Starting phenix.real_space_refine on Fri Sep 11 16:08:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6v3h_21037/09_2026/6v3h_21037.cif Found real_map, /net/cci-nas-00/data/ceres_data/6v3h_21037/09_2026/6v3h_21037.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6v3h_21037/09_2026/6v3h_21037.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6v3h_21037/09_2026/6v3h_21037.cif" model { file = "/net/cci-nas-00/data/ceres_data/6v3h_21037/09_2026/6v3h_21037.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6v3h_21037/09_2026/6v3h_21037.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6v3h_21037/09_2026/6v3h_21037.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6v3h_21037/09_2026/6v3h_21037.map" } resolution = 3.5 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= 0.004 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: 5 Type Number sf(0) Gaussians S 65 5.16 5 C 6406 2.51 5 N 1602 2.21 5 O 1852 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9926 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 9555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1232, 9555 Classifications: {'peptide': 1232} Link IDs: {'PTRANS': 68, 'TRANS': 1163} Chain breaks: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 203 Unusual residues: {'NAG': 6, 'QO1': 1, 'Y01': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 2.24, per 1000 atoms: 0.23 Number of scatterers: 9926 At special positions: 0 Unit cell: (156.699, 98.4665, 85.7612, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 65 16.00 F 1 9.00 O 1852 8.00 N 1602 7.00 C 6406 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 32 " - pdb=" SG CYS A 90 " distance=2.02 Simple disulfide: pdb=" SG CYS A 38 " - pdb=" SG CYS A 56 " distance=2.02 Simple disulfide: pdb=" SG CYS A 77 " - pdb=" SG CYS A 125 " distance=2.03 Simple disulfide: pdb=" SG CYS A 91 " - pdb=" SG CYS A 129 " distance=2.03 Simple disulfide: pdb=" SG CYS A 113 " - pdb=" SG CYS A 254 " distance=2.03 Simple disulfide: pdb=" SG CYS A 116 " - pdb=" SG CYS A 172 " distance=2.02 Simple disulfide: pdb=" SG CYS A 189 " - pdb=" SG CYS A 197 " distance=2.02 Simple disulfide: pdb=" SG CYS A 243 " - pdb=" SG CYS A 259 " distance=2.03 Simple disulfide: pdb=" SG CYS A 256 " - pdb=" SG CYS A 263 " distance=2.02 Simple disulfide: pdb=" SG CYS A 471 " - pdb=" SG CYS A 485 " distance=2.03 Simple disulfide: pdb=" SG CYS A 525 " - pdb=" SG CYS A 542 " distance=2.02 Simple disulfide: pdb=" SG CYS A 920 " - pdb=" SG CYS A 925 " distance=2.02 Simple disulfide: pdb=" SG CYS A 968 " - pdb=" SG CYS A 994 " distance=2.03 Simple disulfide: pdb=" SG CYS A 981 " - pdb=" SG CYS A 990 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " NAG-ASN " NAG A1401 " - " ASN A 53 " " NAG A1406 " - " ASN A 464 " " NAG A1409 " - " ASN A 506 " " NAG A1410 " - " ASN A 606 " " NAG A1413 " - " ASN A 917 " " NAG A1414 " - " ASN A 996 " " NAG B 1 " - " ASN A 138 " " NAG C 1 " - " ASN A 244 " " NAG D 1 " - " ASN A 497 " " NAG E 1 " - " ASN A 909 " " NAG F 1 " - " ASN A1038 " " NAG G 1 " - " ASN A1076 " Time building additional restraints: 0.82 Conformation dependent library (CDL) restraints added in 386.9 milliseconds 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2322 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 13 sheets defined 60.8% alpha, 9.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 66 through 77 Processing helix chain 'A' and resid 92 through 103 Processing helix chain 'A' and resid 103 through 111 Processing helix chain 'A' and resid 113 through 130 removed outlier: 3.689A pdb=" N SER A 130 " --> pdb=" O HIS A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 135 Processing helix chain 'A' and resid 162 through 173 removed outlier: 3.590A pdb=" N CYS A 172 " --> pdb=" O ALA A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 188 Processing helix chain 'A' and resid 193 through 197 removed outlier: 3.880A pdb=" N CYS A 197 " --> pdb=" O SER A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 207 Processing helix chain 'A' and resid 208 through 212 removed outlier: 3.553A pdb=" N ASN A 211 " --> pdb=" O ASP A 208 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY A 212 " --> pdb=" O THR A 209 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 208 through 212' Processing helix chain 'A' and resid 255 through 260 Processing helix chain 'A' and resid 283 through 312 Processing helix chain 'A' and resid 333 through 351 Processing helix chain 'A' and resid 351 through 368 Processing helix chain 'A' and resid 369 through 373 Processing helix chain 'A' and resid 378 through 384 Processing helix chain 'A' and resid 388 through 402 Processing helix chain 'A' and resid 433 through 436 Processing helix chain 'A' and resid 437 through 453 Processing helix chain 'A' and resid 466 through 470 Processing helix chain 'A' and resid 481 through 485 Processing helix chain 'A' and resid 489 through 495 Processing helix chain 'A' and resid 497 through 502 Processing helix chain 'A' and resid 517 through 528 removed outlier: 3.688A pdb=" N HIS A 521 " --> pdb=" O ASP A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 555 Processing helix chain 'A' and resid 563 through 567 Processing helix chain 'A' and resid 584 through 607 removed outlier: 3.780A pdb=" N GLN A 588 " --> pdb=" O PRO A 584 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR A 607 " --> pdb=" O PHE A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 626 removed outlier: 3.737A pdb=" N ASN A 626 " --> pdb=" O GLU A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 637 Processing helix chain 'A' and resid 637 through 651 removed outlier: 3.889A pdb=" N ILE A 641 " --> pdb=" O ALA A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 659 through 664 Processing helix chain 'A' and resid 665 through 690 Processing helix chain 'A' and resid 695 through 700 Processing helix chain 'A' and resid 701 through 724 removed outlier: 3.980A pdb=" N ALA A 711 " --> pdb=" O LEU A 707 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N ASP A 712 " --> pdb=" O ALA A 708 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N ASN A 713 " --> pdb=" O VAL A 709 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N ILE A 714 " --> pdb=" O GLY A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 731 through 762 Proline residue: A 745 - end of helix Processing helix chain 'A' and resid 766 through 788 Processing helix chain 'A' and resid 789 through 804 removed outlier: 3.715A pdb=" N ALA A 804 " --> pdb=" O LYS A 800 " (cutoff:3.500A) Processing helix chain 'A' and resid 826 through 835 Processing helix chain 'A' and resid 835 through 841 removed outlier: 3.560A pdb=" N PHE A 839 " --> pdb=" O ILE A 835 " (cutoff:3.500A) Processing helix chain 'A' and resid 845 through 864 Processing helix chain 'A' and resid 872 through 877 removed outlier: 3.764A pdb=" N ALA A 876 " --> pdb=" O ASP A 872 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU A 877 " --> pdb=" O GLN A 873 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 872 through 877' Processing helix chain 'A' and resid 882 through 894 removed outlier: 3.504A pdb=" N TYR A 886 " --> pdb=" O TYR A 882 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 918 Processing helix chain 'A' and resid 929 through 939 Processing helix chain 'A' and resid 952 through 962 removed outlier: 3.563A pdb=" N ASP A 956 " --> pdb=" O SER A 952 " (cutoff:3.500A) Processing helix chain 'A' and resid 963 through 966 removed outlier: 3.613A pdb=" N SER A 966 " --> pdb=" O PRO A 963 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 963 through 966' Processing helix chain 'A' and resid 1005 through 1017 Proline residue: A1014 - end of helix Processing helix chain 'A' and resid 1028 through 1033 removed outlier: 4.549A pdb=" N ALA A1032 " --> pdb=" O GLY A1028 " (cutoff:3.500A) Processing helix chain 'A' and resid 1059 through 1082 removed outlier: 3.596A pdb=" N ASP A1080 " --> pdb=" O ASN A1076 " (cutoff:3.500A) Processing helix chain 'A' and resid 1099 through 1104 Processing helix chain 'A' and resid 1105 through 1107 No H-bonds generated for 'chain 'A' and resid 1105 through 1107' Processing helix chain 'A' and resid 1108 through 1132 Proline residue: A1123 - end of helix Processing helix chain 'A' and resid 1135 through 1161 Processing helix chain 'A' and resid 1165 through 1179 Processing helix chain 'A' and resid 1179 through 1192 removed outlier: 4.754A pdb=" N HIS A1185 " --> pdb=" O GLU A1181 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N ILE A1186 " --> pdb=" O PHE A1182 " (cutoff:3.500A) Processing helix chain 'A' and resid 1197 through 1227 removed outlier: 4.353A pdb=" N MET A1219 " --> pdb=" O ALA A1215 " (cutoff:3.500A) Proline residue: A1223 - end of helix removed outlier: 3.510A pdb=" N ILE A1227 " --> pdb=" O PRO A1223 " (cutoff:3.500A) Processing helix chain 'A' and resid 1228 through 1231 Processing helix chain 'A' and resid 1233 through 1240 Processing helix chain 'A' and resid 1240 through 1257 Processing helix chain 'A' and resid 1257 through 1267 removed outlier: 3.952A pdb=" N VAL A1261 " --> pdb=" O VAL A1257 " (cutoff:3.500A) Processing helix chain 'A' and resid 1271 through 1282 removed outlier: 3.648A pdb=" N VAL A1275 " --> pdb=" O ASN A1271 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 37 removed outlier: 3.604A pdb=" N PHE A 34 " --> pdb=" O SER A 58 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N SER A 58 " --> pdb=" O PHE A 34 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N GLU A 36 " --> pdb=" O CYS A 56 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 63 through 64 Processing sheet with id=AA3, first strand: chain 'A' and resid 137 through 143 removed outlier: 6.182A pdb=" N ILE A 137 " --> pdb=" O PHE A 159 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N PHE A 159 " --> pdb=" O ILE A 137 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N VAL A 139 " --> pdb=" O GLU A 157 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N GLU A 157 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N VAL A 143 " --> pdb=" O VAL A 153 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N VAL A 153 " --> pdb=" O VAL A 143 " (cutoff:3.500A) removed outlier: 10.191A pdb=" N ASP A 217 " --> pdb=" O ALA A 152 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N VAL A 154 " --> pdb=" O ASP A 217 " (cutoff:3.500A) removed outlier: 8.320A pdb=" N THR A 219 " --> pdb=" O VAL A 154 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N TYR A 156 " --> pdb=" O THR A 219 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N HIS A 221 " --> pdb=" O TYR A 156 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ALA A 158 " --> pdb=" O HIS A 221 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N LEU A 223 " --> pdb=" O ALA A 158 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N TYR A 160 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 176 through 177 Processing sheet with id=AA5, first strand: chain 'A' and resid 277 through 278 Processing sheet with id=AA6, first strand: chain 'A' and resid 487 through 488 Processing sheet with id=AA7, first strand: chain 'A' and resid 487 through 488 Processing sheet with id=AA8, first strand: chain 'A' and resid 420 through 423 Processing sheet with id=AA9, first strand: chain 'A' and resid 456 through 458 removed outlier: 3.649A pdb=" N ARG A 463 " --> pdb=" O SER A 458 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 505 through 509 Processing sheet with id=AB2, first strand: chain 'A' and resid 946 through 948 removed outlier: 6.800A pdb=" N TYR A1053 " --> pdb=" O ALA A 947 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ASN A1038 " --> pdb=" O ILE A1046 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 946 through 948 removed outlier: 6.800A pdb=" N TYR A1053 " --> pdb=" O ALA A 947 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 980 through 981 removed outlier: 3.916A pdb=" N ARG A 969 " --> pdb=" O CYS A 981 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LYS A 992 " --> pdb=" O LEU A 970 " (cutoff:3.500A) 536 hydrogen bonds defined for protein. 1530 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.94 Time building geometry restraints manager: 1.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1564 1.32 - 1.44: 2801 1.44 - 1.57: 5701 1.57 - 1.70: 8 1.70 - 1.83: 90 Bond restraints: 10164 Sorted by residual: bond pdb=" C24 QO1 A1421 " pdb=" N01 QO1 A1421 " ideal model delta sigma weight residual 1.375 1.575 -0.200 2.00e-02 2.50e+03 1.00e+02 bond pdb=" C10 QO1 A1421 " pdb=" C11 QO1 A1421 " ideal model delta sigma weight residual 1.563 1.375 0.188 2.00e-02 2.50e+03 8.87e+01 bond pdb=" C11 QO1 A1421 " pdb=" N01 QO1 A1421 " ideal model delta sigma weight residual 1.483 1.310 0.173 2.00e-02 2.50e+03 7.50e+01 bond pdb=" C10 QO1 A1421 " pdb=" C24 QO1 A1421 " ideal model delta sigma weight residual 1.527 1.697 -0.170 2.00e-02 2.50e+03 7.24e+01 bond pdb=" C11 QO1 A1421 " pdb=" C12 QO1 A1421 " ideal model delta sigma weight residual 1.497 1.656 -0.159 2.00e-02 2.50e+03 6.30e+01 ... (remaining 10159 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.05: 13633 4.05 - 8.11: 189 8.11 - 12.16: 23 12.16 - 16.21: 5 16.21 - 20.27: 3 Bond angle restraints: 13853 Sorted by residual: angle pdb=" C10 QO1 A1421 " pdb=" C24 QO1 A1421 " pdb=" N01 QO1 A1421 " ideal model delta sigma weight residual 92.09 71.82 20.27 3.00e+00 1.11e-01 4.56e+01 angle pdb=" C SER A 275 " pdb=" N PHE A 276 " pdb=" CA PHE A 276 " ideal model delta sigma weight residual 121.54 134.28 -12.74 1.91e+00 2.74e-01 4.45e+01 angle pdb=" N ASP A 231 " pdb=" CA ASP A 231 " pdb=" CB ASP A 231 " ideal model delta sigma weight residual 110.49 100.02 10.47 1.69e+00 3.50e-01 3.84e+01 angle pdb=" C PRO A 230 " pdb=" N ASP A 231 " pdb=" CA ASP A 231 " ideal model delta sigma weight residual 121.54 132.82 -11.28 1.91e+00 2.74e-01 3.48e+01 angle pdb=" O08 QO1 A1421 " pdb=" S01 QO1 A1421 " pdb=" O09 QO1 A1421 " ideal model delta sigma weight residual 119.20 102.42 16.78 3.00e+00 1.11e-01 3.13e+01 ... (remaining 13848 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.17: 5630 21.17 - 42.34: 263 42.34 - 63.51: 50 63.51 - 84.68: 9 84.68 - 105.85: 1 Dihedral angle restraints: 5953 sinusoidal: 2360 harmonic: 3593 Sorted by residual: dihedral pdb=" CB CYS A 525 " pdb=" SG CYS A 525 " pdb=" SG CYS A 542 " pdb=" CB CYS A 542 " ideal model delta sinusoidal sigma weight residual -86.00 -164.06 78.06 1 1.00e+01 1.00e-02 7.61e+01 dihedral pdb=" CB CYS A 243 " pdb=" SG CYS A 243 " pdb=" SG CYS A 259 " pdb=" CB CYS A 259 " ideal model delta sinusoidal sigma weight residual 93.00 149.37 -56.37 1 1.00e+01 1.00e-02 4.28e+01 dihedral pdb=" CB CYS A 38 " pdb=" SG CYS A 38 " pdb=" SG CYS A 56 " pdb=" CB CYS A 56 " ideal model delta sinusoidal sigma weight residual 93.00 147.19 -54.19 1 1.00e+01 1.00e-02 3.98e+01 ... (remaining 5950 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 1355 0.087 - 0.174: 269 0.174 - 0.261: 22 0.261 - 0.348: 5 0.348 - 0.435: 3 Chirality restraints: 1654 Sorted by residual: chirality pdb=" CA PHE A 276 " pdb=" N PHE A 276 " pdb=" C PHE A 276 " pdb=" CB PHE A 276 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.44 2.00e-01 2.50e+01 4.74e+00 chirality pdb=" CG LEU A 223 " pdb=" CB LEU A 223 " pdb=" CD1 LEU A 223 " pdb=" CD2 LEU A 223 " both_signs ideal model delta sigma weight residual False -2.59 -2.22 -0.37 2.00e-01 2.50e+01 3.36e+00 chirality pdb=" C2 NAG B 2 " pdb=" C1 NAG B 2 " pdb=" C3 NAG B 2 " pdb=" N2 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.49 -2.14 -0.36 2.00e-01 2.50e+01 3.16e+00 ... (remaining 1651 not shown) Planarity restraints: 1742 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A1271 " -0.028 2.00e-02 2.50e+03 5.72e-02 3.27e+01 pdb=" CG ASN A1271 " 0.099 2.00e-02 2.50e+03 pdb=" OD1 ASN A1271 " -0.038 2.00e-02 2.50e+03 pdb=" ND2 ASN A1271 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 383 " -0.031 2.00e-02 2.50e+03 3.19e-02 2.55e+01 pdb=" CG TRP A 383 " 0.084 2.00e-02 2.50e+03 pdb=" CD1 TRP A 383 " -0.045 2.00e-02 2.50e+03 pdb=" CD2 TRP A 383 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 383 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP A 383 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP A 383 " -0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 383 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 383 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP A 383 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A1207 " 0.017 2.00e-02 2.50e+03 3.29e-02 1.08e+01 pdb=" C VAL A1207 " -0.057 2.00e-02 2.50e+03 pdb=" O VAL A1207 " 0.021 2.00e-02 2.50e+03 pdb=" N PHE A1208 " 0.019 2.00e-02 2.50e+03 ... (remaining 1739 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 2322 2.80 - 3.33: 9269 3.33 - 3.85: 16374 3.85 - 4.38: 18338 4.38 - 4.90: 32677 Nonbonded interactions: 78980 Sorted by model distance: nonbonded pdb=" OG SER A 620 " pdb=" OH TYR A 882 " model vdw 2.275 3.040 nonbonded pdb=" O GLY A1216 " pdb=" OG1 THR A1220 " model vdw 2.276 3.040 nonbonded pdb=" OD1 ASP A 712 " pdb=" OG1 THR A1220 " model vdw 2.295 3.040 nonbonded pdb=" OH TYR A 169 " pdb=" O CYS A 197 " model vdw 2.313 3.040 nonbonded pdb=" O PRO A1021 " pdb=" O04 QO1 A1421 " model vdw 2.314 3.040 ... (remaining 78975 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 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.260 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.450 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 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 : 0.009 0.200 10196 Z= 0.424 Angle : 1.292 20.265 13935 Z= 0.660 Chirality : 0.069 0.435 1654 Planarity : 0.007 0.057 1730 Dihedral : 12.599 105.846 3589 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.94 % Favored : 96.98 % Rotamer: Outliers : 0.76 % Allowed : 3.41 % Favored : 95.83 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % 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: 0.65 (0.23), residues: 1226 helix: 1.00 (0.19), residues: 612 sheet: 0.27 (0.51), residues: 93 loop : -0.10 (0.26), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A1201 TYR 0.026 0.003 TYR A 689 PHE 0.038 0.003 PHE A 704 TRP 0.084 0.004 TRP A 383 HIS 0.012 0.003 HIS A 126 Details of bonding type rmsd/Z covalent geometry : bond 0.00940 / 0.42 (10164) covalent geometry : angle 1.25819 / 0.65 (13853) SS BOND : bond 0.00649 / 0.38 ( 14) SS BOND : angle 4.41187 / 2.11 ( 28) hydrogen bonds : bond 0.14868 / 9.60 ( 533) hydrogen bonds : angle 6.74947 / 4.89 ( 1530) link_BETA1-4 : bond 0.00552 / 0.28 ( 6) link_BETA1-4 : angle 4.87865 / 2.66 ( 18) link_NAG-ASN : bond 0.00412 / 0.24 ( 12) link_NAG-ASN : angle 3.08053 / 1.52 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 154 time to evaluate : 0.377 Fit side-chains REVERT: A 167 LYS cc_start: 0.8525 (mttt) cc_final: 0.8244 (mttp) REVERT: A 281 MET cc_start: 0.7945 (ptt) cc_final: 0.7745 (ptt) REVERT: A 378 ASP cc_start: 0.8484 (p0) cc_final: 0.8014 (p0) REVERT: A 659 ARG cc_start: 0.6519 (mmm160) cc_final: 0.6089 (ttm170) REVERT: A 684 MET cc_start: 0.9053 (mtt) cc_final: 0.8812 (mtp) outliers start: 8 outliers final: 7 residues processed: 161 average time/residue: 0.1189 time to fit residues: 26.2069 Evaluate side-chains 91 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 84 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 243 CYS Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 381 GLU Chi-restraints excluded: chain A residue 620 SER Chi-restraints excluded: chain A residue 875 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 0.8980 chunk 113 optimal weight: 0.7980 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.7980 chunk 117 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 27 HIS A 200 GLN A 234 GLN A 312 ASN A 397 HIS A 495 GLN A 976 HIS A1254 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.129884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.099269 restraints weight = 14139.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.099514 restraints weight = 8922.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.100789 restraints weight = 8063.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.101144 restraints weight = 6332.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.101956 restraints weight = 5835.355| |-----------------------------------------------------------------------------| r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.1368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 10196 Z= 0.137 Angle : 0.691 18.319 13935 Z= 0.335 Chirality : 0.043 0.253 1654 Planarity : 0.005 0.048 1730 Dihedral : 6.738 56.923 1421 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.42 % Allowed : 7.11 % Favored : 91.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.24), residues: 1226 helix: 1.78 (0.20), residues: 635 sheet: 0.38 (0.52), residues: 101 loop : -0.03 (0.28), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 498 TYR 0.015 0.001 TYR A 646 PHE 0.026 0.001 PHE A 704 TRP 0.025 0.002 TRP A 202 HIS 0.004 0.001 HIS A1054 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.14 (10164) covalent geometry : angle 0.67790 / 0.33 (13853) SS BOND : bond 0.00890 / 0.43 ( 14) SS BOND : angle 1.56964 / 0.79 ( 28) hydrogen bonds : bond 0.05277 / 3.54 ( 533) hydrogen bonds : angle 5.27010 / 3.80 ( 1530) link_BETA1-4 : bond 0.00383 / 0.20 ( 6) link_BETA1-4 : angle 2.39971 / 1.32 ( 18) link_NAG-ASN : bond 0.00223 / 0.15 ( 12) link_NAG-ASN : angle 1.82326 / 1.05 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 103 time to evaluate : 0.383 Fit side-chains REVERT: A 167 LYS cc_start: 0.8541 (mttt) cc_final: 0.8302 (mttm) REVERT: A 520 ASP cc_start: 0.8114 (m-30) cc_final: 0.7891 (m-30) REVERT: A 659 ARG cc_start: 0.6584 (mmm160) cc_final: 0.5796 (ttm110) REVERT: A 932 GLN cc_start: 0.8226 (mt0) cc_final: 0.7846 (tm-30) REVERT: A 1112 GLU cc_start: 0.7456 (mt-10) cc_final: 0.7181 (mt-10) outliers start: 15 outliers final: 11 residues processed: 113 average time/residue: 0.0810 time to fit residues: 14.0804 Evaluate side-chains 102 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 91 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 243 CYS Chi-restraints excluded: chain A residue 478 TYR Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 854 LEU Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain A residue 1120 CYS Chi-restraints excluded: chain A residue 1157 MET Chi-restraints excluded: chain A residue 1207 VAL Chi-restraints excluded: chain A residue 1232 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 80 optimal weight: 4.9990 chunk 106 optimal weight: 0.8980 chunk 90 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 chunk 16 optimal weight: 7.9990 chunk 100 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 chunk 74 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 989 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.130029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.099118 restraints weight = 14153.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.099374 restraints weight = 8876.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.100321 restraints weight = 8008.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.100797 restraints weight = 6426.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.101747 restraints weight = 5889.444| |-----------------------------------------------------------------------------| r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10196 Z= 0.125 Angle : 0.624 18.008 13935 Z= 0.300 Chirality : 0.042 0.253 1654 Planarity : 0.004 0.048 1730 Dihedral : 6.187 57.473 1412 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.80 % Allowed : 7.77 % Favored : 90.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.24), residues: 1226 helix: 1.89 (0.20), residues: 637 sheet: 0.34 (0.53), residues: 100 loop : -0.06 (0.28), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 498 TYR 0.014 0.001 TYR A 646 PHE 0.025 0.001 PHE A 704 TRP 0.019 0.001 TRP A 202 HIS 0.005 0.001 HIS A1054 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (10164) covalent geometry : angle 0.61321 / 0.30 (13853) SS BOND : bond 0.00282 / 0.15 ( 14) SS BOND : angle 1.20046 / 0.68 ( 28) hydrogen bonds : bond 0.04681 / 3.11 ( 533) hydrogen bonds : angle 4.94741 / 3.56 ( 1530) link_BETA1-4 : bond 0.00304 / 0.16 ( 6) link_BETA1-4 : angle 2.29563 / 1.26 ( 18) link_NAG-ASN : bond 0.00169 / 0.11 ( 12) link_NAG-ASN : angle 1.58353 / 0.92 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 103 time to evaluate : 0.323 Fit side-chains revert: symmetry clash REVERT: A 107 LYS cc_start: 0.8823 (mtmt) cc_final: 0.8320 (mtpp) REVERT: A 167 LYS cc_start: 0.8501 (mttt) cc_final: 0.8275 (mttm) REVERT: A 170 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.7686 (mm-30) REVERT: A 659 ARG cc_start: 0.6510 (mmm160) cc_final: 0.5815 (ttm110) REVERT: A 684 MET cc_start: 0.9014 (mtt) cc_final: 0.8779 (mtp) REVERT: A 788 MET cc_start: 0.7996 (mmp) cc_final: 0.7762 (mmp) REVERT: A 932 GLN cc_start: 0.8209 (mt0) cc_final: 0.7833 (tm-30) REVERT: A 1112 GLU cc_start: 0.7565 (mt-10) cc_final: 0.7245 (mt-10) outliers start: 19 outliers final: 11 residues processed: 116 average time/residue: 0.0830 time to fit residues: 14.8786 Evaluate side-chains 103 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 91 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 243 CYS Chi-restraints excluded: chain A residue 478 TYR Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 712 ASP Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain A residue 1120 CYS Chi-restraints excluded: chain A residue 1157 MET Chi-restraints excluded: chain A residue 1176 VAL Chi-restraints excluded: chain A residue 1232 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 84 optimal weight: 0.7980 chunk 45 optimal weight: 3.9990 chunk 81 optimal weight: 5.9990 chunk 43 optimal weight: 0.8980 chunk 13 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 3 optimal weight: 20.0000 chunk 67 optimal weight: 5.9990 chunk 64 optimal weight: 4.9990 chunk 57 optimal weight: 0.9990 chunk 104 optimal weight: 4.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 868 ASN ** A1271 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 = 0.3486 r_free = 0.3486 target = 0.127088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.097187 restraints weight = 14287.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.097124 restraints weight = 9480.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.098354 restraints weight = 8877.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.098724 restraints weight = 6751.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.099001 restraints weight = 6795.473| |-----------------------------------------------------------------------------| r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10196 Z= 0.190 Angle : 0.639 13.215 13935 Z= 0.308 Chirality : 0.043 0.249 1654 Planarity : 0.004 0.047 1730 Dihedral : 5.986 54.143 1410 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.90 % Allowed : 9.48 % Favored : 88.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.24), residues: 1226 helix: 1.82 (0.20), residues: 639 sheet: 0.37 (0.54), residues: 95 loop : 0.02 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 406 TYR 0.013 0.001 TYR A 646 PHE 0.028 0.002 PHE A 704 TRP 0.017 0.001 TRP A 202 HIS 0.005 0.001 HIS A1054 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.19 (10164) covalent geometry : angle 0.62656 / 0.30 (13853) SS BOND : bond 0.00587 / 0.28 ( 14) SS BOND : angle 1.41234 / 0.81 ( 28) hydrogen bonds : bond 0.04784 / 3.18 ( 533) hydrogen bonds : angle 4.92129 / 3.55 ( 1530) link_BETA1-4 : bond 0.00306 / 0.16 ( 6) link_BETA1-4 : angle 2.29045 / 1.25 ( 18) link_NAG-ASN : bond 0.00178 / 0.11 ( 12) link_NAG-ASN : angle 1.64549 / 0.95 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 94 time to evaluate : 0.340 Fit side-chains REVERT: A 107 LYS cc_start: 0.8822 (mtmt) cc_final: 0.8303 (mtpp) REVERT: A 135 LEU cc_start: 0.8605 (mt) cc_final: 0.8394 (mt) REVERT: A 167 LYS cc_start: 0.8544 (mttt) cc_final: 0.8320 (mttp) REVERT: A 278 MET cc_start: 0.8142 (mmm) cc_final: 0.7923 (mmm) REVERT: A 659 ARG cc_start: 0.6456 (mmm160) cc_final: 0.5809 (ttm110) REVERT: A 684 MET cc_start: 0.9033 (mtt) cc_final: 0.8777 (mtp) REVERT: A 727 MET cc_start: 0.6040 (tmm) cc_final: 0.5627 (tmm) REVERT: A 747 MET cc_start: 0.7555 (mtm) cc_final: 0.7303 (mtm) REVERT: A 788 MET cc_start: 0.7920 (mmp) cc_final: 0.7685 (mmp) REVERT: A 932 GLN cc_start: 0.8171 (mt0) cc_final: 0.7880 (tm-30) REVERT: A 1112 GLU cc_start: 0.7577 (mt-10) cc_final: 0.7281 (mt-10) REVERT: A 1152 ASP cc_start: 0.7867 (m-30) cc_final: 0.7404 (m-30) REVERT: A 1246 LEU cc_start: 0.9214 (OUTLIER) cc_final: 0.8847 (mp) outliers start: 20 outliers final: 13 residues processed: 105 average time/residue: 0.0793 time to fit residues: 12.9631 Evaluate side-chains 97 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 83 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 243 CYS Chi-restraints excluded: chain A residue 478 TYR Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 712 ASP Chi-restraints excluded: chain A residue 989 ASN Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain A residue 1120 CYS Chi-restraints excluded: chain A residue 1138 SER Chi-restraints excluded: chain A residue 1157 MET Chi-restraints excluded: chain A residue 1207 VAL Chi-restraints excluded: chain A residue 1232 GLN Chi-restraints excluded: chain A residue 1246 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 96 optimal weight: 0.8980 chunk 24 optimal weight: 30.0000 chunk 51 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 13 optimal weight: 5.9990 chunk 105 optimal weight: 0.9990 chunk 14 optimal weight: 5.9990 chunk 99 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1271 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 = 0.3489 r_free = 0.3489 target = 0.127391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.097169 restraints weight = 14334.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.096140 restraints weight = 10396.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.097180 restraints weight = 9909.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.099708 restraints weight = 7173.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.099672 restraints weight = 5816.861| |-----------------------------------------------------------------------------| r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.902 10196 Z= 0.517 Angle : 0.798 46.607 13935 Z= 0.383 Chirality : 0.043 0.249 1654 Planarity : 0.004 0.047 1730 Dihedral : 5.989 54.143 1410 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.33 % Allowed : 10.24 % Favored : 88.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.24), residues: 1226 helix: 1.82 (0.20), residues: 639 sheet: 0.37 (0.54), residues: 95 loop : 0.02 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 406 TYR 0.013 0.001 TYR A 646 PHE 0.028 0.002 PHE A 704 TRP 0.017 0.001 TRP A 202 HIS 0.005 0.001 HIS A1054 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.19 (10164) covalent geometry : angle 0.62662 / 0.30 (13853) SS BOND : bond 0.25950 / 11.89 ( 14) SS BOND : angle 10.74933 / 4.86 ( 28) hydrogen bonds : bond 0.04783 / 3.18 ( 533) hydrogen bonds : angle 4.92129 / 3.55 ( 1530) link_BETA1-4 : bond 0.00306 / 0.16 ( 6) link_BETA1-4 : angle 2.29044 / 1.25 ( 18) link_NAG-ASN : bond 0.00178 / 0.11 ( 12) link_NAG-ASN : angle 1.64549 / 0.95 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 83 time to evaluate : 0.379 Fit side-chains REVERT: A 107 LYS cc_start: 0.8822 (mtmt) cc_final: 0.8301 (mtpp) REVERT: A 167 LYS cc_start: 0.8551 (mttt) cc_final: 0.8309 (mttp) REVERT: A 278 MET cc_start: 0.8111 (mmm) cc_final: 0.7905 (mmm) REVERT: A 659 ARG cc_start: 0.6466 (mmm160) cc_final: 0.5808 (ttm110) REVERT: A 684 MET cc_start: 0.9015 (mtt) cc_final: 0.8750 (mtp) REVERT: A 727 MET cc_start: 0.6043 (tmm) cc_final: 0.5616 (tmm) REVERT: A 747 MET cc_start: 0.7546 (mtm) cc_final: 0.7281 (mtm) REVERT: A 788 MET cc_start: 0.7929 (mmp) cc_final: 0.7692 (mmp) REVERT: A 932 GLN cc_start: 0.8200 (mt0) cc_final: 0.7849 (tm-30) REVERT: A 1112 GLU cc_start: 0.7587 (mt-10) cc_final: 0.7272 (mt-10) REVERT: A 1152 ASP cc_start: 0.7903 (m-30) cc_final: 0.7421 (m-30) REVERT: A 1246 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8811 (mp) outliers start: 14 outliers final: 13 residues processed: 92 average time/residue: 0.0829 time to fit residues: 11.8927 Evaluate side-chains 97 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 83 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 243 CYS Chi-restraints excluded: chain A residue 478 TYR Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 712 ASP Chi-restraints excluded: chain A residue 989 ASN Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain A residue 1120 CYS Chi-restraints excluded: chain A residue 1138 SER Chi-restraints excluded: chain A residue 1157 MET Chi-restraints excluded: chain A residue 1207 VAL Chi-restraints excluded: chain A residue 1232 GLN Chi-restraints excluded: chain A residue 1246 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 74 optimal weight: 4.9990 chunk 38 optimal weight: 0.0020 chunk 12 optimal weight: 6.9990 chunk 19 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 5 optimal weight: 7.9990 chunk 68 optimal weight: 0.3980 chunk 100 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 89 optimal weight: 0.6980 overall best weight: 1.0192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1271 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 = 0.3485 r_free = 0.3485 target = 0.126969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.097277 restraints weight = 14287.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.096990 restraints weight = 10363.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.099282 restraints weight = 9024.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.099371 restraints weight = 6399.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.099612 restraints weight = 6724.553| |-----------------------------------------------------------------------------| r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.902 10196 Z= 0.517 Angle : 0.798 46.607 13935 Z= 0.383 Chirality : 0.043 0.249 1654 Planarity : 0.004 0.047 1730 Dihedral : 5.986 54.143 1410 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.33 % Allowed : 10.33 % Favored : 88.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.24), residues: 1226 helix: 1.82 (0.20), residues: 639 sheet: 0.37 (0.54), residues: 95 loop : 0.02 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 406 TYR 0.013 0.001 TYR A 646 PHE 0.028 0.002 PHE A 704 TRP 0.017 0.001 TRP A 202 HIS 0.005 0.001 HIS A1054 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.19 (10164) covalent geometry : angle 0.62662 / 0.30 (13853) SS BOND : bond 0.25950 / 11.89 ( 14) SS BOND : angle 10.74933 / 4.86 ( 28) hydrogen bonds : bond 0.04783 / 3.18 ( 533) hydrogen bonds : angle 4.92129 / 3.55 ( 1530) link_BETA1-4 : bond 0.00306 / 0.16 ( 6) link_BETA1-4 : angle 2.29044 / 1.25 ( 18) link_NAG-ASN : bond 0.00178 / 0.11 ( 12) link_NAG-ASN : angle 1.64549 / 0.95 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 83 time to evaluate : 0.366 Fit side-chains REVERT: A 107 LYS cc_start: 0.8816 (mtmt) cc_final: 0.8300 (mtpp) REVERT: A 167 LYS cc_start: 0.8550 (mttt) cc_final: 0.8316 (mttp) REVERT: A 659 ARG cc_start: 0.6437 (mmm160) cc_final: 0.5815 (ttm110) REVERT: A 684 MET cc_start: 0.9034 (mtt) cc_final: 0.8776 (mtp) REVERT: A 727 MET cc_start: 0.6038 (tmm) cc_final: 0.5633 (tmm) REVERT: A 747 MET cc_start: 0.7546 (mtm) cc_final: 0.7290 (mtm) REVERT: A 788 MET cc_start: 0.7922 (mmp) cc_final: 0.7688 (mmp) REVERT: A 932 GLN cc_start: 0.8176 (mt0) cc_final: 0.7874 (tm-30) REVERT: A 1112 GLU cc_start: 0.7580 (mt-10) cc_final: 0.7278 (mt-10) REVERT: A 1152 ASP cc_start: 0.7874 (m-30) cc_final: 0.7405 (m-30) REVERT: A 1246 LEU cc_start: 0.9206 (OUTLIER) cc_final: 0.8842 (mp) outliers start: 14 outliers final: 13 residues processed: 92 average time/residue: 0.0834 time to fit residues: 11.9183 Evaluate side-chains 97 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 83 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 243 CYS Chi-restraints excluded: chain A residue 478 TYR Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 712 ASP Chi-restraints excluded: chain A residue 989 ASN Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain A residue 1120 CYS Chi-restraints excluded: chain A residue 1138 SER Chi-restraints excluded: chain A residue 1157 MET Chi-restraints excluded: chain A residue 1207 VAL Chi-restraints excluded: chain A residue 1232 GLN Chi-restraints excluded: chain A residue 1246 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 5 optimal weight: 8.9990 chunk 109 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 51 optimal weight: 0.5980 chunk 86 optimal weight: 1.9990 chunk 88 optimal weight: 0.0770 chunk 118 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 114 optimal weight: 7.9990 chunk 71 optimal weight: 0.9980 chunk 38 optimal weight: 8.9990 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1271 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 = 0.3502 r_free = 0.3502 target = 0.128335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.098600 restraints weight = 14167.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.098186 restraints weight = 10443.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.099510 restraints weight = 8995.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.100220 restraints weight = 6882.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.101100 restraints weight = 6679.673| |-----------------------------------------------------------------------------| r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 10196 Z= 0.125 Angle : 0.616 11.990 13935 Z= 0.299 Chirality : 0.041 0.254 1654 Planarity : 0.004 0.045 1730 Dihedral : 6.005 54.870 1410 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.52 % Allowed : 10.43 % Favored : 88.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.53 (0.24), residues: 1226 helix: 1.90 (0.20), residues: 638 sheet: 0.41 (0.55), residues: 95 loop : 0.05 (0.29), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 406 TYR 0.013 0.001 TYR A 646 PHE 0.024 0.001 PHE A 704 TRP 0.016 0.001 TRP A 202 HIS 0.004 0.001 HIS A1054 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (10164) covalent geometry : angle 0.59767 / 0.29 (13853) SS BOND : bond 0.00661 / 0.32 ( 14) SS BOND : angle 2.39340 / 1.22 ( 28) hydrogen bonds : bond 0.04639 / 3.09 ( 533) hydrogen bonds : angle 4.88460 / 3.52 ( 1530) link_BETA1-4 : bond 0.00307 / 0.16 ( 6) link_BETA1-4 : angle 2.28563 / 1.25 ( 18) link_NAG-ASN : bond 0.00171 / 0.11 ( 12) link_NAG-ASN : angle 1.59223 / 0.92 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 88 time to evaluate : 0.409 Fit side-chains REVERT: A 80 LEU cc_start: 0.9224 (mt) cc_final: 0.8898 (mp) REVERT: A 107 LYS cc_start: 0.8788 (mtmt) cc_final: 0.8264 (mtpp) REVERT: A 167 LYS cc_start: 0.8521 (mttt) cc_final: 0.8296 (mttp) REVERT: A 659 ARG cc_start: 0.6416 (mmm160) cc_final: 0.5802 (ttm110) REVERT: A 684 MET cc_start: 0.9012 (mtt) cc_final: 0.8755 (mtp) REVERT: A 788 MET cc_start: 0.7884 (mmp) cc_final: 0.7538 (mmp) REVERT: A 932 GLN cc_start: 0.8161 (mt0) cc_final: 0.7897 (tm-30) REVERT: A 1112 GLU cc_start: 0.7554 (mt-10) cc_final: 0.7249 (mt-10) REVERT: A 1246 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.8853 (mp) outliers start: 16 outliers final: 10 residues processed: 98 average time/residue: 0.0830 time to fit residues: 12.7188 Evaluate side-chains 96 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 85 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 243 CYS Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 478 TYR Chi-restraints excluded: chain A residue 989 ASN Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain A residue 1120 CYS Chi-restraints excluded: chain A residue 1157 MET Chi-restraints excluded: chain A residue 1207 VAL Chi-restraints excluded: chain A residue 1232 GLN Chi-restraints excluded: chain A residue 1246 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 70 optimal weight: 4.9990 chunk 75 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 4 optimal weight: 20.0000 chunk 27 optimal weight: 9.9990 chunk 66 optimal weight: 0.7980 chunk 41 optimal weight: 5.9990 chunk 103 optimal weight: 0.6980 chunk 94 optimal weight: 5.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1271 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 = 0.3500 r_free = 0.3500 target = 0.128213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.098142 restraints weight = 14147.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.098075 restraints weight = 9167.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.099229 restraints weight = 8666.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.099650 restraints weight = 6794.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.099817 restraints weight = 6829.233| |-----------------------------------------------------------------------------| r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.021 2.092 10196 Z= 1.046 Angle : 0.770 39.437 13935 Z= 0.371 Chirality : 0.041 0.254 1654 Planarity : 0.004 0.045 1730 Dihedral : 6.006 54.870 1410 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.04 % Allowed : 10.81 % Favored : 88.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.53 (0.24), residues: 1226 helix: 1.90 (0.20), residues: 638 sheet: 0.41 (0.55), residues: 95 loop : 0.05 (0.29), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 406 TYR 0.013 0.001 TYR A 646 PHE 0.024 0.001 PHE A 704 TRP 0.016 0.001 TRP A 202 HIS 0.004 0.001 HIS A1054 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (10164) covalent geometry : angle 0.59769 / 0.29 (13853) SS BOND : bond 0.56032 / 26.65 ( 14) SS BOND : angle 10.55855 / 4.19 ( 28) hydrogen bonds : bond 0.04639 / 3.09 ( 533) hydrogen bonds : angle 4.88460 / 3.52 ( 1530) link_BETA1-4 : bond 0.00307 / 0.16 ( 6) link_BETA1-4 : angle 2.28563 / 1.25 ( 18) link_NAG-ASN : bond 0.00171 / 0.11 ( 12) link_NAG-ASN : angle 1.59223 / 0.92 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 85 time to evaluate : 0.298 Fit side-chains REVERT: A 80 LEU cc_start: 0.9223 (mt) cc_final: 0.8896 (mp) REVERT: A 107 LYS cc_start: 0.8793 (mtmt) cc_final: 0.8267 (mtpp) REVERT: A 167 LYS cc_start: 0.8531 (mttt) cc_final: 0.8299 (mttp) REVERT: A 659 ARG cc_start: 0.6447 (mmm160) cc_final: 0.5800 (ttm110) REVERT: A 684 MET cc_start: 0.9013 (mtt) cc_final: 0.8753 (mtp) REVERT: A 788 MET cc_start: 0.7933 (mmp) cc_final: 0.7539 (mmp) REVERT: A 932 GLN cc_start: 0.8164 (mt0) cc_final: 0.7899 (tm-30) REVERT: A 1112 GLU cc_start: 0.7533 (mt-10) cc_final: 0.7235 (mt-10) REVERT: A 1246 LEU cc_start: 0.9212 (OUTLIER) cc_final: 0.8854 (mp) outliers start: 11 outliers final: 10 residues processed: 91 average time/residue: 0.0836 time to fit residues: 11.6766 Evaluate side-chains 96 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 85 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 243 CYS Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 478 TYR Chi-restraints excluded: chain A residue 989 ASN Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain A residue 1120 CYS Chi-restraints excluded: chain A residue 1157 MET Chi-restraints excluded: chain A residue 1207 VAL Chi-restraints excluded: chain A residue 1232 GLN Chi-restraints excluded: chain A residue 1246 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 69 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 64 optimal weight: 4.9990 chunk 16 optimal weight: 0.4980 chunk 99 optimal weight: 7.9990 chunk 22 optimal weight: 3.9990 chunk 3 optimal weight: 7.9990 chunk 27 optimal weight: 10.0000 chunk 73 optimal weight: 0.9980 chunk 96 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1271 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 = 0.3500 r_free = 0.3500 target = 0.128215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.098139 restraints weight = 14111.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.098037 restraints weight = 9133.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.099211 restraints weight = 8644.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.099626 restraints weight = 6770.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.099820 restraints weight = 6813.266| |-----------------------------------------------------------------------------| r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.021 2.090 10196 Z= 1.045 Angle : 0.769 39.406 13935 Z= 0.371 Chirality : 0.041 0.254 1654 Planarity : 0.004 0.045 1730 Dihedral : 6.020 54.872 1410 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.04 % Allowed : 10.81 % Favored : 88.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.53 (0.24), residues: 1226 helix: 1.90 (0.20), residues: 638 sheet: 0.41 (0.55), residues: 95 loop : 0.05 (0.29), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 406 TYR 0.013 0.001 TYR A 646 PHE 0.024 0.001 PHE A 704 TRP 0.016 0.001 TRP A 202 HIS 0.004 0.001 HIS A1054 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (10164) covalent geometry : angle 0.59766 / 0.29 (13853) SS BOND : bond 0.55980 / 26.63 ( 14) SS BOND : angle 10.55035 / 4.19 ( 28) hydrogen bonds : bond 0.04639 / 3.09 ( 533) hydrogen bonds : angle 4.88459 / 3.52 ( 1530) link_BETA1-4 : bond 0.00307 / 0.16 ( 6) link_BETA1-4 : angle 2.28567 / 1.25 ( 18) link_NAG-ASN : bond 0.00171 / 0.11 ( 12) link_NAG-ASN : angle 1.59222 / 0.92 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 85 time to evaluate : 0.371 Fit side-chains REVERT: A 80 LEU cc_start: 0.9223 (mt) cc_final: 0.8896 (mp) REVERT: A 107 LYS cc_start: 0.8794 (mtmt) cc_final: 0.8267 (mtpp) REVERT: A 167 LYS cc_start: 0.8530 (mttt) cc_final: 0.8299 (mttp) REVERT: A 659 ARG cc_start: 0.6451 (mmm160) cc_final: 0.5800 (ttm110) REVERT: A 684 MET cc_start: 0.9013 (mtt) cc_final: 0.8753 (mtp) REVERT: A 788 MET cc_start: 0.7933 (mmp) cc_final: 0.7539 (mmp) REVERT: A 932 GLN cc_start: 0.8167 (mt0) cc_final: 0.7899 (tm-30) REVERT: A 1112 GLU cc_start: 0.7532 (mt-10) cc_final: 0.7233 (mt-10) REVERT: A 1246 LEU cc_start: 0.9212 (OUTLIER) cc_final: 0.8854 (mp) outliers start: 11 outliers final: 10 residues processed: 91 average time/residue: 0.0832 time to fit residues: 11.7670 Evaluate side-chains 96 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 85 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 243 CYS Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 478 TYR Chi-restraints excluded: chain A residue 989 ASN Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain A residue 1120 CYS Chi-restraints excluded: chain A residue 1157 MET Chi-restraints excluded: chain A residue 1207 VAL Chi-restraints excluded: chain A residue 1232 GLN Chi-restraints excluded: chain A residue 1246 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 67 optimal weight: 4.9990 chunk 12 optimal weight: 6.9990 chunk 41 optimal weight: 6.9990 chunk 80 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 29 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 118 optimal weight: 0.6980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1271 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.126640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.096756 restraints weight = 14091.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.096309 restraints weight = 11551.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.098012 restraints weight = 10489.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.098257 restraints weight = 7117.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.099124 restraints weight = 6685.020| |-----------------------------------------------------------------------------| r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10196 Z= 0.150 Angle : 0.624 10.548 13935 Z= 0.303 Chirality : 0.043 0.253 1654 Planarity : 0.004 0.049 1730 Dihedral : 6.029 54.618 1410 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.33 % Allowed : 10.71 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.24), residues: 1226 helix: 1.97 (0.20), residues: 633 sheet: 0.46 (0.55), residues: 95 loop : -0.09 (0.29), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1071 TYR 0.014 0.001 TYR A1164 PHE 0.026 0.001 PHE A 704 TRP 0.018 0.001 TRP A 202 HIS 0.005 0.001 HIS A1054 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 (10164) covalent geometry : angle 0.61119 / 0.30 (13853) SS BOND : bond 0.00363 / 0.20 ( 14) SS BOND : angle 1.55871 / 0.91 ( 28) hydrogen bonds : bond 0.04616 / 3.08 ( 533) hydrogen bonds : angle 4.82068 / 3.48 ( 1530) link_BETA1-4 : bond 0.00298 / 0.15 ( 6) link_BETA1-4 : angle 2.26920 / 1.24 ( 18) link_NAG-ASN : bond 0.00170 / 0.11 ( 12) link_NAG-ASN : angle 1.60141 / 0.91 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 87 time to evaluate : 0.380 Fit side-chains REVERT: A 107 LYS cc_start: 0.8826 (mtmt) cc_final: 0.8287 (mtpp) REVERT: A 167 LYS cc_start: 0.8543 (mttt) cc_final: 0.8305 (mttp) REVERT: A 659 ARG cc_start: 0.6402 (mmm160) cc_final: 0.5824 (ttm110) REVERT: A 788 MET cc_start: 0.7944 (mmp) cc_final: 0.7617 (mmp) REVERT: A 932 GLN cc_start: 0.8157 (mt0) cc_final: 0.7879 (tm-30) REVERT: A 1112 GLU cc_start: 0.7568 (mt-10) cc_final: 0.7283 (mt-10) REVERT: A 1148 MET cc_start: 0.8712 (mtp) cc_final: 0.8083 (ttm) REVERT: A 1152 ASP cc_start: 0.7898 (m-30) cc_final: 0.7430 (m-30) REVERT: A 1246 LEU cc_start: 0.9302 (OUTLIER) cc_final: 0.8957 (mp) outliers start: 14 outliers final: 9 residues processed: 96 average time/residue: 0.0787 time to fit residues: 11.7113 Evaluate side-chains 94 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 84 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 243 CYS Chi-restraints excluded: chain A residue 259 CYS Chi-restraints excluded: chain A residue 478 TYR Chi-restraints excluded: chain A residue 989 ASN Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain A residue 1120 CYS Chi-restraints excluded: chain A residue 1207 VAL Chi-restraints excluded: chain A residue 1232 GLN Chi-restraints excluded: chain A residue 1246 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 16 optimal weight: 0.0570 chunk 122 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 68 optimal weight: 6.9990 chunk 91 optimal weight: 8.9990 chunk 80 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 72 optimal weight: 1.9990 chunk 50 optimal weight: 6.9990 chunk 75 optimal weight: 0.8980 chunk 1 optimal weight: 7.9990 overall best weight: 1.9904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1271 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 = 0.3449 r_free = 0.3449 target = 0.124417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.095603 restraints weight = 14198.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.094834 restraints weight = 10546.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.096455 restraints weight = 9354.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.096702 restraints weight = 6936.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.097080 restraints weight = 7073.829| |-----------------------------------------------------------------------------| r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10196 Z= 0.181 Angle : 0.655 9.425 13935 Z= 0.319 Chirality : 0.044 0.259 1654 Planarity : 0.004 0.054 1730 Dihedral : 6.051 58.123 1410 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.23 % Allowed : 10.71 % Favored : 88.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.42 (0.24), residues: 1226 helix: 1.88 (0.20), residues: 641 sheet: 0.37 (0.56), residues: 89 loop : -0.14 (0.29), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1071 TYR 0.014 0.002 TYR A1164 PHE 0.030 0.002 PHE A 704 TRP 0.018 0.002 TRP A 202 HIS 0.004 0.001 HIS A1054 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.18 (10164) covalent geometry : angle 0.64023 / 0.31 (13853) SS BOND : bond 0.00467 / 0.27 ( 14) SS BOND : angle 1.87824 / 1.07 ( 28) hydrogen bonds : bond 0.04836 / 3.22 ( 533) hydrogen bonds : angle 4.78412 / 3.46 ( 1530) link_BETA1-4 : bond 0.00271 / 0.14 ( 6) link_BETA1-4 : angle 2.30933 / 1.27 ( 18) link_NAG-ASN : bond 0.00244 / 0.13 ( 12) link_NAG-ASN : angle 1.73458 / 0.99 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1439.72 seconds wall clock time: 25 minutes 44.15 seconds (1544.15 seconds total)