Starting phenix.real_space_refine on Mon Jul 28 09:59:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6v3h_21037/07_2025/6v3h_21037.cif Found real_map, /net/cci-nas-00/data/ceres_data/6v3h_21037/07_2025/6v3h_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6v3h_21037/07_2025/6v3h_21037.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6v3h_21037/07_2025/6v3h_21037.map" model { file = "/net/cci-nas-00/data/ceres_data/6v3h_21037/07_2025/6v3h_21037.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6v3h_21037/07_2025/6v3h_21037.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 6.75, per 1000 atoms: 0.68 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: 2.69 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 1.27 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: 3.79 Time building geometry restraints manager: 3.15 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: 1.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 27.390 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.920 ------------------------------------------------------------------------------- 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 : 3.08 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.084 0.004 TRP A 383 HIS 0.012 0.003 HIS A 126 PHE 0.038 0.003 PHE A 704 TYR 0.026 0.003 TYR A 689 ARG 0.014 0.001 ARG A1201 Details of bonding type rmsd link_NAG-ASN : bond 0.00412 ( 12) link_NAG-ASN : angle 3.08053 ( 36) link_BETA1-4 : bond 0.00552 ( 6) link_BETA1-4 : angle 4.87865 ( 18) hydrogen bonds : bond 0.14868 ( 533) hydrogen bonds : angle 6.74947 ( 1530) SS BOND : bond 0.00649 ( 14) SS BOND : angle 4.41187 ( 28) covalent geometry : bond 0.00940 (10164) covalent geometry : angle 1.25819 (13853) *********************** 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 : 1.057 Fit side-chains REVERT: A 167 LYS cc_start: 0.8525 (mttt) cc_final: 0.8244 (mttp) 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: 0.2597 time to fit residues: 56.7408 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 : 1.034 ------------------------------------------------------------------------------- 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 103 optimal weight: 9.9990 chunk 93 optimal weight: 4.9990 chunk 51 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 96 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 58 optimal weight: 0.5980 chunk 71 optimal weight: 0.9990 chunk 111 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.3527 r_free = 0.3527 target = 0.130318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.099345 restraints weight = 13999.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.099690 restraints weight = 8900.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.100834 restraints weight = 8085.600| |-----------------------------------------------------------------------------| r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.1419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 10196 Z= 0.136 Angle : 0.689 18.820 13935 Z= 0.334 Chirality : 0.043 0.252 1654 Planarity : 0.005 0.047 1730 Dihedral : 8.352 59.931 1915 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.52 % Allowed : 6.92 % Favored : 91.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.24), residues: 1226 helix: 1.78 (0.20), residues: 635 sheet: 0.40 (0.52), residues: 101 loop : -0.04 (0.28), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 202 HIS 0.004 0.001 HIS A1054 PHE 0.026 0.001 PHE A 704 TYR 0.015 0.001 TYR A 646 ARG 0.004 0.000 ARG A 498 Details of bonding type rmsd link_NAG-ASN : bond 0.00237 ( 12) link_NAG-ASN : angle 1.87583 ( 36) link_BETA1-4 : bond 0.00373 ( 6) link_BETA1-4 : angle 2.47640 ( 18) hydrogen bonds : bond 0.05131 ( 533) hydrogen bonds : angle 5.23487 ( 1530) SS BOND : bond 0.00425 ( 14) SS BOND : angle 1.56763 ( 28) covalent geometry : bond 0.00291 (10164) covalent geometry : angle 0.67508 (13853) *********************** 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 124 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 108 time to evaluate : 0.983 Fit side-chains REVERT: A 167 LYS cc_start: 0.8547 (mttt) cc_final: 0.8307 (mttm) REVERT: A 520 ASP cc_start: 0.8130 (m-30) cc_final: 0.7902 (m-30) REVERT: A 659 ARG cc_start: 0.6585 (mmm160) cc_final: 0.5804 (ttm110) REVERT: A 684 MET cc_start: 0.9006 (mtt) cc_final: 0.8766 (mtp) REVERT: A 932 GLN cc_start: 0.8195 (mt0) cc_final: 0.7855 (tm-30) REVERT: A 1112 GLU cc_start: 0.7453 (mt-10) cc_final: 0.7175 (mt-10) REVERT: A 1152 ASP cc_start: 0.7950 (m-30) cc_final: 0.7484 (m-30) outliers start: 16 outliers final: 12 residues processed: 119 average time/residue: 0.1808 time to fit residues: 32.8045 Evaluate side-chains 106 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 94 time to evaluate : 1.010 ------------------------------------------------------------------------------- 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 116 optimal weight: 3.9990 chunk 71 optimal weight: 0.6980 chunk 47 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 63 optimal weight: 7.9990 chunk 91 optimal weight: 4.9990 chunk 67 optimal weight: 0.6980 chunk 29 optimal weight: 7.9990 chunk 84 optimal weight: 0.0040 chunk 25 optimal weight: 0.9980 chunk 14 optimal weight: 6.9990 overall best weight: 1.0794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 868 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 989 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.129601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.099266 restraints weight = 14243.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.098186 restraints weight = 10289.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.099599 restraints weight = 10042.543| |-----------------------------------------------------------------------------| r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10196 Z= 0.133 Angle : 0.640 19.362 13935 Z= 0.305 Chirality : 0.042 0.247 1654 Planarity : 0.004 0.047 1730 Dihedral : 7.744 58.833 1906 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.80 % Allowed : 8.25 % Favored : 89.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.24), residues: 1226 helix: 1.91 (0.20), residues: 631 sheet: 0.33 (0.53), residues: 100 loop : -0.07 (0.28), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 202 HIS 0.005 0.001 HIS A1054 PHE 0.025 0.001 PHE A 704 TYR 0.014 0.001 TYR A 646 ARG 0.003 0.000 ARG A 406 Details of bonding type rmsd link_NAG-ASN : bond 0.00164 ( 12) link_NAG-ASN : angle 1.70281 ( 36) link_BETA1-4 : bond 0.00285 ( 6) link_BETA1-4 : angle 2.39933 ( 18) hydrogen bonds : bond 0.04720 ( 533) hydrogen bonds : angle 4.93106 ( 1530) SS BOND : bond 0.00277 ( 14) SS BOND : angle 1.24117 ( 28) covalent geometry : bond 0.00299 (10164) covalent geometry : angle 0.62765 (13853) *********************** 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: 19 poor density : 102 time to evaluate : 1.058 Fit side-chains revert: symmetry clash REVERT: A 107 LYS cc_start: 0.8851 (mtmt) cc_final: 0.8349 (mtpp) REVERT: A 167 LYS cc_start: 0.8501 (mttt) cc_final: 0.8272 (mttm) REVERT: A 659 ARG cc_start: 0.6523 (mmm160) cc_final: 0.5829 (ttm110) REVERT: A 684 MET cc_start: 0.9030 (mtt) cc_final: 0.8769 (mtp) REVERT: A 788 MET cc_start: 0.7966 (mmp) cc_final: 0.7460 (mmp) REVERT: A 932 GLN cc_start: 0.8146 (mt0) cc_final: 0.7856 (tm-30) REVERT: A 1112 GLU cc_start: 0.7568 (mt-10) cc_final: 0.7244 (mt-10) REVERT: A 1152 ASP cc_start: 0.7882 (m-30) cc_final: 0.7401 (m-30) outliers start: 19 outliers final: 10 residues processed: 115 average time/residue: 0.1836 time to fit residues: 31.9216 Evaluate side-chains 97 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 87 time to evaluate : 1.165 ------------------------------------------------------------------------------- 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 607 THR Chi-restraints excluded: chain A residue 712 ASP Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 989 ASN Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain A residue 1207 VAL Chi-restraints excluded: chain A residue 1232 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 86 optimal weight: 0.8980 chunk 35 optimal weight: 4.9990 chunk 19 optimal weight: 0.9990 chunk 7 optimal weight: 8.9990 chunk 81 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 118 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 = 0.3511 r_free = 0.3511 target = 0.129039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.098470 restraints weight = 13999.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.097786 restraints weight = 9211.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.099012 restraints weight = 9198.247| |-----------------------------------------------------------------------------| r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.1915 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= 0.130 Angle : 0.600 13.755 13935 Z= 0.288 Chirality : 0.041 0.244 1654 Planarity : 0.004 0.045 1730 Dihedral : 7.500 57.672 1904 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.71 % Allowed : 9.19 % Favored : 89.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.24), residues: 1226 helix: 1.96 (0.20), residues: 632 sheet: 0.59 (0.57), residues: 90 loop : -0.03 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 202 HIS 0.004 0.001 HIS A1054 PHE 0.025 0.001 PHE A 704 TYR 0.013 0.001 TYR A 646 ARG 0.002 0.000 ARG A1071 Details of bonding type rmsd link_NAG-ASN : bond 0.00153 ( 12) link_NAG-ASN : angle 1.61770 ( 36) link_BETA1-4 : bond 0.00294 ( 6) link_BETA1-4 : angle 2.33023 ( 18) hydrogen bonds : bond 0.04499 ( 533) hydrogen bonds : angle 4.83290 ( 1530) SS BOND : bond 0.00327 ( 14) SS BOND : angle 1.19799 ( 28) covalent geometry : bond 0.00290 (10164) covalent geometry : angle 0.58740 (13853) *********************** 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 105 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 87 time to evaluate : 1.126 Fit side-chains REVERT: A 107 LYS cc_start: 0.8806 (mtmt) cc_final: 0.8268 (mtpp) REVERT: A 135 LEU cc_start: 0.8568 (mt) cc_final: 0.8353 (mt) REVERT: A 167 LYS cc_start: 0.8588 (mttt) cc_final: 0.8335 (mttp) REVERT: A 659 ARG cc_start: 0.6484 (mmm160) cc_final: 0.5809 (ttm110) REVERT: A 670 LEU cc_start: 0.8788 (tt) cc_final: 0.8497 (tp) REVERT: A 684 MET cc_start: 0.8989 (mtt) cc_final: 0.8728 (mtp) REVERT: A 727 MET cc_start: 0.6154 (tmm) cc_final: 0.5682 (tmm) REVERT: A 788 MET cc_start: 0.7923 (mmp) cc_final: 0.7685 (mmp) REVERT: A 932 GLN cc_start: 0.8126 (mt0) cc_final: 0.7851 (tm-30) REVERT: A 1112 GLU cc_start: 0.7527 (mt-10) cc_final: 0.7293 (mt-10) REVERT: A 1246 LEU cc_start: 0.9224 (OUTLIER) cc_final: 0.8856 (mp) outliers start: 18 outliers final: 12 residues processed: 99 average time/residue: 0.1885 time to fit residues: 28.7047 Evaluate side-chains 97 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 84 time to evaluate : 1.122 ------------------------------------------------------------------------------- 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 690 LEU Chi-restraints excluded: chain A residue 712 ASP Chi-restraints excluded: chain A residue 719 LEU Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain A residue 1176 VAL Chi-restraints excluded: chain A residue 1232 GLN Chi-restraints excluded: chain A residue 1246 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 32 optimal weight: 8.9990 chunk 97 optimal weight: 3.9990 chunk 69 optimal weight: 10.0000 chunk 36 optimal weight: 5.9990 chunk 60 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 17 optimal weight: 6.9990 chunk 5 optimal weight: 9.9990 chunk 53 optimal weight: 0.7980 chunk 79 optimal weight: 2.9990 chunk 6 optimal weight: 8.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 989 ASN ** A1271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.123732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.094305 restraints weight = 14246.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.093099 restraints weight = 9829.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.094687 restraints weight = 9236.796| |-----------------------------------------------------------------------------| r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 10196 Z= 0.232 Angle : 0.678 10.304 13935 Z= 0.333 Chirality : 0.045 0.251 1654 Planarity : 0.004 0.058 1730 Dihedral : 7.718 58.458 1904 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.09 % Allowed : 9.86 % Favored : 88.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.24), residues: 1226 helix: 1.76 (0.20), residues: 641 sheet: 0.35 (0.57), residues: 89 loop : -0.10 (0.29), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 202 HIS 0.007 0.001 HIS A1054 PHE 0.033 0.002 PHE A 704 TYR 0.014 0.002 TYR A 156 ARG 0.004 0.000 ARG A1071 Details of bonding type rmsd link_NAG-ASN : bond 0.00250 ( 12) link_NAG-ASN : angle 1.90916 ( 36) link_BETA1-4 : bond 0.00260 ( 6) link_BETA1-4 : angle 2.45416 ( 18) hydrogen bonds : bond 0.05160 ( 533) hydrogen bonds : angle 4.86937 ( 1530) SS BOND : bond 0.00438 ( 14) SS BOND : angle 2.05922 ( 28) covalent geometry : bond 0.00555 (10164) covalent geometry : angle 0.66038 (13853) *********************** 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 110 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 88 time to evaluate : 1.067 Fit side-chains revert: symmetry clash REVERT: A 107 LYS cc_start: 0.8856 (mtmt) cc_final: 0.8507 (mtmt) REVERT: A 135 LEU cc_start: 0.8678 (mt) cc_final: 0.8462 (mt) REVERT: A 167 LYS cc_start: 0.8640 (mttt) cc_final: 0.8376 (mttp) REVERT: A 502 MET cc_start: 0.7922 (OUTLIER) cc_final: 0.7574 (mtm) REVERT: A 659 ARG cc_start: 0.6762 (mmm160) cc_final: 0.6029 (ttm110) REVERT: A 727 MET cc_start: 0.6413 (tmm) cc_final: 0.6051 (tmm) REVERT: A 788 MET cc_start: 0.7733 (mmp) cc_final: 0.7451 (mmp) REVERT: A 932 GLN cc_start: 0.8195 (mt0) cc_final: 0.7955 (tm-30) REVERT: A 1112 GLU cc_start: 0.7586 (mt-10) cc_final: 0.7364 (mt-10) outliers start: 22 outliers final: 13 residues processed: 104 average time/residue: 0.1782 time to fit residues: 28.6497 Evaluate side-chains 97 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 83 time to evaluate : 1.055 ------------------------------------------------------------------------------- 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 243 CYS Chi-restraints excluded: chain A residue 478 TYR Chi-restraints excluded: chain A residue 502 MET Chi-restraints excluded: chain A residue 531 THR 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 90 optimal weight: 0.6980 chunk 81 optimal weight: 0.0980 chunk 4 optimal weight: 20.0000 chunk 40 optimal weight: 0.8980 chunk 72 optimal weight: 0.9980 chunk 7 optimal weight: 8.9990 chunk 77 optimal weight: 0.7980 chunk 112 optimal weight: 0.9980 chunk 99 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 chunk 83 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3477 r_free = 0.3477 target = 0.126590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.097592 restraints weight = 13981.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.097212 restraints weight = 9327.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.098357 restraints weight = 8978.249| |-----------------------------------------------------------------------------| r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.2200 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= 0.112 Angle : 0.585 10.287 13935 Z= 0.283 Chirality : 0.041 0.249 1654 Planarity : 0.004 0.056 1730 Dihedral : 7.438 59.202 1904 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.18 % Allowed : 10.81 % Favored : 87.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.25), residues: 1226 helix: 2.01 (0.21), residues: 629 sheet: 0.42 (0.57), residues: 89 loop : -0.15 (0.29), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 202 HIS 0.003 0.001 HIS A1054 PHE 0.023 0.001 PHE A 704 TYR 0.012 0.001 TYR A 524 ARG 0.002 0.000 ARG A1071 Details of bonding type rmsd link_NAG-ASN : bond 0.00174 ( 12) link_NAG-ASN : angle 1.62313 ( 36) link_BETA1-4 : bond 0.00314 ( 6) link_BETA1-4 : angle 2.31361 ( 18) hydrogen bonds : bond 0.04397 ( 533) hydrogen bonds : angle 4.77724 ( 1530) SS BOND : bond 0.00311 ( 14) SS BOND : angle 1.78051 ( 28) covalent geometry : bond 0.00239 (10164) covalent geometry : angle 0.56891 (13853) *********************** 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 115 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 92 time to evaluate : 1.149 Fit side-chains revert: symmetry clash REVERT: A 107 LYS cc_start: 0.8799 (mtmt) cc_final: 0.8249 (mtpp) REVERT: A 167 LYS cc_start: 0.8607 (mttt) cc_final: 0.8355 (mttp) REVERT: A 586 MET cc_start: 0.8353 (mmm) cc_final: 0.8054 (tpp) REVERT: A 659 ARG cc_start: 0.6595 (mmm160) cc_final: 0.5978 (ttm110) REVERT: A 727 MET cc_start: 0.6353 (tmm) cc_final: 0.5992 (tmm) REVERT: A 932 GLN cc_start: 0.8174 (mt0) cc_final: 0.7944 (tm-30) REVERT: A 1044 GLN cc_start: 0.7791 (OUTLIER) cc_final: 0.7201 (mm-40) REVERT: A 1112 GLU cc_start: 0.7500 (mt-10) cc_final: 0.7241 (mt-10) outliers start: 23 outliers final: 13 residues processed: 111 average time/residue: 0.1918 time to fit residues: 32.4112 Evaluate side-chains 96 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 82 time to evaluate : 1.037 ------------------------------------------------------------------------------- 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 243 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 989 ASN Chi-restraints excluded: chain A residue 1044 GLN 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 54 optimal weight: 0.9990 chunk 115 optimal weight: 8.9990 chunk 66 optimal weight: 0.0030 chunk 74 optimal weight: 5.9990 chunk 112 optimal weight: 0.1980 chunk 59 optimal weight: 4.9990 chunk 122 optimal weight: 3.9990 chunk 24 optimal weight: 10.0000 chunk 79 optimal weight: 4.9990 chunk 48 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 overall best weight: 1.8396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 989 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.124872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.095889 restraints weight = 14251.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.094855 restraints weight = 10117.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.096509 restraints weight = 9267.573| |-----------------------------------------------------------------------------| r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.2274 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= 0.169 Angle : 0.608 9.423 13935 Z= 0.296 Chirality : 0.042 0.246 1654 Planarity : 0.004 0.054 1730 Dihedral : 7.335 59.030 1904 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.09 % Allowed : 12.04 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.25), residues: 1226 helix: 1.94 (0.21), residues: 635 sheet: 0.43 (0.57), residues: 89 loop : -0.10 (0.29), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 202 HIS 0.005 0.001 HIS A1054 PHE 0.027 0.002 PHE A 704 TYR 0.012 0.001 TYR A 524 ARG 0.003 0.000 ARG A1071 Details of bonding type rmsd link_NAG-ASN : bond 0.00204 ( 12) link_NAG-ASN : angle 1.72841 ( 36) link_BETA1-4 : bond 0.00283 ( 6) link_BETA1-4 : angle 2.36902 ( 18) hydrogen bonds : bond 0.04621 ( 533) hydrogen bonds : angle 4.75424 ( 1530) SS BOND : bond 0.00331 ( 14) SS BOND : angle 1.91156 ( 28) covalent geometry : bond 0.00398 (10164) covalent geometry : angle 0.59098 (13853) *********************** 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 108 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 86 time to evaluate : 1.008 Fit side-chains revert: symmetry clash REVERT: A 28 GLU cc_start: 0.6713 (OUTLIER) cc_final: 0.5850 (pp20) REVERT: A 167 LYS cc_start: 0.8630 (mttt) cc_final: 0.8359 (mttp) REVERT: A 502 MET cc_start: 0.7968 (OUTLIER) cc_final: 0.7617 (mtm) REVERT: A 586 MET cc_start: 0.8391 (mmm) cc_final: 0.8074 (tpp) REVERT: A 659 ARG cc_start: 0.6702 (mmm160) cc_final: 0.5996 (ttm110) REVERT: A 894 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8353 (tp) REVERT: A 932 GLN cc_start: 0.8235 (mt0) cc_final: 0.7953 (tm-30) REVERT: A 1044 GLN cc_start: 0.7879 (OUTLIER) cc_final: 0.7230 (mm-40) REVERT: A 1112 GLU cc_start: 0.7550 (mt-10) cc_final: 0.7326 (mt-10) REVERT: A 1164 TYR cc_start: 0.8975 (t80) cc_final: 0.8667 (t80) outliers start: 22 outliers final: 13 residues processed: 105 average time/residue: 0.1811 time to fit residues: 29.2773 Evaluate side-chains 101 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 84 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 56 CYS Chi-restraints excluded: chain A residue 243 CYS Chi-restraints excluded: chain A residue 259 CYS Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 478 TYR Chi-restraints excluded: chain A residue 502 MET Chi-restraints excluded: chain A residue 712 ASP Chi-restraints excluded: chain A residue 827 LEU Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 1044 GLN 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 20 optimal weight: 1.9990 chunk 121 optimal weight: 0.9990 chunk 113 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 21 optimal weight: 9.9990 chunk 64 optimal weight: 0.7980 chunk 43 optimal weight: 3.9990 chunk 115 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 = 0.3460 r_free = 0.3460 target = 0.125389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.096234 restraints weight = 14103.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.095870 restraints weight = 9498.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.096912 restraints weight = 9232.052| |-----------------------------------------------------------------------------| r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10196 Z= 0.139 Angle : 0.596 12.202 13935 Z= 0.289 Chirality : 0.042 0.248 1654 Planarity : 0.004 0.054 1730 Dihedral : 7.203 59.677 1904 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.18 % Allowed : 12.13 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.25), residues: 1226 helix: 1.96 (0.21), residues: 635 sheet: 0.43 (0.57), residues: 89 loop : -0.12 (0.29), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 202 HIS 0.004 0.001 HIS A1054 PHE 0.025 0.001 PHE A 704 TYR 0.023 0.001 TYR A 35 ARG 0.003 0.000 ARG A 63 Details of bonding type rmsd link_NAG-ASN : bond 0.00182 ( 12) link_NAG-ASN : angle 1.65206 ( 36) link_BETA1-4 : bond 0.00306 ( 6) link_BETA1-4 : angle 2.32678 ( 18) hydrogen bonds : bond 0.04423 ( 533) hydrogen bonds : angle 4.72068 ( 1530) SS BOND : bond 0.00293 ( 14) SS BOND : angle 1.83543 ( 28) covalent geometry : bond 0.00319 (10164) covalent geometry : angle 0.57983 (13853) *********************** 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 111 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 88 time to evaluate : 1.178 Fit side-chains revert: symmetry clash REVERT: A 28 GLU cc_start: 0.6610 (OUTLIER) cc_final: 0.5872 (pp20) REVERT: A 167 LYS cc_start: 0.8589 (mttt) cc_final: 0.8340 (mttp) REVERT: A 502 MET cc_start: 0.7997 (OUTLIER) cc_final: 0.7653 (mtm) REVERT: A 609 ASP cc_start: 0.7747 (t70) cc_final: 0.7348 (t0) REVERT: A 659 ARG cc_start: 0.6622 (mmm160) cc_final: 0.6099 (ttm110) REVERT: A 894 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8318 (tp) REVERT: A 1044 GLN cc_start: 0.7881 (OUTLIER) cc_final: 0.7223 (mm-40) REVERT: A 1112 GLU cc_start: 0.7512 (mt-10) cc_final: 0.7294 (mt-10) REVERT: A 1164 TYR cc_start: 0.9003 (t80) cc_final: 0.8686 (t80) outliers start: 23 outliers final: 11 residues processed: 107 average time/residue: 0.1887 time to fit residues: 31.3649 Evaluate side-chains 98 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 83 time to evaluate : 1.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 56 CYS Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 478 TYR Chi-restraints excluded: chain A residue 502 MET Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 712 ASP Chi-restraints excluded: chain A residue 827 LEU Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 1044 GLN Chi-restraints excluded: chain A residue 1098 ILE 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 48 optimal weight: 3.9990 chunk 75 optimal weight: 6.9990 chunk 14 optimal weight: 3.9990 chunk 71 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 chunk 70 optimal weight: 0.9980 chunk 11 optimal weight: 8.9990 chunk 78 optimal weight: 0.1980 chunk 28 optimal weight: 4.9990 chunk 69 optimal weight: 0.9980 chunk 6 optimal weight: 6.9990 overall best weight: 1.3982 ------------------------------------------------------------------------------- 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 = 0.3461 r_free = 0.3461 target = 0.125315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.096235 restraints weight = 14119.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.095865 restraints weight = 9499.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.096770 restraints weight = 9164.158| |-----------------------------------------------------------------------------| r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10196 Z= 0.144 Angle : 0.606 12.762 13935 Z= 0.294 Chirality : 0.042 0.250 1654 Planarity : 0.004 0.054 1730 Dihedral : 6.969 57.267 1903 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.99 % Allowed : 12.42 % Favored : 85.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.25), residues: 1226 helix: 1.96 (0.21), residues: 635 sheet: 0.44 (0.57), residues: 89 loop : -0.13 (0.29), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 202 HIS 0.004 0.001 HIS A1054 PHE 0.025 0.001 PHE A 704 TYR 0.017 0.001 TYR A 35 ARG 0.002 0.000 ARG A1071 Details of bonding type rmsd link_NAG-ASN : bond 0.00300 ( 12) link_NAG-ASN : angle 1.80542 ( 36) link_BETA1-4 : bond 0.00314 ( 6) link_BETA1-4 : angle 2.29537 ( 18) hydrogen bonds : bond 0.04400 ( 533) hydrogen bonds : angle 4.68725 ( 1530) SS BOND : bond 0.00308 ( 14) SS BOND : angle 1.70969 ( 28) covalent geometry : bond 0.00332 (10164) covalent geometry : angle 0.59036 (13853) *********************** 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 108 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 87 time to evaluate : 1.089 Fit side-chains REVERT: A 28 GLU cc_start: 0.6758 (OUTLIER) cc_final: 0.5779 (pp20) REVERT: A 107 LYS cc_start: 0.8810 (mtmt) cc_final: 0.8288 (mtpp) REVERT: A 167 LYS cc_start: 0.8598 (mttt) cc_final: 0.8345 (mttp) REVERT: A 502 MET cc_start: 0.8032 (OUTLIER) cc_final: 0.7684 (mtm) REVERT: A 609 ASP cc_start: 0.7778 (t70) cc_final: 0.7390 (t0) REVERT: A 659 ARG cc_start: 0.6645 (mmm160) cc_final: 0.6094 (ttm110) REVERT: A 894 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8295 (tp) REVERT: A 1112 GLU cc_start: 0.7510 (mt-10) cc_final: 0.7301 (mt-10) REVERT: A 1164 TYR cc_start: 0.9017 (t80) cc_final: 0.8715 (t80) outliers start: 21 outliers final: 12 residues processed: 104 average time/residue: 0.1932 time to fit residues: 31.4280 Evaluate side-chains 100 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 85 time to evaluate : 1.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 478 TYR Chi-restraints excluded: chain A residue 502 MET Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 712 ASP Chi-restraints excluded: chain A residue 827 LEU Chi-restraints excluded: chain A residue 894 LEU 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 115 optimal weight: 6.9990 chunk 22 optimal weight: 0.2980 chunk 8 optimal weight: 0.9990 chunk 21 optimal weight: 5.9990 chunk 110 optimal weight: 0.9980 chunk 108 optimal weight: 10.0000 chunk 66 optimal weight: 0.1980 chunk 117 optimal weight: 0.7980 chunk 86 optimal weight: 0.9980 chunk 40 optimal weight: 0.6980 chunk 13 optimal weight: 3.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3488 r_free = 0.3488 target = 0.127493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.098446 restraints weight = 14091.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.097631 restraints weight = 10577.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.098675 restraints weight = 10463.655| |-----------------------------------------------------------------------------| r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 10196 Z= 0.110 Angle : 0.600 11.921 13935 Z= 0.286 Chirality : 0.041 0.248 1654 Planarity : 0.004 0.055 1730 Dihedral : 6.875 56.848 1903 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.42 % Allowed : 12.80 % Favored : 85.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.25), residues: 1226 helix: 2.05 (0.21), residues: 636 sheet: 0.75 (0.60), residues: 79 loop : -0.06 (0.29), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 202 HIS 0.003 0.001 HIS A1054 PHE 0.021 0.001 PHE A 704 TYR 0.017 0.001 TYR A 35 ARG 0.002 0.000 ARG A 63 Details of bonding type rmsd link_NAG-ASN : bond 0.00191 ( 12) link_NAG-ASN : angle 1.85857 ( 36) link_BETA1-4 : bond 0.00334 ( 6) link_BETA1-4 : angle 2.31904 ( 18) hydrogen bonds : bond 0.04109 ( 533) hydrogen bonds : angle 4.69147 ( 1530) SS BOND : bond 0.00218 ( 14) SS BOND : angle 1.69507 ( 28) covalent geometry : bond 0.00234 (10164) covalent geometry : angle 0.58331 (13853) ********************** 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 107 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 92 time to evaluate : 1.032 Fit side-chains REVERT: A 28 GLU cc_start: 0.6674 (OUTLIER) cc_final: 0.5704 (pp20) REVERT: A 36 GLU cc_start: 0.7038 (tp30) cc_final: 0.6424 (pp20) REVERT: A 107 LYS cc_start: 0.8826 (mtmt) cc_final: 0.8347 (mtpp) REVERT: A 167 LYS cc_start: 0.8576 (mttt) cc_final: 0.8315 (mttp) REVERT: A 609 ASP cc_start: 0.7752 (t70) cc_final: 0.7383 (t0) REVERT: A 659 ARG cc_start: 0.6558 (mmm160) cc_final: 0.6076 (ttm110) REVERT: A 1164 TYR cc_start: 0.8992 (t80) cc_final: 0.8694 (t80) outliers start: 15 outliers final: 11 residues processed: 104 average time/residue: 0.1841 time to fit residues: 29.7396 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 : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 478 TYR Chi-restraints excluded: chain A residue 712 ASP Chi-restraints excluded: chain A residue 827 LEU 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 2 optimal weight: 7.9990 chunk 103 optimal weight: 3.9990 chunk 84 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 chunk 92 optimal weight: 8.9990 chunk 49 optimal weight: 5.9990 chunk 90 optimal weight: 3.9990 chunk 29 optimal weight: 0.0030 overall best weight: 2.3996 ------------------------------------------------------------------------------- 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 = 0.3442 r_free = 0.3442 target = 0.124009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.094902 restraints weight = 14315.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.094296 restraints weight = 10410.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.095759 restraints weight = 9377.197| |-----------------------------------------------------------------------------| r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 10196 Z= 0.209 Angle : 0.664 11.123 13935 Z= 0.318 Chirality : 0.044 0.253 1654 Planarity : 0.004 0.055 1730 Dihedral : 7.022 57.944 1903 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.23 % Allowed : 13.55 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.25), residues: 1226 helix: 1.88 (0.21), residues: 636 sheet: 0.39 (0.57), residues: 89 loop : -0.13 (0.29), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 202 HIS 0.005 0.001 HIS A1054 PHE 0.029 0.002 PHE A 704 TYR 0.014 0.001 TYR A 35 ARG 0.004 0.000 ARG A 406 Details of bonding type rmsd link_NAG-ASN : bond 0.00233 ( 12) link_NAG-ASN : angle 2.06100 ( 36) link_BETA1-4 : bond 0.00282 ( 6) link_BETA1-4 : angle 2.37858 ( 18) hydrogen bonds : bond 0.04724 ( 533) hydrogen bonds : angle 4.75284 ( 1530) SS BOND : bond 0.00414 ( 14) SS BOND : angle 2.04091 ( 28) covalent geometry : bond 0.00503 (10164) covalent geometry : angle 0.64505 (13853) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2826.01 seconds wall clock time: 50 minutes 27.38 seconds (3027.38 seconds total)