain A residue 840 ILE Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 1015 THR Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1019 ASP Chi-restraints excluded: chain A residue 1023 THR Chi-restraints excluded: chain A residue 1106 VAL Chi-restraints excluded: chain A residue 1171 ASP Chi-restraints excluded: chain A residue 1176 LEU Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain C residue 6 SER Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 37 ARG Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 136 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 71 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 106 optimal weight: 9.9990 chunk 42 optimal weight: 5.9990 chunk 0 optimal weight: 3.9990 chunk 110 optimal weight: 0.8980 chunk 44 optimal weight: 6.9990 chunk 133 optimal weight: 4.9990 chunk 126 optimal weight: 0.5980 chunk 51 optimal weight: 10.0000 chunk 95 optimal weight: 10.0000 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 462 ASN A1238 GLN B 143 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.216125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.171000 restraints weight = 16243.684| |-----------------------------------------------------------------------------| r_work (start): 0.4002 rms_B_bonded: 2.68 r_work: 0.3353 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.3881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 12920 Z= 0.270 Angle : 0.692 12.393 17558 Z= 0.351 Chirality : 0.046 0.270 2031 Planarity : 0.004 0.031 2162 Dihedral : 6.729 101.194 1922 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.48 % Favored : 95.45 % Rotamer: Outliers : 3.75 % Allowed : 19.78 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.09 (0.21), residues: 1584 helix: 1.04 (0.18), residues: 771 sheet: 0.20 (0.32), residues: 275 loop : -1.40 (0.26), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A1103 TYR 0.023 0.002 TYR C 94 PHE 0.029 0.002 PHE A 994 TRP 0.028 0.002 TRP A 232 HIS 0.004 0.001 HIS B 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00645 / 0.27 (12915) covalent geometry : angle 0.69103 / 0.35 (17548) SS BOND : bond 0.00664 / 0.34 ( 5) SS BOND : angle 1.82570 / 0.93 ( 10) hydrogen bonds : bond 0.06775 / 4.39 ( 714) hydrogen bonds : angle 4.82997 / 3.47 ( 2037) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 98 time to evaluate : 0.283 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 364 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7742 (tp30) REVERT: A 418 GLN cc_start: 0.6642 (tp40) cc_final: 0.6228 (tt0) REVERT: A 520 PHE cc_start: 0.3515 (OUTLIER) cc_final: 0.2634 (m-10) REVERT: A 1019 ASP cc_start: 0.2495 (OUTLIER) cc_final: 0.1210 (t0) REVERT: A 1027 MET cc_start: 0.3509 (tpp) cc_final: 0.3024 (tpt) REVERT: B 175 ASP cc_start: 0.8611 (p0) cc_final: 0.8206 (p0) outliers start: 50 outliers final: 36 residues processed: 147 average time/residue: 0.0870 time to fit residues: 19.3666 Evaluate side-chains 129 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 90 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 137 CYS Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 387 ASN Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 520 PHE Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 735 ILE Chi-restraints excluded: chain A residue 752 SER Chi-restraints excluded: chain A residue 821 ASP Chi-restraints excluded: chain A residue 829 ILE Chi-restraints excluded: chain A residue 1004 SER Chi-restraints excluded: chain A residue 1015 THR Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1019 ASP Chi-restraints excluded: chain A residue 1023 THR Chi-restraints excluded: chain A residue 1106 VAL Chi-restraints excluded: chain A residue 1176 LEU Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 101 ARG Chi-restraints excluded: chain C residue 4 VAL Chi-restraints excluded: chain C residue 6 SER Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 37 ARG Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 136 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 85 optimal weight: 0.6980 chunk 93 optimal weight: 0.4980 chunk 101 optimal weight: 9.9990 chunk 53 optimal weight: 20.0000 chunk 25 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 116 optimal weight: 0.9990 chunk 76 optimal weight: 5.9990 chunk 37 optimal weight: 7.9990 chunk 22 optimal weight: 0.7980 chunk 69 optimal weight: 0.4980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 462 ASN A1238 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4510 r_free = 0.4510 target = 0.222364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.178367 restraints weight = 16260.004| |-----------------------------------------------------------------------------| r_work (start): 0.4063 rms_B_bonded: 2.67 r_work: 0.3415 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.4152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12920 Z= 0.124 Angle : 0.550 9.322 17558 Z= 0.277 Chirality : 0.040 0.239 2031 Planarity : 0.003 0.032 2162 Dihedral : 6.131 103.017 1922 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.03 % Favored : 96.91 % Rotamer: Outliers : 3.07 % Allowed : 20.82 % Favored : 76.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.57 (0.21), residues: 1584 helix: 1.57 (0.19), residues: 759 sheet: 0.44 (0.33), residues: 268 loop : -1.32 (0.26), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 905 TYR 0.015 0.001 TYR C 101 PHE 0.033 0.001 PHE A 994 TRP 0.035 0.002 TRP A 232 HIS 0.003 0.001 HIS B 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (12915) covalent geometry : angle 0.54933 / 0.28 (17548) SS BOND : bond 0.00482 / 0.24 ( 5) SS BOND : angle 0.96502 / 0.50 ( 10) hydrogen bonds : bond 0.05139 / 3.33 ( 714) hydrogen bonds : angle 4.36587 / 3.12 ( 2037) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 98 time to evaluate : 0.286 Fit side-chains TARDY: cannot create tardy model for: "CYS B 220 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 413 LEU cc_start: 0.4756 (OUTLIER) cc_final: 0.4159 (pp) REVERT: A 418 GLN cc_start: 0.6592 (tp40) cc_final: 0.6313 (tt0) REVERT: A 440 MET cc_start: 0.5881 (tpt) cc_final: 0.5649 (tpp) REVERT: A 520 PHE cc_start: 0.3673 (OUTLIER) cc_final: 0.2717 (m-10) REVERT: A 876 MET cc_start: 0.7104 (mmm) cc_final: 0.6713 (mmm) REVERT: A 986 MET cc_start: 0.8870 (mtt) cc_final: 0.8627 (mtm) REVERT: A 1019 ASP cc_start: 0.2280 (OUTLIER) cc_final: 0.1270 (m-30) REVERT: A 1027 MET cc_start: 0.3426 (tpp) cc_final: 0.2928 (tpt) REVERT: B 175 ASP cc_start: 0.8612 (p0) cc_final: 0.8176 (p0) outliers start: 41 outliers final: 31 residues processed: 136 average time/residue: 0.0909 time to fit residues: 18.5419 Evaluate side-chains 127 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 93 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 520 PHE Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 735 ILE Chi-restraints excluded: chain A residue 752 SER Chi-restraints excluded: chain A residue 821 ASP Chi-restraints excluded: chain A residue 829 ILE Chi-restraints excluded: chain A residue 1015 THR Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1019 ASP Chi-restraints excluded: chain A residue 1023 THR Chi-restraints excluded: chain A residue 1139 VAL Chi-restraints excluded: chain A residue 1176 LEU Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 220 CYS Chi-restraints excluded: chain C residue 6 SER Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 37 ARG Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 136 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 52 optimal weight: 4.9990 chunk 102 optimal weight: 3.9990 chunk 155 optimal weight: 9.9990 chunk 146 optimal weight: 1.9990 chunk 78 optimal weight: 6.9990 chunk 21 optimal weight: 0.6980 chunk 131 optimal weight: 7.9990 chunk 151 optimal weight: 0.9990 chunk 94 optimal weight: 20.0000 chunk 137 optimal weight: 1.9990 chunk 95 optimal weight: 6.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 462 ASN ** A1130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.217097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.171999 restraints weight = 16128.294| |-----------------------------------------------------------------------------| r_work (start): 0.4011 rms_B_bonded: 2.65 r_work: 0.3345 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.4191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 12920 Z= 0.219 Angle : 0.642 11.349 17558 Z= 0.323 Chirality : 0.044 0.256 2031 Planarity : 0.004 0.031 2162 Dihedral : 6.435 102.761 1922 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.23 % Favored : 95.71 % Rotamer: Outliers : 2.77 % Allowed : 21.27 % Favored : 75.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.21), residues: 1584 helix: 1.35 (0.18), residues: 762 sheet: 0.42 (0.33), residues: 269 loop : -1.38 (0.26), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 193 TYR 0.022 0.002 TYR C 94 PHE 0.024 0.002 PHE A 994 TRP 0.036 0.002 TRP A 232 HIS 0.003 0.001 HIS B 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00517 / 0.22 (12915) covalent geometry : angle 0.64152 / 0.32 (17548) SS BOND : bond 0.00611 / 0.31 ( 5) SS BOND : angle 1.50441 / 0.77 ( 10) hydrogen bonds : bond 0.06114 / 3.96 ( 714) hydrogen bonds : angle 4.60324 / 3.30 ( 2037) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 96 time to evaluate : 0.479 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "CYS B 220 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 111 MET cc_start: 0.8401 (mmp) cc_final: 0.8086 (mmp) REVERT: A 418 GLN cc_start: 0.6710 (tp40) cc_final: 0.6353 (tt0) REVERT: A 520 PHE cc_start: 0.3743 (OUTLIER) cc_final: 0.2946 (m-10) REVERT: A 876 MET cc_start: 0.7176 (mmm) cc_final: 0.6790 (mmm) REVERT: A 986 MET cc_start: 0.8928 (mtt) cc_final: 0.8671 (mtm) REVERT: A 1019 ASP cc_start: 0.2439 (OUTLIER) cc_final: 0.0935 (t0) REVERT: A 1027 MET cc_start: 0.3445 (tpp) cc_final: 0.2939 (tpt) REVERT: A 1064 GLN cc_start: 0.6525 (pt0) cc_final: 0.6179 (pp30) REVERT: B 123 PHE cc_start: 0.5257 (m-80) cc_final: 0.5020 (m-80) REVERT: B 174 LYS cc_start: 0.8202 (mtmp) cc_final: 0.7754 (ttpt) outliers start: 37 outliers final: 34 residues processed: 131 average time/residue: 0.1017 time to fit residues: 20.1569 Evaluate side-chains 130 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 94 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 520 PHE Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 735 ILE Chi-restraints excluded: chain A residue 752 SER Chi-restraints excluded: chain A residue 821 ASP Chi-restraints excluded: chain A residue 829 ILE Chi-restraints excluded: chain A residue 1015 THR Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1019 ASP Chi-restraints excluded: chain A residue 1023 THR Chi-restraints excluded: chain A residue 1106 VAL Chi-restraints excluded: chain A residue 1139 VAL Chi-restraints excluded: chain A residue 1176 LEU Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 101 ARG Chi-restraints excluded: chain B residue 220 CYS Chi-restraints excluded: chain C residue 4 VAL Chi-restraints excluded: chain C residue 6 SER Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 144 optimal weight: 3.9990 chunk 96 optimal weight: 6.9990 chunk 2 optimal weight: 0.8980 chunk 85 optimal weight: 0.0980 chunk 132 optimal weight: 3.9990 chunk 130 optimal weight: 8.9990 chunk 53 optimal weight: 20.0000 chunk 19 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 88 optimal weight: 5.9990 chunk 34 optimal weight: 10.0000 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 462 ASN ** A1130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.219389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.174886 restraints weight = 16336.664| |-----------------------------------------------------------------------------| r_work (start): 0.4039 rms_B_bonded: 2.63 r_work: 0.3402 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.4423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12920 Z= 0.169 Angle : 0.597 10.680 17558 Z= 0.299 Chirality : 0.042 0.251 2031 Planarity : 0.003 0.032 2162 Dihedral : 6.274 103.342 1922 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.72 % Favored : 96.21 % Rotamer: Outliers : 3.00 % Allowed : 20.97 % Favored : 76.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.49 (0.21), residues: 1584 helix: 1.45 (0.19), residues: 766 sheet: 0.48 (0.33), residues: 264 loop : -1.36 (0.26), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 100 TYR 0.019 0.001 TYR C 94 PHE 0.016 0.001 PHE A 994 TRP 0.034 0.002 TRP A 232 HIS 0.003 0.001 HIS A 612 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.17 (12915) covalent geometry : angle 0.59605 / 0.30 (17548) SS BOND : bond 0.00568 / 0.29 ( 5) SS BOND : angle 1.28047 / 0.65 ( 10) hydrogen bonds : bond 0.05572 / 3.60 ( 714) hydrogen bonds : angle 4.45059 / 3.19 ( 2037) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 95 time to evaluate : 0.489 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "CYS B 220 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 111 MET cc_start: 0.8319 (mmp) cc_final: 0.7971 (mmp) REVERT: A 413 LEU cc_start: 0.4502 (OUTLIER) cc_final: 0.3945 (pp) REVERT: A 418 GLN cc_start: 0.6606 (tp40) cc_final: 0.6320 (tt0) REVERT: A 520 PHE cc_start: 0.3746 (OUTLIER) cc_final: 0.2871 (m-10) REVERT: A 876 MET cc_start: 0.7218 (mmm) cc_final: 0.6839 (mmm) REVERT: A 986 MET cc_start: 0.8912 (mtt) cc_final: 0.8664 (mtm) REVERT: A 1019 ASP cc_start: 0.2455 (OUTLIER) cc_final: 0.1428 (m-30) REVERT: A 1027 MET cc_start: 0.3510 (tpp) cc_final: 0.3014 (tpt) REVERT: B 123 PHE cc_start: 0.5485 (m-80) cc_final: 0.5251 (m-80) REVERT: B 174 LYS cc_start: 0.8207 (mtmp) cc_final: 0.7699 (ttpt) outliers start: 40 outliers final: 36 residues processed: 132 average time/residue: 0.1014 time to fit residues: 20.3803 Evaluate side-chains 132 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 93 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 374 SER Chi-restraints excluded: chain A residue 387 ASN Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 520 PHE Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 735 ILE Chi-restraints excluded: chain A residue 752 SER Chi-restraints excluded: chain A residue 821 ASP Chi-restraints excluded: chain A residue 829 ILE Chi-restraints excluded: chain A residue 1015 THR Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1019 ASP Chi-restraints excluded: chain A residue 1023 THR Chi-restraints excluded: chain A residue 1106 VAL Chi-restraints excluded: chain A residue 1139 VAL Chi-restraints excluded: chain A residue 1176 LEU Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 101 ARG Chi-restraints excluded: chain B residue 220 CYS Chi-restraints excluded: chain C residue 6 SER Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 76 optimal weight: 1.9990 chunk 144 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 138 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 98 optimal weight: 9.9990 chunk 4 optimal weight: 0.5980 chunk 46 optimal weight: 0.9980 chunk 54 optimal weight: 8.9990 chunk 40 optimal weight: 0.6980 chunk 151 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1130 ASN ** 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 = 0.4504 r_free = 0.4504 target = 0.221842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.177348 restraints weight = 16409.358| |-----------------------------------------------------------------------------| r_work (start): 0.4060 rms_B_bonded: 2.66 r_work: 0.3422 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.4637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12920 Z= 0.125 Angle : 0.552 9.859 17558 Z= 0.276 Chirality : 0.040 0.241 2031 Planarity : 0.003 0.031 2162 Dihedral : 6.013 104.158 1922 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.28 % Favored : 96.65 % Rotamer: Outliers : 3.07 % Allowed : 20.97 % Favored : 75.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.72 (0.21), residues: 1584 helix: 1.68 (0.19), residues: 765 sheet: 0.47 (0.33), residues: 274 loop : -1.28 (0.26), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 905 TYR 0.015 0.001 TYR C 94 PHE 0.011 0.001 PHE B 94 TRP 0.030 0.002 TRP A 232 HIS 0.003 0.001 HIS A 612 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.13 (12915) covalent geometry : angle 0.55170 / 0.28 (17548) SS BOND : bond 0.00486 / 0.25 ( 5) SS BOND : angle 0.95140 / 0.50 ( 10) hydrogen bonds : bond 0.04903 / 3.17 ( 714) hydrogen bonds : angle 4.25711 / 3.05 ( 2037) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2715.88 seconds wall clock time: 47 minutes 26.72 seconds (2846.72 seconds total)