Starting phenix.real_space_refine on Sat Jun 28 18:11:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wcd_32421/06_2025/7wcd_32421.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wcd_32421/06_2025/7wcd_32421.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wcd_32421/06_2025/7wcd_32421.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wcd_32421/06_2025/7wcd_32421.map" model { file = "/net/cci-nas-00/data/ceres_data/7wcd_32421/06_2025/7wcd_32421.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wcd_32421/06_2025/7wcd_32421.cif" } resolution = 3.3 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 147 5.16 5 C 21297 2.51 5 N 5514 2.21 5 O 6567 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 78 residue(s): 0.18s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 33525 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 7803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1000, 7803 Classifications: {'peptide': 1000} Link IDs: {'PTRANS': 50, 'TRANS': 949} Chain breaks: 10 Chain: "A" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1643 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 11, 'TRANS': 202} Chain breaks: 1 Chain: "B" Number of atoms: 1575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1575 Classifications: {'peptide': 214} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 198} Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Restraints were copied for chains: E, G, H, J, F, I Time building chain proxies: 24.02, per 1000 atoms: 0.72 Number of scatterers: 33525 At special positions: 0 Unit cell: (147.44, 148.41, 231.83, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 147 16.00 O 6567 8.00 N 5514 7.00 C 21297 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=17, symmetry=0 Simple disulfide: pdb=" SG CYS H 131 " - pdb=" SG CYS H 166 " distance=2.03 Simple disulfide: pdb=" SG CYS H 291 " - pdb=" SG CYS H 301 " distance=2.03 Simple disulfide: pdb=" SG CYS H 336 " - pdb=" SG CYS H 361 " distance=2.03 Simple disulfide: pdb=" SG CYS H 379 " - pdb=" SG CYS H 432 " distance=2.03 Simple disulfide: pdb=" SG CYS H 391 " - pdb=" SG CYS H 525 " distance=2.03 Simple disulfide: pdb=" SG CYS H 480 " - pdb=" SG CYS H 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 538 " - pdb=" SG CYS H 590 " distance=2.03 Simple disulfide: pdb=" SG CYS H 617 " - pdb=" SG CYS H 649 " distance=2.04 Simple disulfide: pdb=" SG CYS H 662 " - pdb=" SG CYS H 671 " distance=2.03 Simple disulfide: pdb=" SG CYS H 738 " - pdb=" SG CYS H 760 " distance=2.03 Simple disulfide: pdb=" SG CYS H 743 " - pdb=" SG CYS H 749 " distance=2.03 Simple disulfide: pdb=" SG CYS H1032 " - pdb=" SG CYS H1043 " distance=2.03 Simple disulfide: pdb=" SG CYS H1082 " - pdb=" SG CYS H1126 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 153 " - pdb=" SG CYS E 209 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 90 " distance=2.03 Simple disulfide: pdb=" SG CYS F 140 " - pdb=" SG CYS F 199 " 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 NAG-ASN " NAG C1301 " - " ASN C1074 " " NAG C1302 " - " ASN C 234 " " NAG C1303 " - " ASN C 282 " " NAG C1304 " - " ASN C1134 " " NAG C1305 " - " ASN C1098 " " NAG C1306 " - " ASN C 801 " " NAG C1307 " - " ASN C 709 " " NAG C1308 " - " ASN C 657 " " NAG C1309 " - " ASN C 616 " " NAG C1310 " - " ASN C 603 " " NAG C1311 " - " ASN C 165 " " NAG H1301 " - " ASN H1074 " " NAG H1302 " - " ASN H 234 " " NAG H1303 " - " ASN H 282 " " NAG H1304 " - " ASN H1134 " " NAG H1305 " - " ASN H1098 " " NAG H1306 " - " ASN H 801 " " NAG H1307 " - " ASN H 709 " " NAG H1308 " - " ASN H 657 " " NAG H1309 " - " ASN H 616 " " NAG H1310 " - " ASN H 603 " " NAG H1311 " - " ASN H 165 " " NAG J1301 " - " ASN J1074 " " NAG J1302 " - " ASN J 234 " " NAG J1303 " - " ASN J 282 " " NAG J1304 " - " ASN J1134 " " NAG J1305 " - " ASN J1098 " " NAG J1306 " - " ASN J 801 " " NAG J1307 " - " ASN J 709 " " NAG J1308 " - " ASN J 657 " " NAG J1309 " - " ASN J 616 " " NAG J1310 " - " ASN J 603 " " NAG J1311 " - " ASN J 165 " Time building additional restraints: 8.42 Conformation dependent library (CDL) restraints added in 3.9 seconds 8400 Ramachandran restraints generated. 4200 Oldfield, 0 Emsley, 4200 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7962 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 75 sheets defined 19.3% alpha, 30.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.19 Creating SS restraints... Processing helix chain 'H' and resid 294 through 304 Processing helix chain 'H' and resid 338 through 343 Processing helix chain 'H' and resid 365 through 371 Processing helix chain 'H' and resid 384 through 388 removed outlier: 3.729A pdb=" N LEU H 387 " --> pdb=" O PRO H 384 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ASN H 388 " --> pdb=" O THR H 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 384 through 388' Processing helix chain 'H' and resid 405 through 410 removed outlier: 4.296A pdb=" N ARG H 408 " --> pdb=" O ASP H 405 " (cutoff:3.500A) Processing helix chain 'H' and resid 416 through 422 Processing helix chain 'H' and resid 737 through 743 Processing helix chain 'H' and resid 746 through 755 removed outlier: 3.844A pdb=" N GLN H 755 " --> pdb=" O ASN H 751 " (cutoff:3.500A) Processing helix chain 'H' and resid 758 through 783 removed outlier: 3.630A pdb=" N GLN H 762 " --> pdb=" O SER H 758 " (cutoff:3.500A) Processing helix chain 'H' and resid 816 through 826 removed outlier: 3.614A pdb=" N VAL H 826 " --> pdb=" O LEU H 822 " (cutoff:3.500A) Processing helix chain 'H' and resid 866 through 885 Processing helix chain 'H' and resid 886 through 890 Processing helix chain 'H' and resid 897 through 909 removed outlier: 3.518A pdb=" N ILE H 909 " --> pdb=" O ARG H 905 " (cutoff:3.500A) Processing helix chain 'H' and resid 912 through 919 removed outlier: 4.177A pdb=" N LEU H 916 " --> pdb=" O THR H 912 " (cutoff:3.500A) Processing helix chain 'H' and resid 919 through 941 Processing helix chain 'H' and resid 945 through 966 Processing helix chain 'H' and resid 976 through 984 removed outlier: 3.594A pdb=" N ILE H 980 " --> pdb=" O VAL H 976 " (cutoff:3.500A) Processing helix chain 'H' and resid 985 through 1033 removed outlier: 4.848A pdb=" N VAL H 991 " --> pdb=" O PRO H 987 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N GLN H 992 " --> pdb=" O GLU H 988 " (cutoff:3.500A) Processing helix chain 'H' and resid 1140 through 1146 Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'F' and resid 81 through 85 removed outlier: 3.846A pdb=" N GLU F 85 " --> pdb=" O ALA F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 127 through 133 Processing helix chain 'F' and resid 187 through 193 Processing helix chain 'J' and resid 294 through 304 Processing helix chain 'J' and resid 338 through 343 Processing helix chain 'J' and resid 365 through 371 Processing helix chain 'J' and resid 384 through 388 removed outlier: 3.729A pdb=" N LEU J 387 " --> pdb=" O PRO J 384 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ASN J 388 " --> pdb=" O THR J 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 384 through 388' Processing helix chain 'J' and resid 405 through 410 removed outlier: 4.296A pdb=" N ARG J 408 " --> pdb=" O ASP J 405 " (cutoff:3.500A) Processing helix chain 'J' and resid 416 through 422 Processing helix chain 'J' and resid 737 through 743 Processing helix chain 'J' and resid 746 through 755 removed outlier: 3.844A pdb=" N GLN J 755 " --> pdb=" O ASN J 751 " (cutoff:3.500A) Processing helix chain 'J' and resid 758 through 783 removed outlier: 3.630A pdb=" N GLN J 762 " --> pdb=" O SER J 758 " (cutoff:3.500A) Processing helix chain 'J' and resid 816 through 826 removed outlier: 3.614A pdb=" N VAL J 826 " --> pdb=" O LEU J 822 " (cutoff:3.500A) Processing helix chain 'J' and resid 866 through 885 Processing helix chain 'J' and resid 886 through 890 Processing helix chain 'J' and resid 897 through 909 removed outlier: 3.517A pdb=" N ILE J 909 " --> pdb=" O ARG J 905 " (cutoff:3.500A) Processing helix chain 'J' and resid 912 through 919 removed outlier: 4.178A pdb=" N LEU J 916 " --> pdb=" O THR J 912 " (cutoff:3.500A) Processing helix chain 'J' and resid 919 through 941 Processing helix chain 'J' and resid 945 through 966 Processing helix chain 'J' and resid 976 through 984 removed outlier: 3.594A pdb=" N ILE J 980 " --> pdb=" O VAL J 976 " (cutoff:3.500A) Processing helix chain 'J' and resid 985 through 1033 removed outlier: 4.849A pdb=" N VAL J 991 " --> pdb=" O PRO J 987 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N GLN J 992 " --> pdb=" O GLU J 988 " (cutoff:3.500A) Processing helix chain 'J' and resid 1140 through 1146 Processing helix chain 'G' and resid 87 through 91 Processing helix chain 'I' and resid 81 through 85 removed outlier: 3.846A pdb=" N GLU I 85 " --> pdb=" O ALA I 82 " (cutoff:3.500A) Processing helix chain 'I' and resid 127 through 133 Processing helix chain 'I' and resid 187 through 193 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 384 through 388 removed outlier: 3.729A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 384 through 388' Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.296A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.844A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.630A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.614A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.518A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.178A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 966 Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.594A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.848A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 Processing helix chain 'A' and resid 87 through 91 Processing helix chain 'B' and resid 81 through 85 removed outlier: 3.846A pdb=" N GLU B 85 " --> pdb=" O ALA B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 133 Processing helix chain 'B' and resid 187 through 193 Processing sheet with id=AA1, first strand: chain 'H' and resid 28 through 30 removed outlier: 7.941A pdb=" N ASN H 61 " --> pdb=" O TYR H 269 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N TYR H 269 " --> pdb=" O ASN H 61 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLU H 191 " --> pdb=" O LYS H 206 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE H 203 " --> pdb=" O LEU H 226 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N HIS H 207 " --> pdb=" O ALA H 222 " (cutoff:3.500A) removed outlier: 9.600A pdb=" N ALA H 222 " --> pdb=" O HIS H 207 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N VAL H 36 " --> pdb=" O LEU H 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 42 through 43 removed outlier: 6.279A pdb=" N PHE H 43 " --> pdb=" O ARG C 567 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N THR C 572 " --> pdb=" O ASP C 568 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 8.309A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 48 through 55 removed outlier: 7.393A pdb=" N THR H 274 " --> pdb=" O ASP H 290 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N ASP H 290 " --> pdb=" O THR H 274 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N LEU H 276 " --> pdb=" O ALA H 288 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ALA H 288 " --> pdb=" O LEU H 276 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N LYS H 278 " --> pdb=" O THR H 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 169 through 172 Processing sheet with id=AA5, first strand: chain 'H' and resid 311 through 319 removed outlier: 5.667A pdb=" N ILE H 312 " --> pdb=" O THR H 599 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N THR H 599 " --> pdb=" O ILE H 312 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N GLN H 314 " --> pdb=" O VAL H 597 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N VAL H 597 " --> pdb=" O GLN H 314 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N SER H 316 " --> pdb=" O VAL H 595 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 324 through 325 removed outlier: 6.833A pdb=" N GLU H 324 " --> pdb=" O ASN H 540 " (cutoff:3.500A) removed outlier: 8.309A pdb=" N ASN H 542 " --> pdb=" O GLU H 324 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N ASP H 574 " --> pdb=" O ILE H 587 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N THR H 572 " --> pdb=" O ASP H 568 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N GLY H 566 " --> pdb=" O ASP H 574 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 356 through 358 Processing sheet with id=AA8, first strand: chain 'H' and resid 361 through 362 removed outlier: 6.540A pdb=" N CYS H 361 " --> pdb=" O CYS H 525 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'H' and resid 654 through 655 removed outlier: 6.284A pdb=" N GLU H 654 " --> pdb=" O ALA H 694 " (cutoff:3.500A) removed outlier: 8.658A pdb=" N THR H 696 " --> pdb=" O GLU H 654 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ALA H 672 " --> pdb=" O PRO H 665 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 711 through 713 removed outlier: 3.583A pdb=" N THR H1076 " --> pdb=" O SER H1097 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA H1078 " --> pdb=" O PHE H1095 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N PHE H1095 " --> pdb=" O ALA H1078 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 717 through 718 Processing sheet with id=AB4, first strand: chain 'H' and resid 721 through 728 removed outlier: 3.602A pdb=" N GLY H1059 " --> pdb=" O ALA H1056 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N TYR H1067 " --> pdb=" O HIS H1048 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N HIS H1048 " --> pdb=" O TYR H1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 733 through 736 removed outlier: 4.233A pdb=" N LYS H 733 " --> pdb=" O LEU H 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 1120 through 1125 removed outlier: 4.836A pdb=" N ALA H1087 " --> pdb=" O SER H1123 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 3 through 6 Processing sheet with id=AB8, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.421A pdb=" N GLU E 10 " --> pdb=" O THR E 123 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N TYR E 33 " --> pdb=" O GLY E 99 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASN E 59 " --> pdb=" O TRP E 50 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 133 through 136 removed outlier: 3.703A pdb=" N ASP E 157 " --> pdb=" O TYR E 189 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N TYR E 189 " --> pdb=" O ASP E 157 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 133 through 136 removed outlier: 3.703A pdb=" N ASP E 157 " --> pdb=" O TYR E 189 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N TYR E 189 " --> pdb=" O ASP E 157 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 164 through 167 removed outlier: 3.991A pdb=" N TYR E 207 " --> pdb=" O VAL E 224 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 9 through 12 removed outlier: 3.721A pdb=" N THR F 110 " --> pdb=" O VAL F 10 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLY F 12 " --> pdb=" O THR F 110 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N GLN F 39 " --> pdb=" O LEU F 48 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N LEU F 48 " --> pdb=" O GLN F 39 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 9 through 12 removed outlier: 3.721A pdb=" N THR F 110 " --> pdb=" O VAL F 10 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLY F 12 " --> pdb=" O THR F 110 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 17 through 23 Processing sheet with id=AC6, first strand: chain 'F' and resid 120 through 124 removed outlier: 3.562A pdb=" N ASP F 144 " --> pdb=" O TYR F 178 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N TYR F 178 " --> pdb=" O ASP F 144 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 120 through 124 removed outlier: 3.562A pdb=" N ASP F 144 " --> pdb=" O TYR F 178 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N TYR F 178 " --> pdb=" O ASP F 144 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 151 through 154 Processing sheet with id=AC9, first strand: chain 'J' and resid 28 through 30 removed outlier: 7.941A pdb=" N ASN J 61 " --> pdb=" O TYR J 269 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N TYR J 269 " --> pdb=" O ASN J 61 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLU J 191 " --> pdb=" O LYS J 206 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE J 203 " --> pdb=" O LEU J 226 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N HIS J 207 " --> pdb=" O ALA J 222 " (cutoff:3.500A) removed outlier: 9.600A pdb=" N ALA J 222 " --> pdb=" O HIS J 207 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N VAL J 36 " --> pdb=" O LEU J 223 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 48 through 55 removed outlier: 7.393A pdb=" N THR J 274 " --> pdb=" O ASP J 290 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N ASP J 290 " --> pdb=" O THR J 274 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N LEU J 276 " --> pdb=" O ALA J 288 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ALA J 288 " --> pdb=" O LEU J 276 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N LYS J 278 " --> pdb=" O THR J 286 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'J' and resid 169 through 172 Processing sheet with id=AD3, first strand: chain 'J' and resid 311 through 319 removed outlier: 5.667A pdb=" N ILE J 312 " --> pdb=" O THR J 599 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N THR J 599 " --> pdb=" O ILE J 312 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N GLN J 314 " --> pdb=" O VAL J 597 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N VAL J 597 " --> pdb=" O GLN J 314 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N SER J 316 " --> pdb=" O VAL J 595 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'J' and resid 324 through 325 removed outlier: 6.834A pdb=" N GLU J 324 " --> pdb=" O ASN J 540 " (cutoff:3.500A) removed outlier: 8.310A pdb=" N ASN J 542 " --> pdb=" O GLU J 324 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N ASP J 574 " --> pdb=" O ILE J 587 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N THR J 572 " --> pdb=" O ASP J 568 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N GLY J 566 " --> pdb=" O ASP J 574 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 356 through 358 Processing sheet with id=AD6, first strand: chain 'J' and resid 361 through 362 removed outlier: 6.540A pdb=" N CYS J 361 " --> pdb=" O CYS J 525 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 452 through 454 Processing sheet with id=AD8, first strand: chain 'J' and resid 654 through 655 removed outlier: 6.283A pdb=" N GLU J 654 " --> pdb=" O ALA J 694 " (cutoff:3.500A) removed outlier: 8.658A pdb=" N THR J 696 " --> pdb=" O GLU J 654 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ALA J 672 " --> pdb=" O PRO J 665 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 711 through 713 removed outlier: 3.583A pdb=" N THR J1076 " --> pdb=" O SER J1097 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA J1078 " --> pdb=" O PHE J1095 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N PHE J1095 " --> pdb=" O ALA J1078 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 717 through 718 Processing sheet with id=AE2, first strand: chain 'J' and resid 721 through 728 removed outlier: 3.602A pdb=" N GLY J1059 " --> pdb=" O ALA J1056 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N TYR J1067 " --> pdb=" O HIS J1048 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N HIS J1048 " --> pdb=" O TYR J1067 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 733 through 736 removed outlier: 4.233A pdb=" N LYS J 733 " --> pdb=" O LEU J 861 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 1120 through 1125 removed outlier: 4.837A pdb=" N ALA J1087 " --> pdb=" O SER J1123 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AE6, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.420A pdb=" N GLU G 10 " --> pdb=" O THR G 123 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N TYR G 33 " --> pdb=" O GLY G 99 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASN G 59 " --> pdb=" O TRP G 50 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 133 through 136 removed outlier: 3.703A pdb=" N ASP G 157 " --> pdb=" O TYR G 189 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N TYR G 189 " --> pdb=" O ASP G 157 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 133 through 136 removed outlier: 3.703A pdb=" N ASP G 157 " --> pdb=" O TYR G 189 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N TYR G 189 " --> pdb=" O ASP G 157 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'G' and resid 164 through 167 removed outlier: 3.991A pdb=" N TYR G 207 " --> pdb=" O VAL G 224 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'I' and resid 9 through 12 removed outlier: 3.721A pdb=" N THR I 110 " --> pdb=" O VAL I 10 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLY I 12 " --> pdb=" O THR I 110 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N GLN I 39 " --> pdb=" O LEU I 48 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N LEU I 48 " --> pdb=" O GLN I 39 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'I' and resid 9 through 12 removed outlier: 3.721A pdb=" N THR I 110 " --> pdb=" O VAL I 10 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLY I 12 " --> pdb=" O THR I 110 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'I' and resid 17 through 23 Processing sheet with id=AF4, first strand: chain 'I' and resid 120 through 124 removed outlier: 3.562A pdb=" N ASP I 144 " --> pdb=" O TYR I 178 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N TYR I 178 " --> pdb=" O ASP I 144 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'I' and resid 120 through 124 removed outlier: 3.562A pdb=" N ASP I 144 " --> pdb=" O TYR I 178 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N TYR I 178 " --> pdb=" O ASP I 144 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'I' and resid 151 through 154 Processing sheet with id=AF7, first strand: chain 'C' and resid 28 through 30 removed outlier: 7.941A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLU C 191 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 9.600A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 48 through 55 removed outlier: 7.393A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 169 through 172 Processing sheet with id=AG1, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.667A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'C' and resid 356 through 358 Processing sheet with id=AG3, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.540A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AG5, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.284A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.658A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'C' and resid 711 through 713 removed outlier: 3.583A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'C' and resid 717 through 718 Processing sheet with id=AG8, first strand: chain 'C' and resid 721 through 728 removed outlier: 3.602A pdb=" N GLY C1059 " --> pdb=" O ALA C1056 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.233A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.837A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'A' and resid 3 through 6 Processing sheet with id=AH3, first strand: chain 'A' and resid 10 through 12 removed outlier: 6.420A pdb=" N GLU A 10 " --> pdb=" O THR A 123 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N TYR A 33 " --> pdb=" O GLY A 99 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N ARG A 38 " --> pdb=" O TRP A 47 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N TRP A 47 " --> pdb=" O ARG A 38 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASN A 59 " --> pdb=" O TRP A 50 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'A' and resid 133 through 136 removed outlier: 3.703A pdb=" N ASP A 157 " --> pdb=" O TYR A 189 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N TYR A 189 " --> pdb=" O ASP A 157 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'A' and resid 133 through 136 removed outlier: 3.703A pdb=" N ASP A 157 " --> pdb=" O TYR A 189 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N TYR A 189 " --> pdb=" O ASP A 157 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'A' and resid 164 through 167 removed outlier: 3.991A pdb=" N TYR A 207 " --> pdb=" O VAL A 224 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'B' and resid 9 through 12 removed outlier: 3.721A pdb=" N THR B 110 " --> pdb=" O VAL B 10 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLY B 12 " --> pdb=" O THR B 110 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N GLN B 39 " --> pdb=" O LEU B 48 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N LEU B 48 " --> pdb=" O GLN B 39 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'B' and resid 9 through 12 removed outlier: 3.721A pdb=" N THR B 110 " --> pdb=" O VAL B 10 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLY B 12 " --> pdb=" O THR B 110 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'B' and resid 17 through 23 Processing sheet with id=AI1, first strand: chain 'B' and resid 120 through 124 removed outlier: 3.563A pdb=" N ASP B 144 " --> pdb=" O TYR B 178 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N TYR B 178 " --> pdb=" O ASP B 144 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'B' and resid 120 through 124 removed outlier: 3.563A pdb=" N ASP B 144 " --> pdb=" O TYR B 178 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N TYR B 178 " --> pdb=" O ASP B 144 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'B' and resid 151 through 154 1378 hydrogen bonds defined for protein. 3630 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: 18.83 Time building geometry restraints manager: 9.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10635 1.34 - 1.46: 7842 1.46 - 1.58: 15639 1.58 - 1.70: 0 1.70 - 1.81: 186 Bond restraints: 34302 Sorted by residual: bond pdb=" N ASN E 52 " pdb=" CA ASN E 52 " ideal model delta sigma weight residual 1.457 1.512 -0.055 1.41e-02 5.03e+03 1.52e+01 bond pdb=" N ASN A 52 " pdb=" CA ASN A 52 " ideal model delta sigma weight residual 1.457 1.512 -0.055 1.41e-02 5.03e+03 1.52e+01 bond pdb=" N ASN G 52 " pdb=" CA ASN G 52 " ideal model delta sigma weight residual 1.457 1.511 -0.054 1.41e-02 5.03e+03 1.48e+01 bond pdb=" N LEU J 650 " pdb=" CA LEU J 650 " ideal model delta sigma weight residual 1.454 1.490 -0.036 1.19e-02 7.06e+03 9.21e+00 bond pdb=" N LEU H 650 " pdb=" CA LEU H 650 " ideal model delta sigma weight residual 1.454 1.490 -0.036 1.19e-02 7.06e+03 9.21e+00 ... (remaining 34297 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.39: 46014 2.39 - 4.77: 637 4.77 - 7.16: 41 7.16 - 9.55: 6 9.55 - 11.93: 12 Bond angle restraints: 46710 Sorted by residual: angle pdb=" N ASN E 54 " pdb=" CA ASN E 54 " pdb=" C ASN E 54 " ideal model delta sigma weight residual 111.11 121.37 -10.26 1.20e+00 6.94e-01 7.31e+01 angle pdb=" N ASN A 54 " pdb=" CA ASN A 54 " pdb=" C ASN A 54 " ideal model delta sigma weight residual 111.11 121.37 -10.26 1.20e+00 6.94e-01 7.31e+01 angle pdb=" N ASN G 54 " pdb=" CA ASN G 54 " pdb=" C ASN G 54 " ideal model delta sigma weight residual 111.11 121.36 -10.25 1.20e+00 6.94e-01 7.29e+01 angle pdb=" N SER H 375 " pdb=" CA SER H 375 " pdb=" C SER H 375 " ideal model delta sigma weight residual 112.45 101.45 11.00 1.39e+00 5.18e-01 6.26e+01 angle pdb=" N SER C 375 " pdb=" CA SER C 375 " pdb=" C SER C 375 " ideal model delta sigma weight residual 112.45 101.47 10.98 1.39e+00 5.18e-01 6.24e+01 ... (remaining 46705 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.43: 19333 21.43 - 42.87: 1108 42.87 - 64.30: 171 64.30 - 85.73: 34 85.73 - 107.16: 51 Dihedral angle restraints: 20697 sinusoidal: 8286 harmonic: 12411 Sorted by residual: dihedral pdb=" CB CYS H 336 " pdb=" SG CYS H 336 " pdb=" SG CYS H 361 " pdb=" CB CYS H 361 " ideal model delta sinusoidal sigma weight residual 93.00 25.78 67.22 1 1.00e+01 1.00e-02 5.88e+01 dihedral pdb=" CB CYS E 22 " pdb=" SG CYS E 22 " pdb=" SG CYS E 96 " pdb=" CB CYS E 96 " ideal model delta sinusoidal sigma weight residual 93.00 42.89 50.11 1 1.00e+01 1.00e-02 3.44e+01 dihedral pdb=" CB CYS E 153 " pdb=" SG CYS E 153 " pdb=" SG CYS E 209 " pdb=" CB CYS E 209 " ideal model delta sinusoidal sigma weight residual 93.00 47.32 45.68 1 1.00e+01 1.00e-02 2.89e+01 ... (remaining 20694 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 4947 0.094 - 0.189: 423 0.189 - 0.283: 9 0.283 - 0.378: 6 0.378 - 0.472: 9 Chirality restraints: 5394 Sorted by residual: chirality pdb=" CA PRO G 53 " pdb=" N PRO G 53 " pdb=" C PRO G 53 " pdb=" CB PRO G 53 " both_signs ideal model delta sigma weight residual False 2.72 2.25 0.47 2.00e-01 2.50e+01 5.57e+00 chirality pdb=" CA PRO A 53 " pdb=" N PRO A 53 " pdb=" C PRO A 53 " pdb=" CB PRO A 53 " both_signs ideal model delta sigma weight residual False 2.72 2.25 0.47 2.00e-01 2.50e+01 5.56e+00 chirality pdb=" CA PRO E 53 " pdb=" N PRO E 53 " pdb=" C PRO E 53 " pdb=" CB PRO E 53 " both_signs ideal model delta sigma weight residual False 2.72 2.25 0.47 2.00e-01 2.50e+01 5.55e+00 ... (remaining 5391 not shown) Planarity restraints: 5994 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER J 967 " 0.018 2.00e-02 2.50e+03 3.68e-02 1.35e+01 pdb=" C SER J 967 " -0.064 2.00e-02 2.50e+03 pdb=" O SER J 967 " 0.025 2.00e-02 2.50e+03 pdb=" N SER J 968 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER H 967 " 0.018 2.00e-02 2.50e+03 3.68e-02 1.35e+01 pdb=" C SER H 967 " -0.064 2.00e-02 2.50e+03 pdb=" O SER H 967 " 0.025 2.00e-02 2.50e+03 pdb=" N SER H 968 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER C 967 " 0.018 2.00e-02 2.50e+03 3.68e-02 1.35e+01 pdb=" C SER C 967 " -0.064 2.00e-02 2.50e+03 pdb=" O SER C 967 " 0.025 2.00e-02 2.50e+03 pdb=" N SER C 968 " 0.021 2.00e-02 2.50e+03 ... (remaining 5991 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 351 2.60 - 3.18: 28009 3.18 - 3.75: 48889 3.75 - 4.33: 68241 4.33 - 4.90: 117660 Nonbonded interactions: 263150 Sorted by model distance: nonbonded pdb=" SG CYS J1032 " pdb=" SG CYS J1043 " model vdw 2.026 3.760 nonbonded pdb=" SG CYS C1032 " pdb=" SG CYS C1043 " model vdw 2.026 3.760 nonbonded pdb=" SG CYS C 336 " pdb=" SG CYS C 361 " model vdw 2.027 3.760 nonbonded pdb=" SG CYS J 336 " pdb=" SG CYS J 361 " model vdw 2.028 3.760 nonbonded pdb=" SG CYS C 391 " pdb=" SG CYS C 525 " model vdw 2.030 3.760 ... (remaining 263145 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: 0.24 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'C' selection = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.140 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: 0.050 Extract box with map and model: 1.380 Check model and map are aligned: 0.220 Set scattering table: 0.400 Process input model: 85.610 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.130 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 93.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 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 : 0.004 0.055 34352 Z= 0.254 Angle : 0.652 11.933 46843 Z= 0.395 Chirality : 0.051 0.472 5394 Planarity : 0.004 0.044 5961 Dihedral : 14.742 107.164 12684 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 0.24 % Allowed : 0.84 % Favored : 98.92 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 1.32 % 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: 0.01 (0.14), residues: 4200 helix: 1.58 (0.20), residues: 780 sheet: 0.79 (0.15), residues: 1305 loop : -1.14 (0.14), residues: 2115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP E 36 HIS 0.003 0.001 HIS F 203 PHE 0.017 0.001 PHE J 906 TYR 0.012 0.001 TYR C1067 ARG 0.005 0.000 ARG E 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00294 ( 33) link_NAG-ASN : angle 1.78343 ( 99) hydrogen bonds : bond 0.19410 ( 1303) hydrogen bonds : angle 7.43335 ( 3630) SS BOND : bond 0.00232 ( 17) SS BOND : angle 1.02077 ( 34) covalent geometry : bond 0.00411 (34302) covalent geometry : angle 0.64728 (46710) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8400 Ramachandran restraints generated. 4200 Oldfield, 0 Emsley, 4200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8400 Ramachandran restraints generated. 4200 Oldfield, 0 Emsley, 4200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 3702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 377 time to evaluate : 3.991 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 70 MET cc_start: 0.6169 (mmt) cc_final: 0.5875 (mmt) outliers start: 9 outliers final: 3 residues processed: 383 average time/residue: 0.4347 time to fit residues: 279.3030 Evaluate side-chains 279 residues out of total 3702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 276 time to evaluate : 3.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 373 SER Chi-restraints excluded: chain J residue 373 SER Chi-restraints excluded: chain C residue 373 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 359 optimal weight: 3.9990 chunk 322 optimal weight: 10.0000 chunk 179 optimal weight: 0.8980 chunk 110 optimal weight: 0.9990 chunk 217 optimal weight: 2.9990 chunk 172 optimal weight: 3.9990 chunk 333 optimal weight: 6.9990 chunk 129 optimal weight: 9.9990 chunk 203 optimal weight: 1.9990 chunk 248 optimal weight: 5.9990 chunk 386 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 52 GLN H 207 HIS H 540 ASN H 675 GLN H 751 ASN E 52 ASN J 207 HIS J 675 GLN J 751 ASN G 52 ASN C 207 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.192109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.161002 restraints weight = 48541.264| |-----------------------------------------------------------------------------| r_work (start): 0.3866 rms_B_bonded: 2.09 r_work: 0.3602 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3514 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.1216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 34352 Z= 0.187 Angle : 0.595 8.501 46843 Z= 0.306 Chirality : 0.047 0.245 5394 Planarity : 0.004 0.047 5961 Dihedral : 9.736 81.614 5268 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 1.22 % Allowed : 6.89 % Favored : 91.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % 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: -0.05 (0.13), residues: 4200 helix: 1.44 (0.19), residues: 768 sheet: 0.83 (0.15), residues: 1254 loop : -1.14 (0.13), residues: 2178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 50 HIS 0.008 0.001 HIS B 100 PHE 0.023 0.002 PHE E 29 TYR 0.017 0.002 TYR A 94 ARG 0.004 0.000 ARG A 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00299 ( 33) link_NAG-ASN : angle 1.58368 ( 99) hydrogen bonds : bond 0.05360 ( 1303) hydrogen bonds : angle 5.53769 ( 3630) SS BOND : bond 0.00400 ( 17) SS BOND : angle 1.02089 ( 34) covalent geometry : bond 0.00444 (34302) covalent geometry : angle 0.59025 (46710) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8400 Ramachandran restraints generated. 4200 Oldfield, 0 Emsley, 4200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8400 Ramachandran restraints generated. 4200 Oldfield, 0 Emsley, 4200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 3702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 323 time to evaluate : 3.883 Fit side-chains REVERT: E 81 MET cc_start: 0.6341 (tmm) cc_final: 0.5862 (tmm) REVERT: E 105 ASP cc_start: 0.8544 (t0) cc_final: 0.8343 (t0) REVERT: J 1041 ASP cc_start: 0.7955 (t0) cc_final: 0.7716 (t0) REVERT: J 1144 GLU cc_start: 0.7435 (tp30) cc_final: 0.7220 (tp30) REVERT: G 118 GLN cc_start: 0.7536 (mm-40) cc_final: 0.7198 (mm-40) REVERT: C 1041 ASP cc_start: 0.8144 (t0) cc_final: 0.7849 (t0) REVERT: A 81 MET cc_start: 0.6158 (tmm) cc_final: 0.5822 (tmm) REVERT: A 105 ASP cc_start: 0.8550 (t0) cc_final: 0.8268 (t0) outliers start: 45 outliers final: 33 residues processed: 354 average time/residue: 0.4117 time to fit residues: 247.9184 Evaluate side-chains 318 residues out of total 3702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 285 time to evaluate : 3.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain H residue 307 THR Chi-restraints excluded: chain H residue 540 ASN Chi-restraints excluded: chain H residue 553 THR Chi-restraints excluded: chain H residue 602 THR Chi-restraints excluded: chain H residue 720 ILE Chi-restraints excluded: chain H residue 723 THR Chi-restraints excluded: chain H residue 1061 VAL Chi-restraints excluded: chain H residue 1128 VAL Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain J residue 63 THR Chi-restraints excluded: chain J residue 307 THR Chi-restraints excluded: chain J residue 373 SER Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 723 THR Chi-restraints excluded: chain J residue 934 ILE Chi-restraints excluded: chain J residue 1092 GLU Chi-restraints excluded: chain J residue 1128 VAL Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 1061 VAL Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain B residue 72 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 272 optimal weight: 9.9990 chunk 76 optimal weight: 0.9980 chunk 399 optimal weight: 10.0000 chunk 59 optimal weight: 0.9980 chunk 412 optimal weight: 20.0000 chunk 95 optimal weight: 2.9990 chunk 13 optimal weight: 0.3980 chunk 196 optimal weight: 8.9990 chunk 411 optimal weight: 4.9990 chunk 163 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 613 GLN ** E 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 613 GLN ** G 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN A 59 ASN ** B 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.192093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.160579 restraints weight = 48875.626| |-----------------------------------------------------------------------------| r_work (start): 0.3862 rms_B_bonded: 2.07 r_work: 0.3607 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3526 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.1482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 34352 Z= 0.161 Angle : 0.556 9.039 46843 Z= 0.284 Chirality : 0.046 0.291 5394 Planarity : 0.004 0.063 5961 Dihedral : 7.379 56.516 5266 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 1.49 % Allowed : 9.83 % Favored : 88.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % 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: -0.03 (0.13), residues: 4200 helix: 1.47 (0.19), residues: 774 sheet: 0.82 (0.15), residues: 1266 loop : -1.13 (0.13), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP E 36 HIS 0.010 0.001 HIS I 100 PHE 0.025 0.001 PHE A 29 TYR 0.018 0.001 TYR C1067 ARG 0.003 0.000 ARG J 815 Details of bonding type rmsd link_NAG-ASN : bond 0.00340 ( 33) link_NAG-ASN : angle 1.60878 ( 99) hydrogen bonds : bond 0.04923 ( 1303) hydrogen bonds : angle 5.17730 ( 3630) SS BOND : bond 0.00307 ( 17) SS BOND : angle 0.82948 ( 34) covalent geometry : bond 0.00383 (34302) covalent geometry : angle 0.55123 (46710) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8400 Ramachandran restraints generated. 4200 Oldfield, 0 Emsley, 4200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8400 Ramachandran restraints generated. 4200 Oldfield, 0 Emsley, 4200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 3702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 309 time to evaluate : 3.742 Fit side-chains REVERT: H 1144 GLU cc_start: 0.7304 (tp30) cc_final: 0.7071 (tp30) REVERT: E 81 MET cc_start: 0.6346 (tmm) cc_final: 0.5872 (tmm) REVERT: J 1041 ASP cc_start: 0.7997 (t0) cc_final: 0.7661 (t0) REVERT: G 81 MET cc_start: 0.6172 (tmm) cc_final: 0.5932 (tmm) REVERT: G 118 GLN cc_start: 0.7441 (mm-40) cc_final: 0.7091 (mm-40) REVERT: C 1144 GLU cc_start: 0.7270 (tp30) cc_final: 0.7043 (tp30) REVERT: A 81 MET cc_start: 0.6179 (tmm) cc_final: 0.5789 (tmm) REVERT: A 105 ASP cc_start: 0.8521 (t0) cc_final: 0.8253 (t0) outliers start: 55 outliers final: 40 residues processed: 348 average time/residue: 0.4293 time to fit residues: 252.0193 Evaluate side-chains 315 residues out of total 3702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 275 time to evaluate : 3.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 229 LEU Chi-restraints excluded: chain H residue 307 THR Chi-restraints excluded: chain H residue 540 ASN Chi-restraints excluded: chain H residue 553 THR Chi-restraints excluded: chain H residue 602 THR Chi-restraints excluded: chain H residue 642 VAL Chi-restraints excluded: chain H residue 720 ILE Chi-restraints excluded: chain H residue 723 THR Chi-restraints excluded: chain H residue 1092 GLU Chi-restraints excluded: chain H residue 1128 VAL Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain J residue 63 THR Chi-restraints excluded: chain J residue 130 VAL Chi-restraints excluded: chain J residue 307 THR Chi-restraints excluded: chain J residue 512 VAL Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 642 VAL Chi-restraints excluded: chain J residue 723 THR Chi-restraints excluded: chain J residue 856 ASN Chi-restraints excluded: chain J residue 934 ILE Chi-restraints excluded: chain J residue 1092 GLU Chi-restraints excluded: chain J residue 1128 VAL Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 1061 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain B residue 72 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 336 optimal weight: 2.9990 chunk 282 optimal weight: 40.0000 chunk 16 optimal weight: 6.9990 chunk 186 optimal weight: 6.9990 chunk 20 optimal weight: 5.9990 chunk 360 optimal weight: 0.5980 chunk 2 optimal weight: 0.6980 chunk 157 optimal weight: 9.9990 chunk 135 optimal weight: 0.9990 chunk 107 optimal weight: 5.9990 chunk 223 optimal weight: 0.6980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 540 ASN E 39 GLN ** E 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 540 ASN J1002 GLN G 39 GLN ** G 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 540 ASN C 613 GLN ** A 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.192549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.159174 restraints weight = 48694.221| |-----------------------------------------------------------------------------| r_work (start): 0.3830 rms_B_bonded: 2.13 r_work: 0.3569 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3477 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 34352 Z= 0.130 Angle : 0.522 8.155 46843 Z= 0.266 Chirality : 0.045 0.309 5394 Planarity : 0.004 0.054 5961 Dihedral : 5.676 41.613 5265 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 1.78 % Allowed : 11.05 % Favored : 87.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % 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: 0.03 (0.13), residues: 4200 helix: 1.67 (0.20), residues: 759 sheet: 0.81 (0.15), residues: 1269 loop : -1.11 (0.13), residues: 2172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP G 50 HIS 0.009 0.001 HIS I 100 PHE 0.019 0.001 PHE A 29 TYR 0.015 0.001 TYR C1067 ARG 0.007 0.000 ARG J 646 Details of bonding type rmsd link_NAG-ASN : bond 0.00381 ( 33) link_NAG-ASN : angle 1.57185 ( 99) hydrogen bonds : bond 0.04472 ( 1303) hydrogen bonds : angle 4.94035 ( 3630) SS BOND : bond 0.00348 ( 17) SS BOND : angle 0.72392 ( 34) covalent geometry : bond 0.00303 (34302) covalent geometry : angle 0.51736 (46710) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8400 Ramachandran restraints generated. 4200 Oldfield, 0 Emsley, 4200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8400 Ramachandran restraints generated. 4200 Oldfield, 0 Emsley, 4200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 3702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 296 time to evaluate : 3.396 Fit side-chains revert: symmetry clash REVERT: H 1144 GLU cc_start: 0.7347 (tp30) cc_final: 0.7124 (tp30) REVERT: E 81 MET cc_start: 0.6631 (tmm) cc_final: 0.6160 (tmm) REVERT: J 1041 ASP cc_start: 0.8044 (t0) cc_final: 0.7815 (t0) REVERT: J 1144 GLU cc_start: 0.7528 (tp30) cc_final: 0.7279 (tp30) REVERT: G 81 MET cc_start: 0.6301 (tmm) cc_final: 0.5965 (tmm) REVERT: G 118 GLN cc_start: 0.7444 (mm-40) cc_final: 0.7131 (mm-40) REVERT: A 81 MET cc_start: 0.6221 (tmm) cc_final: 0.5847 (tmm) REVERT: A 105 ASP cc_start: 0.8547 (t0) cc_final: 0.8299 (t0) outliers start: 66 outliers final: 51 residues processed: 347 average time/residue: 0.4005 time to fit residues: 236.7502 Evaluate side-chains 320 residues out of total 3702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 269 time to evaluate : 3.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain H residue 227 VAL Chi-restraints excluded: chain H residue 229 LEU Chi-restraints excluded: chain H residue 307 THR Chi-restraints excluded: chain H residue 540 ASN Chi-restraints excluded: chain H residue 553 THR Chi-restraints excluded: chain H residue 602 THR Chi-restraints excluded: chain H residue 720 ILE Chi-restraints excluded: chain H residue 723 THR Chi-restraints excluded: chain H residue 856 ASN Chi-restraints excluded: chain H residue 1061 VAL Chi-restraints excluded: chain H residue 1068 VAL Chi-restraints excluded: chain H residue 1128 VAL Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain J residue 94 SER Chi-restraints excluded: chain J residue 130 VAL Chi-restraints excluded: chain J residue 159 VAL Chi-restraints excluded: chain J residue 307 THR Chi-restraints excluded: chain J residue 512 VAL Chi-restraints excluded: chain J residue 551 VAL Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 705 VAL Chi-restraints excluded: chain J residue 723 THR Chi-restraints excluded: chain J residue 856 ASN Chi-restraints excluded: chain J residue 934 ILE Chi-restraints excluded: chain J residue 1068 VAL Chi-restraints excluded: chain J residue 1092 GLU Chi-restraints excluded: chain J residue 1128 VAL Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain G residue 111 SER Chi-restraints excluded: chain I residue 22 CYS Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 1068 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain B residue 22 CYS Chi-restraints excluded: chain B residue 72 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 154 optimal weight: 6.9990 chunk 214 optimal weight: 0.7980 chunk 132 optimal weight: 20.0000 chunk 405 optimal weight: 20.0000 chunk 171 optimal weight: 0.4980 chunk 311 optimal weight: 6.9990 chunk 24 optimal weight: 10.0000 chunk 45 optimal weight: 0.8980 chunk 194 optimal weight: 0.8980 chunk 267 optimal weight: 20.0000 chunk 97 optimal weight: 3.9990 overall best weight: 1.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 168 ASN ** E 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J1002 GLN ** G 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.192068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.160169 restraints weight = 48607.255| |-----------------------------------------------------------------------------| r_work (start): 0.3830 rms_B_bonded: 2.14 r_work: 0.3489 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 34352 Z= 0.140 Angle : 0.516 6.826 46843 Z= 0.265 Chirality : 0.045 0.304 5394 Planarity : 0.004 0.045 5961 Dihedral : 4.980 36.382 5265 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 2.35 % Allowed : 11.94 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % 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: 0.06 (0.13), residues: 4200 helix: 1.71 (0.20), residues: 756 sheet: 0.80 (0.15), residues: 1269 loop : -1.08 (0.13), residues: 2175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 50 HIS 0.008 0.001 HIS I 100 PHE 0.024 0.001 PHE G 113 TYR 0.016 0.001 TYR C1067 ARG 0.007 0.000 ARG J 646 Details of bonding type rmsd link_NAG-ASN : bond 0.00366 ( 33) link_NAG-ASN : angle 1.61827 ( 99) hydrogen bonds : bond 0.04518 ( 1303) hydrogen bonds : angle 4.83990 ( 3630) SS BOND : bond 0.00265 ( 17) SS BOND : angle 0.70909 ( 34) covalent geometry : bond 0.00331 (34302) covalent geometry : angle 0.51118 (46710) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8400 Ramachandran restraints generated. 4200 Oldfield, 0 Emsley, 4200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8400 Ramachandran restraints generated. 4200 Oldfield, 0 Emsley, 4200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 3702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 283 time to evaluate : 3.447 Fit side-chains revert: symmetry clash REVERT: H 237 ARG cc_start: 0.7308 (mtp180) cc_final: 0.7097 (mtm180) REVERT: E 81 MET cc_start: 0.6616 (tmm) cc_final: 0.6244 (tmm) REVERT: E 118 GLN cc_start: 0.7690 (mm-40) cc_final: 0.7239 (mm-40) REVERT: J 646 ARG cc_start: 0.7916 (tpt-90) cc_final: 0.7696 (tpt90) REVERT: G 81 MET cc_start: 0.6271 (tmm) cc_final: 0.5561 (tmm) REVERT: G 118 GLN cc_start: 0.7495 (mm-40) cc_final: 0.7129 (mm-40) REVERT: A 81 MET cc_start: 0.6347 (tmm) cc_final: 0.5911 (tmm) outliers start: 87 outliers final: 68 residues processed: 350 average time/residue: 0.4165 time to fit residues: 249.5859 Evaluate side-chains 335 residues out of total 3702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 267 time to evaluate : 3.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain H residue 208 THR Chi-restraints excluded: chain H residue 229 LEU Chi-restraints excluded: chain H residue 307 THR Chi-restraints excluded: chain H residue 553 THR Chi-restraints excluded: chain H residue 588 THR Chi-restraints excluded: chain H residue 602 THR Chi-restraints excluded: chain H residue 720 ILE Chi-restraints excluded: chain H residue 723 THR Chi-restraints excluded: chain H residue 856 ASN Chi-restraints excluded: chain H residue 1050 MET Chi-restraints excluded: chain H residue 1061 VAL Chi-restraints excluded: chain H residue 1068 VAL Chi-restraints excluded: chain H residue 1092 GLU Chi-restraints excluded: chain H residue 1128 VAL Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain F residue 28 ASP Chi-restraints excluded: chain J residue 94 SER Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain J residue 108 THR Chi-restraints excluded: chain J residue 130 VAL Chi-restraints excluded: chain J residue 159 VAL Chi-restraints excluded: chain J residue 208 THR Chi-restraints excluded: chain J residue 229 LEU Chi-restraints excluded: chain J residue 512 VAL Chi-restraints excluded: chain J residue 551 VAL Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 588 THR Chi-restraints excluded: chain J residue 705 VAL Chi-restraints excluded: chain J residue 723 THR Chi-restraints excluded: chain J residue 856 ASN Chi-restraints excluded: chain J residue 934 ILE Chi-restraints excluded: chain J residue 1068 VAL Chi-restraints excluded: chain J residue 1092 GLU Chi-restraints excluded: chain J residue 1128 VAL Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain G residue 111 SER Chi-restraints excluded: chain I residue 22 CYS Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 1061 VAL Chi-restraints excluded: chain C residue 1068 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain B residue 22 CYS Chi-restraints excluded: chain B residue 72 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 215 optimal weight: 0.7980 chunk 261 optimal weight: 20.0000 chunk 183 optimal weight: 0.9990 chunk 12 optimal weight: 7.9990 chunk 235 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 177 optimal weight: 4.9990 chunk 54 optimal weight: 0.9990 chunk 170 optimal weight: 3.9990 chunk 368 optimal weight: 0.7980 chunk 93 optimal weight: 5.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 540 ASN ** E 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 540 ASN ** G 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 540 ASN ** A 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.192641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.161003 restraints weight = 48797.760| |-----------------------------------------------------------------------------| r_work (start): 0.3848 rms_B_bonded: 2.13 r_work: 0.3597 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3524 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 34352 Z= 0.122 Angle : 0.500 7.520 46843 Z= 0.257 Chirality : 0.044 0.279 5394 Planarity : 0.004 0.046 5961 Dihedral : 4.643 35.614 5265 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 2.38 % Allowed : 12.48 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % 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: 0.12 (0.13), residues: 4200 helix: 1.81 (0.20), residues: 753 sheet: 0.83 (0.15), residues: 1269 loop : -1.05 (0.13), residues: 2178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP E 36 HIS 0.009 0.001 HIS I 100 PHE 0.012 0.001 PHE J 86 TYR 0.015 0.001 TYR C 904 ARG 0.007 0.000 ARG J 646 Details of bonding type rmsd link_NAG-ASN : bond 0.00333 ( 33) link_NAG-ASN : angle 1.58816 ( 99) hydrogen bonds : bond 0.04279 ( 1303) hydrogen bonds : angle 4.73241 ( 3630) SS BOND : bond 0.00288 ( 17) SS BOND : angle 0.76439 ( 34) covalent geometry : bond 0.00284 (34302) covalent geometry : angle 0.49539 (46710) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8400 Ramachandran restraints generated. 4200 Oldfield, 0 Emsley, 4200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8400 Ramachandran restraints generated. 4200 Oldfield, 0 Emsley, 4200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 3702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 277 time to evaluate : 3.949 Fit side-chains revert: symmetry clash REVERT: H 981 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8565 (mm) REVERT: E 81 MET cc_start: 0.6430 (tmm) cc_final: 0.6100 (tmm) REVERT: E 118 GLN cc_start: 0.7569 (mm-40) cc_final: 0.7166 (mm-40) REVERT: F 88 TYR cc_start: 0.7036 (m-10) cc_final: 0.6573 (m-10) REVERT: J 646 ARG cc_start: 0.7949 (tpt-90) cc_final: 0.7707 (tpt90) REVERT: J 981 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8732 (mm) REVERT: J 1144 GLU cc_start: 0.7403 (tp30) cc_final: 0.7193 (tp30) REVERT: G 81 MET cc_start: 0.6097 (tmm) cc_final: 0.5310 (tmm) REVERT: G 118 GLN cc_start: 0.7431 (mm-40) cc_final: 0.7109 (mm-40) REVERT: A 81 MET cc_start: 0.6271 (tmm) cc_final: 0.5881 (tmm) outliers start: 88 outliers final: 66 residues processed: 350 average time/residue: 0.4302 time to fit residues: 257.0929 Evaluate side-chains 331 residues out of total 3702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 263 time to evaluate : 3.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain H residue 208 THR Chi-restraints excluded: chain H residue 229 LEU Chi-restraints excluded: chain H residue 307 THR Chi-restraints excluded: chain H residue 540 ASN Chi-restraints excluded: chain H residue 553 THR Chi-restraints excluded: chain H residue 588 THR Chi-restraints excluded: chain H residue 602 THR Chi-restraints excluded: chain H residue 720 ILE Chi-restraints excluded: chain H residue 723 THR Chi-restraints excluded: chain H residue 856 ASN Chi-restraints excluded: chain H residue 916 LEU Chi-restraints excluded: chain H residue 981 LEU Chi-restraints excluded: chain H residue 1061 VAL Chi-restraints excluded: chain H residue 1068 VAL Chi-restraints excluded: chain H residue 1128 VAL Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain J residue 63 THR Chi-restraints excluded: chain J residue 94 SER Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain J residue 130 VAL Chi-restraints excluded: chain J residue 159 VAL Chi-restraints excluded: chain J residue 208 THR Chi-restraints excluded: chain J residue 229 LEU Chi-restraints excluded: chain J residue 401 VAL Chi-restraints excluded: chain J residue 512 VAL Chi-restraints excluded: chain J residue 540 ASN Chi-restraints excluded: chain J residue 551 VAL Chi-restraints excluded: chain J residue 588 THR Chi-restraints excluded: chain J residue 705 VAL Chi-restraints excluded: chain J residue 723 THR Chi-restraints excluded: chain J residue 856 ASN Chi-restraints excluded: chain J residue 934 ILE Chi-restraints excluded: chain J residue 981 LEU Chi-restraints excluded: chain J residue 1068 VAL Chi-restraints excluded: chain J residue 1128 VAL Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain I residue 22 CYS Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1061 VAL Chi-restraints excluded: chain C residue 1068 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain B residue 22 CYS Chi-restraints excluded: chain B residue 72 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 354 optimal weight: 7.9990 chunk 187 optimal weight: 4.9990 chunk 133 optimal weight: 20.0000 chunk 3 optimal weight: 5.9990 chunk 130 optimal weight: 9.9990 chunk 216 optimal weight: 2.9990 chunk 214 optimal weight: 0.7980 chunk 170 optimal weight: 3.9990 chunk 164 optimal weight: 1.9990 chunk 288 optimal weight: 0.2980 chunk 158 optimal weight: 0.0270 overall best weight: 1.2242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 54 ASN ** E 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J1002 GLN ** G 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 59 ASN ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.192409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.158190 restraints weight = 48579.624| |-----------------------------------------------------------------------------| r_work (start): 0.3814 rms_B_bonded: 2.18 r_work: 0.3569 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3499 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 34352 Z= 0.126 Angle : 0.504 9.986 46843 Z= 0.258 Chirality : 0.044 0.271 5394 Planarity : 0.004 0.046 5961 Dihedral : 4.533 35.411 5265 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 2.35 % Allowed : 12.94 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % 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: 0.15 (0.13), residues: 4200 helix: 1.84 (0.20), residues: 753 sheet: 0.84 (0.15), residues: 1275 loop : -1.02 (0.13), residues: 2172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP G 36 HIS 0.008 0.001 HIS I 100 PHE 0.014 0.001 PHE G 113 TYR 0.019 0.001 TYR C 904 ARG 0.005 0.000 ARG J 646 Details of bonding type rmsd link_NAG-ASN : bond 0.00311 ( 33) link_NAG-ASN : angle 1.56134 ( 99) hydrogen bonds : bond 0.04308 ( 1303) hydrogen bonds : angle 4.68800 ( 3630) SS BOND : bond 0.00232 ( 17) SS BOND : angle 0.78370 ( 34) covalent geometry : bond 0.00297 (34302) covalent geometry : angle 0.49957 (46710) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8400 Ramachandran restraints generated. 4200 Oldfield, 0 Emsley, 4200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8400 Ramachandran restraints generated. 4200 Oldfield, 0 Emsley, 4200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 3702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 275 time to evaluate : 3.713 Fit side-chains revert: symmetry clash REVERT: H 740 MET cc_start: 0.8650 (OUTLIER) cc_final: 0.8223 (ttt) REVERT: H 981 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8592 (mm) REVERT: E 81 MET cc_start: 0.6441 (tmm) cc_final: 0.6112 (tmm) REVERT: E 118 GLN cc_start: 0.7579 (mm-40) cc_final: 0.7175 (mm-40) REVERT: F 88 TYR cc_start: 0.7114 (m-10) cc_final: 0.6663 (m-10) REVERT: J 646 ARG cc_start: 0.8032 (tpt-90) cc_final: 0.7770 (tpt90) REVERT: J 981 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8757 (mm) REVERT: J 1144 GLU cc_start: 0.7410 (tp30) cc_final: 0.7174 (tp30) REVERT: G 81 MET cc_start: 0.6127 (tmm) cc_final: 0.5335 (tmm) REVERT: G 118 GLN cc_start: 0.7444 (mm-40) cc_final: 0.7145 (mm-40) REVERT: C 1144 GLU cc_start: 0.7325 (tp30) cc_final: 0.7110 (tp30) REVERT: A 81 MET cc_start: 0.6269 (tmm) cc_final: 0.5887 (tmm) outliers start: 87 outliers final: 78 residues processed: 343 average time/residue: 0.4428 time to fit residues: 256.9151 Evaluate side-chains 344 residues out of total 3702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 263 time to evaluate : 4.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain H residue 208 THR Chi-restraints excluded: chain H residue 227 VAL Chi-restraints excluded: chain H residue 229 LEU Chi-restraints excluded: chain H residue 307 THR Chi-restraints excluded: chain H residue 340 GLU Chi-restraints excluded: chain H residue 553 THR Chi-restraints excluded: chain H residue 588 THR Chi-restraints excluded: chain H residue 602 THR Chi-restraints excluded: chain H residue 720 ILE Chi-restraints excluded: chain H residue 723 THR Chi-restraints excluded: chain H residue 740 MET Chi-restraints excluded: chain H residue 856 ASN Chi-restraints excluded: chain H residue 896 ILE Chi-restraints excluded: chain H residue 916 LEU Chi-restraints excluded: chain H residue 981 LEU Chi-restraints excluded: chain H residue 1061 VAL Chi-restraints excluded: chain H residue 1068 VAL Chi-restraints excluded: chain H residue 1128 VAL Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 111 SER Chi-restraints excluded: chain F residue 28 ASP Chi-restraints excluded: chain J residue 63 THR Chi-restraints excluded: chain J residue 94 SER Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain J residue 108 THR Chi-restraints excluded: chain J residue 130 VAL Chi-restraints excluded: chain J residue 159 VAL Chi-restraints excluded: chain J residue 208 THR Chi-restraints excluded: chain J residue 229 LEU Chi-restraints excluded: chain J residue 401 VAL Chi-restraints excluded: chain J residue 512 VAL Chi-restraints excluded: chain J residue 551 VAL Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 588 THR Chi-restraints excluded: chain J residue 705 VAL Chi-restraints excluded: chain J residue 723 THR Chi-restraints excluded: chain J residue 856 ASN Chi-restraints excluded: chain J residue 934 ILE Chi-restraints excluded: chain J residue 981 LEU Chi-restraints excluded: chain J residue 1061 VAL Chi-restraints excluded: chain J residue 1068 VAL Chi-restraints excluded: chain J residue 1128 VAL Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain G residue 111 SER Chi-restraints excluded: chain I residue 22 CYS Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1061 VAL Chi-restraints excluded: chain C residue 1068 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain B residue 22 CYS Chi-restraints excluded: chain B residue 72 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 399 optimal weight: 50.0000 chunk 302 optimal weight: 1.9990 chunk 323 optimal weight: 10.0000 chunk 11 optimal weight: 10.0000 chunk 148 optimal weight: 10.0000 chunk 237 optimal weight: 3.9990 chunk 125 optimal weight: 9.9990 chunk 31 optimal weight: 0.9980 chunk 336 optimal weight: 4.9990 chunk 333 optimal weight: 0.8980 chunk 228 optimal weight: 2.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 540 ASN E 54 ASN ** E 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 540 ASN ** G 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 39 GLN I 71 ASN C 540 ASN ** A 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 59 ASN A 118 GLN A 168 ASN ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 39 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.190766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.157411 restraints weight = 48495.129| |-----------------------------------------------------------------------------| r_work (start): 0.3795 rms_B_bonded: 2.17 r_work: 0.3544 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3471 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 34352 Z= 0.188 Angle : 0.548 7.711 46843 Z= 0.282 Chirality : 0.046 0.305 5394 Planarity : 0.004 0.048 5961 Dihedral : 4.734 38.390 5265 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 2.78 % Allowed : 12.75 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % 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: 0.03 (0.13), residues: 4200 helix: 1.62 (0.20), residues: 753 sheet: 0.82 (0.15), residues: 1293 loop : -1.11 (0.13), residues: 2154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 36 HIS 0.007 0.001 HIS I 100 PHE 0.023 0.002 PHE G 113 TYR 0.023 0.001 TYR H 904 ARG 0.004 0.000 ARG E 72 Details of bonding type rmsd link_NAG-ASN : bond 0.00349 ( 33) link_NAG-ASN : angle 1.66649 ( 99) hydrogen bonds : bond 0.05131 ( 1303) hydrogen bonds : angle 4.78608 ( 3630) SS BOND : bond 0.00340 ( 17) SS BOND : angle 1.31371 ( 34) covalent geometry : bond 0.00457 (34302) covalent geometry : angle 0.54202 (46710) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8400 Ramachandran restraints generated. 4200 Oldfield, 0 Emsley, 4200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8400 Ramachandran restraints generated. 4200 Oldfield, 0 Emsley, 4200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 3702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 272 time to evaluate : 3.545 Fit side-chains REVERT: H 740 MET cc_start: 0.8660 (OUTLIER) cc_final: 0.8449 (ttt) REVERT: H 981 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8607 (mm) REVERT: E 81 MET cc_start: 0.6460 (tmm) cc_final: 0.5907 (tmm) REVERT: E 118 GLN cc_start: 0.7562 (mm-40) cc_final: 0.7153 (mm-40) REVERT: J 981 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8739 (mm) REVERT: J 1144 GLU cc_start: 0.7461 (tp30) cc_final: 0.7258 (tp30) REVERT: G 81 MET cc_start: 0.6046 (tmm) cc_final: 0.5335 (tmm) REVERT: G 118 GLN cc_start: 0.7504 (mm-40) cc_final: 0.7184 (mm-40) REVERT: C 340 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.8220 (pp20) REVERT: A 81 MET cc_start: 0.6273 (tmm) cc_final: 0.5907 (tmm) outliers start: 103 outliers final: 77 residues processed: 356 average time/residue: 0.4324 time to fit residues: 260.5776 Evaluate side-chains 344 residues out of total 3702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 263 time to evaluate : 3.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain H residue 208 THR Chi-restraints excluded: chain H residue 227 VAL Chi-restraints excluded: chain H residue 229 LEU Chi-restraints excluded: chain H residue 307 THR Chi-restraints excluded: chain H residue 340 GLU Chi-restraints excluded: chain H residue 540 ASN Chi-restraints excluded: chain H residue 553 THR Chi-restraints excluded: chain H residue 588 THR Chi-restraints excluded: chain H residue 602 THR Chi-restraints excluded: chain H residue 720 ILE Chi-restraints excluded: chain H residue 723 THR Chi-restraints excluded: chain H residue 740 MET Chi-restraints excluded: chain H residue 896 ILE Chi-restraints excluded: chain H residue 916 LEU Chi-restraints excluded: chain H residue 981 LEU Chi-restraints excluded: chain H residue 1061 VAL Chi-restraints excluded: chain H residue 1068 VAL Chi-restraints excluded: chain H residue 1128 VAL Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 111 SER Chi-restraints excluded: chain F residue 28 ASP Chi-restraints excluded: chain J residue 63 THR Chi-restraints excluded: chain J residue 94 SER Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain J residue 108 THR Chi-restraints excluded: chain J residue 130 VAL Chi-restraints excluded: chain J residue 159 VAL Chi-restraints excluded: chain J residue 208 THR Chi-restraints excluded: chain J residue 401 VAL Chi-restraints excluded: chain J residue 512 VAL Chi-restraints excluded: chain J residue 540 ASN Chi-restraints excluded: chain J residue 551 VAL Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 588 THR Chi-restraints excluded: chain J residue 705 VAL Chi-restraints excluded: chain J residue 723 THR Chi-restraints excluded: chain J residue 856 ASN Chi-restraints excluded: chain J residue 934 ILE Chi-restraints excluded: chain J residue 976 VAL Chi-restraints excluded: chain J residue 981 LEU Chi-restraints excluded: chain J residue 1061 VAL Chi-restraints excluded: chain J residue 1068 VAL Chi-restraints excluded: chain J residue 1128 VAL Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 340 GLU Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1061 VAL Chi-restraints excluded: chain C residue 1068 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain B residue 22 CYS Chi-restraints excluded: chain B residue 72 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 373 optimal weight: 0.9980 chunk 339 optimal weight: 0.2980 chunk 273 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 363 optimal weight: 8.9990 chunk 200 optimal weight: 0.0770 chunk 248 optimal weight: 6.9990 chunk 221 optimal weight: 7.9990 chunk 128 optimal weight: 20.0000 chunk 213 optimal weight: 0.7980 chunk 333 optimal weight: 0.7980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 540 ASN ** E 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 540 ASN G 59 ASN G 168 ASN ** G 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 39 GLN I 71 ASN C 540 ASN ** A 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 59 ASN ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 39 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.192819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.159184 restraints weight = 48597.293| |-----------------------------------------------------------------------------| r_work (start): 0.3832 rms_B_bonded: 2.17 r_work: 0.3528 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3441 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 34352 Z= 0.103 Angle : 0.502 12.078 46843 Z= 0.257 Chirality : 0.044 0.281 5394 Planarity : 0.004 0.044 5961 Dihedral : 4.437 36.066 5265 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 1.97 % Allowed : 13.67 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % 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: 0.17 (0.13), residues: 4200 helix: 1.88 (0.20), residues: 753 sheet: 0.87 (0.15), residues: 1272 loop : -1.04 (0.13), residues: 2175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.001 TRP E 36 HIS 0.008 0.001 HIS B 100 PHE 0.041 0.001 PHE C 541 TYR 0.021 0.001 TYR H 904 ARG 0.007 0.000 ARG A 72 Details of bonding type rmsd link_NAG-ASN : bond 0.00315 ( 33) link_NAG-ASN : angle 1.53299 ( 99) hydrogen bonds : bond 0.04116 ( 1303) hydrogen bonds : angle 4.62583 ( 3630) SS BOND : bond 0.00208 ( 17) SS BOND : angle 1.05661 ( 34) covalent geometry : bond 0.00225 (34302) covalent geometry : angle 0.49652 (46710) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8400 Ramachandran restraints generated. 4200 Oldfield, 0 Emsley, 4200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8400 Ramachandran restraints generated. 4200 Oldfield, 0 Emsley, 4200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 3702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 288 time to evaluate : 3.768 Fit side-chains revert: symmetry clash REVERT: H 740 MET cc_start: 0.8616 (OUTLIER) cc_final: 0.8210 (ttt) REVERT: E 81 MET cc_start: 0.6528 (tmm) cc_final: 0.5993 (tmm) REVERT: E 118 GLN cc_start: 0.7693 (mm-40) cc_final: 0.7262 (mm-40) REVERT: G 81 MET cc_start: 0.6146 (tmm) cc_final: 0.5408 (tmm) REVERT: G 118 GLN cc_start: 0.7380 (mm-40) cc_final: 0.7048 (mm-40) REVERT: I 55 LYS cc_start: 0.7949 (ptpp) cc_final: 0.7749 (pttm) REVERT: A 81 MET cc_start: 0.6356 (tmm) cc_final: 0.5951 (tmm) outliers start: 73 outliers final: 64 residues processed: 351 average time/residue: 0.4614 time to fit residues: 272.1093 Evaluate side-chains 338 residues out of total 3702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 273 time to evaluate : 3.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain H residue 208 THR Chi-restraints excluded: chain H residue 227 VAL Chi-restraints excluded: chain H residue 229 LEU Chi-restraints excluded: chain H residue 307 THR Chi-restraints excluded: chain H residue 340 GLU Chi-restraints excluded: chain H residue 540 ASN Chi-restraints excluded: chain H residue 588 THR Chi-restraints excluded: chain H residue 602 THR Chi-restraints excluded: chain H residue 720 ILE Chi-restraints excluded: chain H residue 740 MET Chi-restraints excluded: chain H residue 856 ASN Chi-restraints excluded: chain H residue 896 ILE Chi-restraints excluded: chain H residue 916 LEU Chi-restraints excluded: chain H residue 1061 VAL Chi-restraints excluded: chain H residue 1068 VAL Chi-restraints excluded: chain H residue 1128 VAL Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 111 SER Chi-restraints excluded: chain J residue 94 SER Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain J residue 108 THR Chi-restraints excluded: chain J residue 130 VAL Chi-restraints excluded: chain J residue 159 VAL Chi-restraints excluded: chain J residue 208 THR Chi-restraints excluded: chain J residue 401 VAL Chi-restraints excluded: chain J residue 512 VAL Chi-restraints excluded: chain J residue 540 ASN Chi-restraints excluded: chain J residue 551 VAL Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 588 THR Chi-restraints excluded: chain J residue 705 VAL Chi-restraints excluded: chain J residue 723 THR Chi-restraints excluded: chain J residue 856 ASN Chi-restraints excluded: chain J residue 934 ILE Chi-restraints excluded: chain J residue 1068 VAL Chi-restraints excluded: chain J residue 1128 VAL Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 1061 VAL Chi-restraints excluded: chain C residue 1068 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain B residue 22 CYS Chi-restraints excluded: chain B residue 72 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 147 optimal weight: 8.9990 chunk 152 optimal weight: 0.9990 chunk 86 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 159 optimal weight: 2.9990 chunk 236 optimal weight: 0.9990 chunk 353 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 253 optimal weight: 6.9990 chunk 8 optimal weight: 8.9990 chunk 370 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 59 ASN ** G 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 118 GLN ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.191780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.157369 restraints weight = 48472.890| |-----------------------------------------------------------------------------| r_work (start): 0.3794 rms_B_bonded: 2.18 r_work: 0.3557 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3484 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 34352 Z= 0.147 Angle : 0.519 7.744 46843 Z= 0.266 Chirality : 0.045 0.291 5394 Planarity : 0.004 0.045 5961 Dihedral : 4.466 36.520 5265 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 2.03 % Allowed : 13.78 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % 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: 0.12 (0.13), residues: 4200 helix: 1.80 (0.20), residues: 753 sheet: 0.85 (0.15), residues: 1287 loop : -1.07 (0.13), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.001 TRP E 36 HIS 0.008 0.001 HIS F 100 PHE 0.015 0.001 PHE H 86 TYR 0.027 0.001 TYR H 904 ARG 0.005 0.000 ARG A 72 Details of bonding type rmsd link_NAG-ASN : bond 0.00283 ( 33) link_NAG-ASN : angle 1.56652 ( 99) hydrogen bonds : bond 0.04522 ( 1303) hydrogen bonds : angle 4.66396 ( 3630) SS BOND : bond 0.00299 ( 17) SS BOND : angle 1.13103 ( 34) covalent geometry : bond 0.00352 (34302) covalent geometry : angle 0.51398 (46710) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8400 Ramachandran restraints generated. 4200 Oldfield, 0 Emsley, 4200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8400 Ramachandran restraints generated. 4200 Oldfield, 0 Emsley, 4200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 3702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 273 time to evaluate : 3.942 Fit side-chains REVERT: H 740 MET cc_start: 0.8636 (OUTLIER) cc_final: 0.8419 (ttt) REVERT: E 81 MET cc_start: 0.6333 (tmm) cc_final: 0.5838 (tmm) REVERT: E 118 GLN cc_start: 0.7586 (mm-40) cc_final: 0.7192 (mm-40) REVERT: G 81 MET cc_start: 0.5984 (tmm) cc_final: 0.5270 (tmm) REVERT: G 118 GLN cc_start: 0.7319 (mm-40) cc_final: 0.7023 (mm-40) REVERT: I 55 LYS cc_start: 0.7919 (ptpp) cc_final: 0.7706 (pttm) REVERT: C 900 MET cc_start: 0.9158 (mtp) cc_final: 0.8919 (mtm) REVERT: C 1144 GLU cc_start: 0.7323 (tp30) cc_final: 0.7112 (tp30) REVERT: A 81 MET cc_start: 0.6205 (tmm) cc_final: 0.5840 (tmm) outliers start: 75 outliers final: 68 residues processed: 334 average time/residue: 0.4504 time to fit residues: 254.3405 Evaluate side-chains 335 residues out of total 3702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 266 time to evaluate : 3.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain H residue 208 THR Chi-restraints excluded: chain H residue 227 VAL Chi-restraints excluded: chain H residue 229 LEU Chi-restraints excluded: chain H residue 307 THR Chi-restraints excluded: chain H residue 340 GLU Chi-restraints excluded: chain H residue 588 THR Chi-restraints excluded: chain H residue 602 THR Chi-restraints excluded: chain H residue 720 ILE Chi-restraints excluded: chain H residue 740 MET Chi-restraints excluded: chain H residue 896 ILE Chi-restraints excluded: chain H residue 916 LEU Chi-restraints excluded: chain H residue 1061 VAL Chi-restraints excluded: chain H residue 1068 VAL Chi-restraints excluded: chain H residue 1128 VAL Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 72 ARG Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 111 SER Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 94 SER Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain J residue 108 THR Chi-restraints excluded: chain J residue 130 VAL Chi-restraints excluded: chain J residue 159 VAL Chi-restraints excluded: chain J residue 208 THR Chi-restraints excluded: chain J residue 401 VAL Chi-restraints excluded: chain J residue 512 VAL Chi-restraints excluded: chain J residue 551 VAL Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 588 THR Chi-restraints excluded: chain J residue 705 VAL Chi-restraints excluded: chain J residue 723 THR Chi-restraints excluded: chain J residue 856 ASN Chi-restraints excluded: chain J residue 934 ILE Chi-restraints excluded: chain J residue 1068 VAL Chi-restraints excluded: chain J residue 1128 VAL Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1061 VAL Chi-restraints excluded: chain C residue 1068 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain B residue 72 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 377 optimal weight: 0.9980 chunk 164 optimal weight: 3.9990 chunk 323 optimal weight: 0.6980 chunk 222 optimal weight: 2.9990 chunk 421 optimal weight: 10.0000 chunk 292 optimal weight: 0.5980 chunk 60 optimal weight: 0.6980 chunk 374 optimal weight: 0.8980 chunk 349 optimal weight: 3.9990 chunk 127 optimal weight: 9.9990 chunk 27 optimal weight: 6.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 540 ASN ** E 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 540 ASN ** G 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 71 ASN C 540 ASN ** A 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 71 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.193067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.158979 restraints weight = 48422.404| |-----------------------------------------------------------------------------| r_work (start): 0.3813 rms_B_bonded: 2.19 r_work: 0.3570 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3503 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 34352 Z= 0.105 Angle : 0.499 12.136 46843 Z= 0.255 Chirality : 0.044 0.279 5394 Planarity : 0.004 0.045 5961 Dihedral : 4.263 34.892 5265 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 2.05 % Allowed : 13.67 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % 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: 0.17 (0.13), residues: 4200 helix: 1.89 (0.20), residues: 756 sheet: 0.86 (0.15), residues: 1287 loop : -1.05 (0.13), residues: 2157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP E 36 HIS 0.008 0.001 HIS F 100 PHE 0.027 0.001 PHE A 113 TYR 0.021 0.001 TYR H 904 ARG 0.006 0.000 ARG A 72 Details of bonding type rmsd link_NAG-ASN : bond 0.00286 ( 33) link_NAG-ASN : angle 1.49017 ( 99) hydrogen bonds : bond 0.03981 ( 1303) hydrogen bonds : angle 4.56542 ( 3630) SS BOND : bond 0.00196 ( 17) SS BOND : angle 0.92808 ( 34) covalent geometry : bond 0.00239 (34302) covalent geometry : angle 0.49464 (46710) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17257.45 seconds wall clock time: 297 minutes 33.55 seconds (17853.55 seconds total)