Starting phenix.real_space_refine on Wed Mar 4 02:41:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6v3h_21037/03_2026/6v3h_21037.cif Found real_map, /net/cci-nas-00/data/ceres_data/6v3h_21037/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/6v3h_21037/03_2026/6v3h_21037.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6v3h_21037/03_2026/6v3h_21037.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6v3h_21037/03_2026/6v3h_21037.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6v3h_21037/03_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 1.99, per 1000 atoms: 0.20 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: 0.72 Conformation dependent library (CDL) restraints added in 464.8 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: 1.64 Time building geometry restraints manager: 0.96 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: 6080 21.17 - 42.34: 288 42.34 - 63.51: 69 63.51 - 84.68: 9 84.68 - 105.85: 1 Dihedral angle restraints: 6447 sinusoidal: 2854 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 6444 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: 1.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.540 Find NCS groups from input model: 0.040 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:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 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 : 12.720 105.846 4083 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 covalent geometry : bond 0.00940 (10164) covalent geometry : angle 1.25819 (13853) SS BOND : bond 0.00649 ( 14) SS BOND : angle 4.41187 ( 28) hydrogen bonds : bond 0.14868 ( 533) hydrogen bonds : angle 6.74947 ( 1530) link_BETA1-4 : bond 0.00552 ( 6) link_BETA1-4 : angle 4.87865 ( 18) link_NAG-ASN : bond 0.00412 ( 12) link_NAG-ASN : angle 3.08053 ( 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 : 0.327 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: 0.1162 time to fit residues: 25.3299 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 : 0.346 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 27 HIS A 200 GLN A 234 GLN A 312 ASN A 397 HIS A 976 HIS A1254 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.130065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.099594 restraints weight = 14144.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.099765 restraints weight = 8972.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.100981 restraints weight = 8218.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.101413 restraints weight = 6339.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.101596 restraints weight = 6301.060| |-----------------------------------------------------------------------------| r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.1428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 10196 Z= 0.136 Angle : 0.686 18.649 13935 Z= 0.332 Chirality : 0.043 0.243 1654 Planarity : 0.005 0.048 1730 Dihedral : 8.368 59.532 1915 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.61 % Allowed : 6.73 % Favored : 91.66 % 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: 1.39 (0.24), residues: 1226 helix: 1.78 (0.20), residues: 637 sheet: 0.38 (0.52), residues: 101 loop : -0.02 (0.28), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 726 TYR 0.015 0.001 TYR A 646 PHE 0.026 0.001 PHE A 704 TRP 0.024 0.002 TRP A 202 HIS 0.004 0.001 HIS A 976 Details of bonding type rmsd covalent geometry : bond 0.00296 (10164) covalent geometry : angle 0.67238 (13853) SS BOND : bond 0.00405 ( 14) SS BOND : angle 1.54220 ( 28) hydrogen bonds : bond 0.05062 ( 533) hydrogen bonds : angle 5.21897 ( 1530) link_BETA1-4 : bond 0.00312 ( 6) link_BETA1-4 : angle 2.42700 ( 18) link_NAG-ASN : bond 0.00216 ( 12) link_NAG-ASN : angle 1.86351 ( 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 122 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 105 time to evaluate : 0.348 Fit side-chains REVERT: A 167 LYS cc_start: 0.8548 (mttt) cc_final: 0.8309 (mttm) REVERT: A 520 ASP cc_start: 0.8123 (m-30) cc_final: 0.7888 (m-30) REVERT: A 659 ARG cc_start: 0.6587 (mmm160) cc_final: 0.5797 (ttm110) REVERT: A 932 GLN cc_start: 0.8230 (mt0) cc_final: 0.7863 (tm-30) REVERT: A 1112 GLU cc_start: 0.7435 (mt-10) cc_final: 0.7155 (mt-10) REVERT: A 1152 ASP cc_start: 0.7943 (m-30) cc_final: 0.7477 (m-30) outliers start: 17 outliers final: 12 residues processed: 117 average time/residue: 0.0787 time to fit residues: 14.1320 Evaluate side-chains 107 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 95 time to evaluate : 0.248 ------------------------------------------------------------------------------- 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 1176 VAL 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: 5.9990 chunk 106 optimal weight: 0.8980 chunk 90 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 23 optimal weight: 0.0870 chunk 74 optimal weight: 0.3980 chunk 82 optimal weight: 1.9990 overall best weight: 0.6760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 495 GLN A 989 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.130824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.100065 restraints weight = 14127.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.099668 restraints weight = 9035.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.101022 restraints weight = 9471.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.101505 restraints weight = 6337.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.102691 restraints weight = 6053.464| |-----------------------------------------------------------------------------| r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10196 Z= 0.118 Angle : 0.619 18.403 13935 Z= 0.295 Chirality : 0.041 0.249 1654 Planarity : 0.004 0.046 1730 Dihedral : 7.786 57.976 1906 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.52 % Allowed : 7.96 % Favored : 90.52 % 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: 1.50 (0.24), residues: 1226 helix: 1.90 (0.20), residues: 639 sheet: 0.36 (0.52), residues: 100 loop : -0.02 (0.28), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 406 TYR 0.014 0.001 TYR A 646 PHE 0.024 0.001 PHE A 704 TRP 0.018 0.001 TRP A 202 HIS 0.004 0.001 HIS A1054 Details of bonding type rmsd covalent geometry : bond 0.00246 (10164) covalent geometry : angle 0.60711 (13853) SS BOND : bond 0.00409 ( 14) SS BOND : angle 1.14270 ( 28) hydrogen bonds : bond 0.04613 ( 533) hydrogen bonds : angle 4.94905 ( 1530) link_BETA1-4 : bond 0.00360 ( 6) link_BETA1-4 : angle 2.40179 ( 18) link_NAG-ASN : bond 0.00174 ( 12) link_NAG-ASN : angle 1.66542 ( 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 121 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 105 time to evaluate : 0.395 Fit side-chains revert: symmetry clash REVERT: A 107 LYS cc_start: 0.8779 (mtmt) cc_final: 0.8263 (mtpp) REVERT: A 167 LYS cc_start: 0.8513 (mttt) cc_final: 0.8304 (mttm) REVERT: A 170 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.7668 (mm-30) REVERT: A 659 ARG cc_start: 0.6511 (mmm160) cc_final: 0.5811 (ttm110) REVERT: A 684 MET cc_start: 0.9020 (mtt) cc_final: 0.8798 (mtp) REVERT: A 932 GLN cc_start: 0.8200 (mt0) cc_final: 0.7820 (tm-30) REVERT: A 1112 GLU cc_start: 0.7528 (mt-10) cc_final: 0.7205 (mt-10) REVERT: A 1152 ASP cc_start: 0.7876 (m-30) cc_final: 0.7392 (m-30) outliers start: 16 outliers final: 10 residues processed: 116 average time/residue: 0.0775 time to fit residues: 13.5873 Evaluate side-chains 99 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 88 time to evaluate : 0.340 ------------------------------------------------------------------------------- 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 1232 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 84 optimal weight: 0.0970 chunk 45 optimal weight: 3.9990 chunk 81 optimal weight: 6.9990 chunk 43 optimal weight: 0.9990 chunk 13 optimal weight: 6.9990 chunk 80 optimal weight: 1.9990 chunk 3 optimal weight: 10.0000 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: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 868 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.127200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.097411 restraints weight = 14242.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.096578 restraints weight = 10836.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.098029 restraints weight = 10941.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.098510 restraints weight = 7277.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.099078 restraints weight = 6813.068| |-----------------------------------------------------------------------------| r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10196 Z= 0.158 Angle : 0.623 13.044 13935 Z= 0.302 Chirality : 0.043 0.244 1654 Planarity : 0.004 0.047 1730 Dihedral : 7.550 57.539 1904 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.09 % Allowed : 9.38 % Favored : 88.53 % 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: 1.57 (0.24), residues: 1226 helix: 1.96 (0.20), residues: 633 sheet: 0.70 (0.58), residues: 85 loop : -0.01 (0.28), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1071 TYR 0.013 0.001 TYR A 646 PHE 0.027 0.001 PHE A 704 TRP 0.018 0.001 TRP A 202 HIS 0.006 0.001 HIS A1054 Details of bonding type rmsd covalent geometry : bond 0.00367 (10164) covalent geometry : angle 0.61027 (13853) SS BOND : bond 0.00441 ( 14) SS BOND : angle 1.33402 ( 28) hydrogen bonds : bond 0.04714 ( 533) hydrogen bonds : angle 4.84832 ( 1530) link_BETA1-4 : bond 0.00290 ( 6) link_BETA1-4 : angle 2.35657 ( 18) link_NAG-ASN : bond 0.00159 ( 12) link_NAG-ASN : angle 1.71772 ( 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 113 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 91 time to evaluate : 0.342 Fit side-chains REVERT: A 107 LYS cc_start: 0.8817 (mtmt) cc_final: 0.8280 (mtpp) REVERT: A 135 LEU cc_start: 0.8601 (mt) cc_final: 0.8373 (mt) REVERT: A 167 LYS cc_start: 0.8545 (mttt) cc_final: 0.8319 (mttp) REVERT: A 659 ARG cc_start: 0.6430 (mmm160) cc_final: 0.5822 (ttm110) REVERT: A 932 GLN cc_start: 0.8150 (mt0) cc_final: 0.7895 (tm-30) REVERT: A 1112 GLU cc_start: 0.7569 (mt-10) cc_final: 0.7289 (mt-10) outliers start: 22 outliers final: 11 residues processed: 104 average time/residue: 0.0757 time to fit residues: 12.2009 Evaluate side-chains 95 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 84 time to evaluate : 0.262 ------------------------------------------------------------------------------- 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 719 LEU Chi-restraints excluded: chain A residue 989 ASN Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain A residue 1176 VAL Chi-restraints excluded: chain A residue 1207 VAL Chi-restraints excluded: chain A residue 1232 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 96 optimal weight: 1.9990 chunk 24 optimal weight: 30.0000 chunk 51 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 121 optimal weight: 5.9990 chunk 79 optimal weight: 7.9990 chunk 13 optimal weight: 5.9990 chunk 105 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 99 optimal weight: 0.0470 chunk 101 optimal weight: 2.9990 overall best weight: 1.4082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.127129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.097587 restraints weight = 14212.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.096970 restraints weight = 10658.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.098175 restraints weight = 11212.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.098817 restraints weight = 7301.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.099636 restraints weight = 6743.169| |-----------------------------------------------------------------------------| r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10196 Z= 0.143 Angle : 0.608 10.375 13935 Z= 0.294 Chirality : 0.042 0.243 1654 Planarity : 0.004 0.060 1730 Dihedral : 7.477 57.102 1904 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.80 % Allowed : 10.43 % Favored : 87.77 % 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: 1.54 (0.24), residues: 1226 helix: 1.97 (0.20), residues: 633 sheet: 0.48 (0.55), residues: 95 loop : -0.04 (0.29), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1071 TYR 0.013 0.001 TYR A1164 PHE 0.026 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 covalent geometry : bond 0.00329 (10164) covalent geometry : angle 0.59106 (13853) SS BOND : bond 0.00285 ( 14) SS BOND : angle 2.07486 ( 28) hydrogen bonds : bond 0.04571 ( 533) hydrogen bonds : angle 4.80441 ( 1530) link_BETA1-4 : bond 0.00282 ( 6) link_BETA1-4 : angle 2.34076 ( 18) link_NAG-ASN : bond 0.00157 ( 12) link_NAG-ASN : angle 1.65782 ( 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 111 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 92 time to evaluate : 0.280 Fit side-chains REVERT: A 107 LYS cc_start: 0.8808 (mtmt) cc_final: 0.8256 (mtpp) REVERT: A 135 LEU cc_start: 0.8570 (mt) cc_final: 0.8315 (mt) REVERT: A 167 LYS cc_start: 0.8591 (mttt) cc_final: 0.8334 (mttp) REVERT: A 659 ARG cc_start: 0.6607 (mmm160) cc_final: 0.5965 (ttm110) REVERT: A 932 GLN cc_start: 0.8168 (mt0) cc_final: 0.7896 (tm-30) REVERT: A 1112 GLU cc_start: 0.7515 (mt-10) cc_final: 0.7231 (mt-10) outliers start: 19 outliers final: 12 residues processed: 105 average time/residue: 0.0739 time to fit residues: 12.1872 Evaluate side-chains 100 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 88 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 719 LEU 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 74 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 12 optimal weight: 7.9990 chunk 19 optimal weight: 0.4980 chunk 46 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 5 optimal weight: 7.9990 chunk 68 optimal weight: 8.9990 chunk 100 optimal weight: 0.6980 chunk 40 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.127262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.097599 restraints weight = 14271.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.096862 restraints weight = 10679.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.098734 restraints weight = 9179.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.098936 restraints weight = 6803.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.099234 restraints weight = 7061.034| |-----------------------------------------------------------------------------| r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10196 Z= 0.145 Angle : 0.608 10.557 13935 Z= 0.294 Chirality : 0.042 0.241 1654 Planarity : 0.004 0.057 1730 Dihedral : 7.433 57.883 1904 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.09 % Allowed : 10.14 % Favored : 87.77 % 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: 1.55 (0.24), residues: 1226 helix: 1.97 (0.21), residues: 635 sheet: 0.69 (0.58), residues: 85 loop : -0.08 (0.29), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1071 TYR 0.012 0.001 TYR A 646 PHE 0.025 0.001 PHE A 704 TRP 0.015 0.001 TRP A 202 HIS 0.005 0.001 HIS A1054 Details of bonding type rmsd covalent geometry : bond 0.00337 (10164) covalent geometry : angle 0.58953 (13853) SS BOND : bond 0.00359 ( 14) SS BOND : angle 2.31824 ( 28) hydrogen bonds : bond 0.04480 ( 533) hydrogen bonds : angle 4.75394 ( 1530) link_BETA1-4 : bond 0.00284 ( 6) link_BETA1-4 : angle 2.31640 ( 18) link_NAG-ASN : bond 0.00162 ( 12) link_NAG-ASN : angle 1.64687 ( 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 116 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 94 time to evaluate : 0.361 Fit side-chains REVERT: A 135 LEU cc_start: 0.8598 (mt) cc_final: 0.8320 (mt) REVERT: A 167 LYS cc_start: 0.8577 (mttt) cc_final: 0.8333 (mttp) REVERT: A 659 ARG cc_start: 0.6625 (mmm160) cc_final: 0.5998 (ttm110) REVERT: A 932 GLN cc_start: 0.8187 (mt0) cc_final: 0.7948 (tm-30) REVERT: A 1112 GLU cc_start: 0.7491 (mt-10) cc_final: 0.7232 (mt-10) outliers start: 22 outliers final: 14 residues processed: 110 average time/residue: 0.0763 time to fit residues: 13.1393 Evaluate side-chains 103 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 0.345 ------------------------------------------------------------------------------- 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 712 ASP Chi-restraints excluded: chain A residue 719 LEU Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 989 ASN Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain A residue 1098 ILE Chi-restraints excluded: chain A residue 1138 SER Chi-restraints excluded: chain A residue 1176 VAL Chi-restraints excluded: chain A residue 1207 VAL Chi-restraints excluded: chain A residue 1232 GLN 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: 0.7980 chunk 65 optimal weight: 0.5980 chunk 51 optimal weight: 0.5980 chunk 86 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 114 optimal weight: 6.9990 chunk 71 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.128745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.098888 restraints weight = 13965.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.098984 restraints weight = 9439.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.100389 restraints weight = 9094.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.100662 restraints weight = 6701.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.101155 restraints weight = 6502.698| |-----------------------------------------------------------------------------| r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10196 Z= 0.109 Angle : 0.568 9.473 13935 Z= 0.273 Chirality : 0.040 0.240 1654 Planarity : 0.004 0.057 1730 Dihedral : 7.155 58.186 1904 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.09 % Allowed : 10.43 % Favored : 87.49 % 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: 1.62 (0.25), residues: 1226 helix: 2.07 (0.21), residues: 631 sheet: 0.65 (0.60), residues: 84 loop : -0.06 (0.29), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 656 TYR 0.012 0.001 TYR A 646 PHE 0.021 0.001 PHE A 704 TRP 0.015 0.001 TRP A 202 HIS 0.003 0.001 HIS A1054 Details of bonding type rmsd covalent geometry : bond 0.00237 (10164) covalent geometry : angle 0.55266 (13853) SS BOND : bond 0.00284 ( 14) SS BOND : angle 1.83911 ( 28) hydrogen bonds : bond 0.04087 ( 533) hydrogen bonds : angle 4.67479 ( 1530) link_BETA1-4 : bond 0.00323 ( 6) link_BETA1-4 : angle 2.24632 ( 18) link_NAG-ASN : bond 0.00193 ( 12) link_NAG-ASN : angle 1.48264 ( 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 115 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 93 time to evaluate : 0.370 Fit side-chains REVERT: A 107 LYS cc_start: 0.8807 (mtmt) cc_final: 0.8271 (mtpp) REVERT: A 167 LYS cc_start: 0.8563 (mttt) cc_final: 0.8316 (mttp) REVERT: A 609 ASP cc_start: 0.7696 (t70) cc_final: 0.7247 (t0) REVERT: A 659 ARG cc_start: 0.6554 (mmm160) cc_final: 0.6098 (ttm110) REVERT: A 932 GLN cc_start: 0.8200 (mt0) cc_final: 0.7895 (tm-30) REVERT: A 1044 GLN cc_start: 0.7755 (OUTLIER) cc_final: 0.7158 (mm-40) REVERT: A 1112 GLU cc_start: 0.7470 (mt-10) cc_final: 0.7202 (mt-10) outliers start: 22 outliers final: 11 residues processed: 111 average time/residue: 0.0883 time to fit residues: 14.7535 Evaluate side-chains 98 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 86 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 478 TYR Chi-restraints excluded: chain A residue 712 ASP Chi-restraints excluded: chain A residue 719 LEU Chi-restraints excluded: chain A residue 989 ASN Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain A residue 1044 GLN Chi-restraints excluded: chain A residue 1098 ILE Chi-restraints excluded: chain A residue 1135 ASP Chi-restraints excluded: chain A residue 1138 SER Chi-restraints excluded: chain A residue 1207 VAL Chi-restraints excluded: chain A residue 1232 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 70 optimal weight: 6.9990 chunk 75 optimal weight: 6.9990 chunk 30 optimal weight: 0.9980 chunk 72 optimal weight: 0.9990 chunk 86 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 27 optimal weight: 0.7980 chunk 66 optimal weight: 0.0060 chunk 41 optimal weight: 4.9990 chunk 103 optimal weight: 0.8980 chunk 94 optimal weight: 10.0000 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.128451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.099761 restraints weight = 14005.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.099282 restraints weight = 10637.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.100806 restraints weight = 10377.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.101247 restraints weight = 6948.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.101913 restraints weight = 6580.119| |-----------------------------------------------------------------------------| r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.099 10196 Z= 0.115 Angle : 0.583 9.656 13935 Z= 0.282 Chirality : 0.041 0.235 1654 Planarity : 0.004 0.073 1730 Dihedral : 6.985 56.935 1903 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.80 % Allowed : 11.47 % Favored : 86.73 % 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: 1.64 (0.25), residues: 1226 helix: 2.09 (0.21), residues: 631 sheet: 0.69 (0.59), residues: 84 loop : -0.06 (0.29), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1071 TYR 0.017 0.001 TYR A 971 PHE 0.021 0.001 PHE A 704 TRP 0.013 0.001 TRP A 202 HIS 0.003 0.001 HIS A1054 Details of bonding type rmsd covalent geometry : bond 0.00262 (10164) covalent geometry : angle 0.56738 (13853) SS BOND : bond 0.00694 ( 14) SS BOND : angle 1.92299 ( 28) hydrogen bonds : bond 0.04077 ( 533) hydrogen bonds : angle 4.67357 ( 1530) link_BETA1-4 : bond 0.00375 ( 6) link_BETA1-4 : angle 2.26756 ( 18) link_NAG-ASN : bond 0.00265 ( 12) link_NAG-ASN : angle 1.43760 ( 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 112 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 93 time to evaluate : 0.347 Fit side-chains REVERT: A 56 CYS cc_start: 0.6201 (OUTLIER) cc_final: 0.5959 (m) REVERT: A 107 LYS cc_start: 0.8819 (mtmt) cc_final: 0.8267 (mtpp) REVERT: A 167 LYS cc_start: 0.8563 (mttt) cc_final: 0.8327 (mttp) REVERT: A 609 ASP cc_start: 0.7725 (t70) cc_final: 0.7277 (t0) REVERT: A 659 ARG cc_start: 0.6539 (mmm160) cc_final: 0.6066 (ttm110) REVERT: A 894 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.7668 (tp) REVERT: A 932 GLN cc_start: 0.8184 (mt0) cc_final: 0.7880 (tm-30) REVERT: A 1112 GLU cc_start: 0.7472 (mt-10) cc_final: 0.7194 (mt-10) outliers start: 19 outliers final: 12 residues processed: 109 average time/residue: 0.0810 time to fit residues: 13.7520 Evaluate side-chains 103 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 56 CYS Chi-restraints excluded: chain A residue 478 TYR Chi-restraints excluded: chain A residue 712 ASP Chi-restraints excluded: chain A residue 719 LEU Chi-restraints excluded: chain A residue 827 LEU Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 989 ASN Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain A residue 1098 ILE Chi-restraints excluded: chain A residue 1135 ASP Chi-restraints excluded: chain A residue 1138 SER Chi-restraints excluded: chain A residue 1207 VAL Chi-restraints excluded: chain A residue 1232 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 69 optimal weight: 0.8980 chunk 46 optimal weight: 4.9990 chunk 64 optimal weight: 0.6980 chunk 16 optimal weight: 0.0770 chunk 99 optimal weight: 6.9990 chunk 22 optimal weight: 0.0980 chunk 3 optimal weight: 5.9990 chunk 27 optimal weight: 0.8980 chunk 73 optimal weight: 0.9980 chunk 96 optimal weight: 0.7980 chunk 57 optimal weight: 0.9980 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1254 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.128282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.099618 restraints weight = 13987.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.099275 restraints weight = 10480.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.100635 restraints weight = 10559.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.101121 restraints weight = 7018.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.101762 restraints weight = 6570.439| |-----------------------------------------------------------------------------| r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.018 1.801 10196 Z= 0.899 Angle : 0.882 62.114 13935 Z= 0.423 Chirality : 0.041 0.235 1654 Planarity : 0.004 0.073 1730 Dihedral : 6.988 56.935 1903 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.33 % Allowed : 11.94 % Favored : 86.73 % 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: 1.64 (0.25), residues: 1226 helix: 2.09 (0.21), residues: 631 sheet: 0.69 (0.59), residues: 84 loop : -0.06 (0.29), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1071 TYR 0.017 0.001 TYR A 971 PHE 0.021 0.001 PHE A 704 TRP 0.013 0.001 TRP A 202 HIS 0.003 0.001 HIS A1054 Details of bonding type rmsd covalent geometry : bond 0.00262 (10164) covalent geometry : angle 0.56741 (13853) SS BOND : bond 0.48136 ( 14) SS BOND : angle 14.88802 ( 28) hydrogen bonds : bond 0.04077 ( 533) hydrogen bonds : angle 4.67357 ( 1530) link_BETA1-4 : bond 0.00374 ( 6) link_BETA1-4 : angle 2.26753 ( 18) link_NAG-ASN : bond 0.00265 ( 12) link_NAG-ASN : angle 1.43760 ( 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 103 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 0.355 Fit side-chains REVERT: A 56 CYS cc_start: 0.6208 (OUTLIER) cc_final: 0.5968 (m) REVERT: A 107 LYS cc_start: 0.8817 (mtmt) cc_final: 0.8265 (mtpp) REVERT: A 167 LYS cc_start: 0.8564 (mttt) cc_final: 0.8322 (mttp) REVERT: A 609 ASP cc_start: 0.7720 (t70) cc_final: 0.7273 (t0) REVERT: A 659 ARG cc_start: 0.6530 (mmm160) cc_final: 0.6069 (ttm110) REVERT: A 794 LEU cc_start: 0.9001 (tp) cc_final: 0.8733 (tt) REVERT: A 894 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.8168 (tp) REVERT: A 932 GLN cc_start: 0.8170 (mt0) cc_final: 0.7884 (tm-30) REVERT: A 1112 GLU cc_start: 0.7483 (mt-10) cc_final: 0.7204 (mt-10) outliers start: 14 outliers final: 12 residues processed: 101 average time/residue: 0.0806 time to fit residues: 12.6576 Evaluate side-chains 102 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 88 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 56 CYS Chi-restraints excluded: chain A residue 478 TYR Chi-restraints excluded: chain A residue 712 ASP Chi-restraints excluded: chain A residue 719 LEU Chi-restraints excluded: chain A residue 827 LEU Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 989 ASN Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain A residue 1098 ILE Chi-restraints excluded: chain A residue 1135 ASP Chi-restraints excluded: chain A residue 1138 SER Chi-restraints excluded: chain A residue 1207 VAL Chi-restraints excluded: chain A residue 1232 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 67 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 41 optimal weight: 5.9990 chunk 80 optimal weight: 4.9990 chunk 104 optimal weight: 3.9990 chunk 84 optimal weight: 0.0370 chunk 49 optimal weight: 2.9990 chunk 29 optimal weight: 0.0570 chunk 50 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 118 optimal weight: 2.9990 overall best weight: 1.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1254 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.128247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.099551 restraints weight = 13890.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.099486 restraints weight = 10308.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.101038 restraints weight = 8911.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.101253 restraints weight = 6621.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.101685 restraints weight = 6826.931| |-----------------------------------------------------------------------------| r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.018 1.795 10196 Z= 0.896 Angle : 0.881 62.044 13935 Z= 0.423 Chirality : 0.041 0.235 1654 Planarity : 0.004 0.073 1730 Dihedral : 7.010 56.935 1903 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.33 % Allowed : 11.94 % Favored : 86.73 % 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: 1.64 (0.25), residues: 1226 helix: 2.09 (0.21), residues: 631 sheet: 0.69 (0.59), residues: 84 loop : -0.06 (0.29), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1071 TYR 0.017 0.001 TYR A 971 PHE 0.021 0.001 PHE A 704 TRP 0.013 0.001 TRP A 202 HIS 0.003 0.001 HIS A1054 Details of bonding type rmsd covalent geometry : bond 0.00262 (10164) covalent geometry : angle 0.56746 (13853) SS BOND : bond 0.47986 ( 14) SS BOND : angle 14.86835 ( 28) hydrogen bonds : bond 0.04077 ( 533) hydrogen bonds : angle 4.67356 ( 1530) link_BETA1-4 : bond 0.00372 ( 6) link_BETA1-4 : angle 2.26730 ( 18) link_NAG-ASN : bond 0.00265 ( 12) link_NAG-ASN : angle 1.43758 ( 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 102 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 88 time to evaluate : 0.359 Fit side-chains REVERT: A 56 CYS cc_start: 0.6206 (OUTLIER) cc_final: 0.5964 (m) REVERT: A 107 LYS cc_start: 0.8816 (mtmt) cc_final: 0.8265 (mtpp) REVERT: A 167 LYS cc_start: 0.8565 (mttt) cc_final: 0.8324 (mttp) REVERT: A 609 ASP cc_start: 0.7716 (t70) cc_final: 0.7268 (t0) REVERT: A 659 ARG cc_start: 0.6534 (mmm160) cc_final: 0.6065 (ttm110) REVERT: A 794 LEU cc_start: 0.8998 (tp) cc_final: 0.8730 (tt) REVERT: A 894 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.8165 (tp) REVERT: A 932 GLN cc_start: 0.8181 (mt0) cc_final: 0.7885 (tm-30) REVERT: A 1112 GLU cc_start: 0.7459 (mt-10) cc_final: 0.7183 (mt-10) outliers start: 14 outliers final: 12 residues processed: 100 average time/residue: 0.0814 time to fit residues: 12.6827 Evaluate side-chains 102 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 88 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 56 CYS Chi-restraints excluded: chain A residue 478 TYR Chi-restraints excluded: chain A residue 712 ASP Chi-restraints excluded: chain A residue 719 LEU Chi-restraints excluded: chain A residue 827 LEU Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 989 ASN Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain A residue 1098 ILE Chi-restraints excluded: chain A residue 1135 ASP Chi-restraints excluded: chain A residue 1138 SER Chi-restraints excluded: chain A residue 1207 VAL Chi-restraints excluded: chain A residue 1232 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 16 optimal weight: 0.9990 chunk 122 optimal weight: 0.9980 chunk 6 optimal weight: 6.9990 chunk 68 optimal weight: 10.0000 chunk 91 optimal weight: 7.9990 chunk 80 optimal weight: 4.9990 chunk 55 optimal weight: 5.9990 chunk 72 optimal weight: 0.7980 chunk 50 optimal weight: 6.9990 chunk 75 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.123763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.094863 restraints weight = 14277.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.094388 restraints weight = 10775.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.095968 restraints weight = 9344.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.096313 restraints weight = 6935.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.096586 restraints weight = 7016.741| |-----------------------------------------------------------------------------| r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 10196 Z= 0.236 Angle : 0.694 13.450 13935 Z= 0.332 Chirality : 0.045 0.253 1654 Planarity : 0.004 0.067 1730 Dihedral : 7.197 58.432 1903 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.23 % Allowed : 11.94 % Favored : 86.82 % 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 (0.25), residues: 1226 helix: 1.87 (0.21), residues: 641 sheet: 0.44 (0.57), residues: 89 loop : -0.08 (0.30), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A1071 TYR 0.012 0.002 TYR A 156 PHE 0.031 0.002 PHE A 704 TRP 0.014 0.002 TRP A 383 HIS 0.005 0.001 HIS A1054 Details of bonding type rmsd covalent geometry : bond 0.00566 (10164) covalent geometry : angle 0.67451 (13853) SS BOND : bond 0.00485 ( 14) SS BOND : angle 2.19081 ( 28) hydrogen bonds : bond 0.05007 ( 533) hydrogen bonds : angle 4.78084 ( 1530) link_BETA1-4 : bond 0.00280 ( 6) link_BETA1-4 : angle 2.38793 ( 18) link_NAG-ASN : bond 0.00353 ( 12) link_NAG-ASN : angle 2.18989 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1385.32 seconds wall clock time: 24 minutes 46.84 seconds (1486.84 seconds total)