Starting phenix.real_space_refine on Tue Jun 10 00:08:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7bsp_30163/06_2025/7bsp_30163_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7bsp_30163/06_2025/7bsp_30163.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7bsp_30163/06_2025/7bsp_30163.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7bsp_30163/06_2025/7bsp_30163.map" model { file = "/net/cci-nas-00/data/ceres_data/7bsp_30163/06_2025/7bsp_30163_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7bsp_30163/06_2025/7bsp_30163_trim.cif" } resolution = 4.0 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 58 5.16 5 C 7112 2.51 5 N 1807 2.21 5 O 2030 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 11010 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 8311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1028, 8311 Classifications: {'peptide': 1028} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 25, 'TRANS': 1002} Chain breaks: 3 Chain: "C" Number of atoms: 2613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2613 Classifications: {'peptide': 324} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 25, 'TRANS': 298} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ACP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 6.53, per 1000 atoms: 0.59 Number of scatterers: 11010 At special positions: 0 Unit cell: (107.07, 87.15, 161.02, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 58 16.00 P 3 15.00 O 2030 8.00 N 1807 7.00 C 7112 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS C 91 " - pdb=" SG CYS C 104 " distance=2.03 Simple disulfide: pdb=" SG CYS C 94 " - pdb=" SG CYS C 102 " distance=2.03 Simple disulfide: pdb=" SG CYS C 157 " - pdb=" SG CYS C 171 " 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=1, symmetry=0 Links applied BETA1-3 " NAG B 1 " - " NAG B 2 " NAG-ASN " NAG B 1 " - " ASN C 180 " " NAG C 403 " - " ASN C 294 " " NAG C 404 " - " ASN C 107 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.89 Conformation dependent library (CDL) restraints added in 1.4 seconds 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2562 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 12 sheets defined 44.3% alpha, 9.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.24 Creating SS restraints... Processing helix chain 'A' and resid 54 through 65 removed outlier: 4.360A pdb=" N PHE A 61 " --> pdb=" O PRO A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 82 removed outlier: 3.646A pdb=" N PHE A 72 " --> pdb=" O ALA A 68 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N LEU A 73 " --> pdb=" O ASN A 69 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE A 76 " --> pdb=" O PHE A 72 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLN A 79 " --> pdb=" O ILE A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 121 Proline residue: A 94 - end of helix removed outlier: 4.232A pdb=" N VAL A 98 " --> pdb=" O PRO A 94 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE A 99 " --> pdb=" O LEU A 95 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR A 102 " --> pdb=" O VAL A 98 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LYS A 105 " --> pdb=" O VAL A 101 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ASP A 110 " --> pdb=" O GLN A 106 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N ARG A 113 " --> pdb=" O GLU A 109 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N HIS A 114 " --> pdb=" O ASP A 110 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLU A 119 " --> pdb=" O ARG A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 194 Processing helix chain 'A' and resid 270 through 275 removed outlier: 3.736A pdb=" N TYR A 274 " --> pdb=" O ALA A 271 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N GLN A 275 " --> pdb=" O LEU A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 296 removed outlier: 3.911A pdb=" N LEU A 292 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ILE A 293 " --> pdb=" O ASN A 289 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL A 294 " --> pdb=" O ALA A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 314 removed outlier: 3.791A pdb=" N CYS A 306 " --> pdb=" O LYS A 302 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LEU A 309 " --> pdb=" O VAL A 305 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N LYS A 310 " --> pdb=" O CYS A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 333 removed outlier: 3.515A pdb=" N GLU A 333 " --> pdb=" O GLN A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 345 removed outlier: 4.078A pdb=" N PHE A 344 " --> pdb=" O MET A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 350 removed outlier: 3.689A pdb=" N VAL A 349 " --> pdb=" O LEU A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 355 Processing helix chain 'A' and resid 358 through 370 removed outlier: 3.725A pdb=" N THR A 362 " --> pdb=" O SER A 358 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N GLU A 364 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LYS A 367 " --> pdb=" O VAL A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 377 removed outlier: 3.552A pdb=" N ASP A 377 " --> pdb=" O PHE A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 400 removed outlier: 4.181A pdb=" N GLU A 398 " --> pdb=" O ASP A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 414 removed outlier: 3.757A pdb=" N THR A 413 " --> pdb=" O ASP A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 468 Processing helix chain 'A' and resid 495 through 508 removed outlier: 3.640A pdb=" N ILE A 499 " --> pdb=" O SER A 495 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N LEU A 501 " --> pdb=" O ASP A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 569 Processing helix chain 'A' and resid 574 through 576 No H-bonds generated for 'chain 'A' and resid 574 through 576' Processing helix chain 'A' and resid 577 through 591 removed outlier: 3.761A pdb=" N THR A 581 " --> pdb=" O GLU A 577 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL A 583 " --> pdb=" O GLU A 579 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N HIS A 584 " --> pdb=" O LEU A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 617 removed outlier: 3.553A pdb=" N GLU A 609 " --> pdb=" O PRO A 605 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ARG A 610 " --> pdb=" O ASP A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 635 removed outlier: 3.583A pdb=" N VAL A 632 " --> pdb=" O LYS A 628 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE A 633 " --> pdb=" O MET A 629 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ASP A 635 " --> pdb=" O LYS A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 658 through 666 removed outlier: 3.767A pdb=" N HIS A 664 " --> pdb=" O ILE A 660 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ALA A 665 " --> pdb=" O GLU A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 677 through 689 removed outlier: 3.669A pdb=" N TYR A 686 " --> pdb=" O LYS A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 724 removed outlier: 3.901A pdb=" N ASP A 713 " --> pdb=" O GLU A 709 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N TYR A 722 " --> pdb=" O LEU A 718 " (cutoff:3.500A) Processing helix chain 'A' and resid 752 through 762 removed outlier: 3.806A pdb=" N SER A 757 " --> pdb=" O GLY A 753 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE A 759 " --> pdb=" O THR A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 780 removed outlier: 3.797A pdb=" N GLN A 777 " --> pdb=" O SER A 773 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE A 778 " --> pdb=" O ILE A 774 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N CYS A 779 " --> pdb=" O PHE A 775 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N MET A 780 " --> pdb=" O LEU A 776 " (cutoff:3.500A) Processing helix chain 'A' and resid 793 through 804 removed outlier: 4.616A pdb=" N VAL A 799 " --> pdb=" O LYS A 795 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 819 No H-bonds generated for 'chain 'A' and resid 817 through 819' Processing helix chain 'A' and resid 820 through 825 removed outlier: 3.670A pdb=" N LEU A 825 " --> pdb=" O VAL A 821 " (cutoff:3.500A) Processing helix chain 'A' and resid 853 through 860 removed outlier: 4.298A pdb=" N LYS A 857 " --> pdb=" O LYS A 853 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU A 859 " --> pdb=" O LEU A 855 " (cutoff:3.500A) Processing helix chain 'A' and resid 864 through 869 Processing helix chain 'A' and resid 870 through 875 Processing helix chain 'A' and resid 875 through 880 Processing helix chain 'A' and resid 880 through 885 removed outlier: 3.738A pdb=" N PHE A 884 " --> pdb=" O LYS A 880 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 891 Processing helix chain 'A' and resid 905 through 914 removed outlier: 4.035A pdb=" N MET A 910 " --> pdb=" O ALA A 906 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N TYR A 911 " --> pdb=" O TYR A 907 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N ASN A 912 " --> pdb=" O LEU A 908 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ILE A 913 " --> pdb=" O THR A 909 " (cutoff:3.500A) Processing helix chain 'A' and resid 917 through 926 removed outlier: 3.657A pdb=" N TYR A 923 " --> pdb=" O PRO A 919 " (cutoff:3.500A) Processing helix chain 'A' and resid 931 through 937 removed outlier: 3.832A pdb=" N THR A 936 " --> pdb=" O ILE A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 948 through 951 Processing helix chain 'A' and resid 952 through 976 removed outlier: 3.604A pdb=" N LEU A 957 " --> pdb=" O LEU A 953 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR A 958 " --> pdb=" O GLY A 954 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N PHE A 965 " --> pdb=" O PHE A 961 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N PHE A 970 " --> pdb=" O GLU A 966 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE A 971 " --> pdb=" O GLY A 967 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N PHE A 976 " --> pdb=" O PHE A 972 " (cutoff:3.500A) Processing helix chain 'A' and resid 977 through 979 No H-bonds generated for 'chain 'A' and resid 977 through 979' Processing helix chain 'A' and resid 993 through 1005 removed outlier: 3.938A pdb=" N ILE A 998 " --> pdb=" O THR A 994 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL A 999 " --> pdb=" O PHE A 995 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N LEU A1003 " --> pdb=" O VAL A 999 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE A1005 " --> pdb=" O THR A1001 " (cutoff:3.500A) Processing helix chain 'A' and resid 1005 through 1013 removed outlier: 3.619A pdb=" N LEU A1009 " --> pdb=" O PHE A1005 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N LEU A1011 " --> pdb=" O VAL A1007 " (cutoff:3.500A) Processing helix chain 'A' and resid 1019 through 1042 removed outlier: 3.704A pdb=" N HIS A1023 " --> pdb=" O THR A1019 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N TRP A1027 " --> pdb=" O HIS A1023 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ALA A1031 " --> pdb=" O TRP A1027 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N PHE A1032 " --> pdb=" O GLY A1028 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N PHE A1035 " --> pdb=" O ALA A1031 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N PHE A1038 " --> pdb=" O VAL A1034 " (cutoff:3.500A) Processing helix chain 'A' and resid 1055 through 1061 Processing helix chain 'A' and resid 1063 through 1079 removed outlier: 3.825A pdb=" N TRP A1067 " --> pdb=" O SER A1063 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LEU A1068 " --> pdb=" O VAL A1064 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ALA A1069 " --> pdb=" O SER A1065 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU A1072 " --> pdb=" O LEU A1068 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N PHE A1075 " --> pdb=" O ILE A1071 " (cutoff:3.500A) Processing helix chain 'A' and resid 1081 through 1090 removed outlier: 3.582A pdb=" N ILE A1085 " --> pdb=" O GLU A1081 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N VAL A1086 " --> pdb=" O ILE A1082 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 74 Proline residue: C 52 - end of helix removed outlier: 3.669A pdb=" N PHE C 55 " --> pdb=" O LEU C 51 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ILE C 57 " --> pdb=" O ILE C 53 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LEU C 59 " --> pdb=" O PHE C 55 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE C 60 " --> pdb=" O ILE C 56 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ILE C 62 " --> pdb=" O GLY C 58 " (cutoff:3.500A) Proline residue: C 63 - end of helix removed outlier: 3.811A pdb=" N GLY C 67 " --> pdb=" O PRO C 63 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N THR C 71 " --> pdb=" O GLY C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 95 Processing helix chain 'C' and resid 131 through 136 removed outlier: 3.515A pdb=" N LYS C 136 " --> pdb=" O ARG C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 144 removed outlier: 3.526A pdb=" N LEU C 143 " --> pdb=" O ASP C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 152 removed outlier: 3.818A pdb=" N LEU C 151 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ASN C 152 " --> pdb=" O SER C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 177 Processing helix chain 'C' and resid 207 through 212 removed outlier: 3.503A pdb=" N VAL C 212 " --> pdb=" O THR C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 243 Processing helix chain 'C' and resid 246 through 250 removed outlier: 3.735A pdb=" N ASN C 250 " --> pdb=" O PRO C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 262 Processing helix chain 'C' and resid 323 through 333 Processing helix chain 'C' and resid 335 through 349 removed outlier: 3.769A pdb=" N LEU C 339 " --> pdb=" O ILE C 335 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N VAL C 341 " --> pdb=" O PHE C 337 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 124 through 128 removed outlier: 3.583A pdb=" N LYS A 136 " --> pdb=" O VAL A 125 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 146 through 150 removed outlier: 3.681A pdb=" N VAL A 149 " --> pdb=" O ILE A 257 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER A 163 " --> pdb=" O TYR A 258 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 159 through 160 removed outlier: 3.517A pdb=" N LEU A 245 " --> pdb=" O LEU A 159 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 185 through 188 removed outlier: 3.527A pdb=" N HIS A 187 " --> pdb=" O CYS A 171 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N CYS A 171 " --> pdb=" O HIS A 187 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N THR A 250 " --> pdb=" O THR A 174 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 224 through 227 removed outlier: 3.891A pdb=" N ILE A 227 " --> pdb=" O VAL A 235 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL A 235 " --> pdb=" O ILE A 227 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 381 through 382 removed outlier: 3.665A pdb=" N GLU A 387 " --> pdb=" O ASP A 382 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 390 through 391 removed outlier: 6.198A pdb=" N TYR A 405 " --> pdb=" O LEU A 812 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N ILE A 814 " --> pdb=" O TYR A 405 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N PHE A 407 " --> pdb=" O ILE A 814 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N VAL A 406 " --> pdb=" O TRP A 671 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 420 through 421 removed outlier: 3.659A pdb=" N GLU A 420 " --> pdb=" O GLU A 649 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU A 649 " --> pdb=" O GLU A 420 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 420 through 421 removed outlier: 3.659A pdb=" N GLU A 420 " --> pdb=" O GLU A 649 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU A 649 " --> pdb=" O GLU A 420 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N LEU A 642 " --> pdb=" O PHE A 600 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N PHE A 600 " --> pdb=" O LEU A 642 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N HIS A 536 " --> pdb=" O ILE A 550 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N LYS A 552 " --> pdb=" O LEU A 534 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N LEU A 534 " --> pdb=" O LYS A 552 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 698 through 699 removed outlier: 6.391A pdb=" N LEU A 698 " --> pdb=" O ILE A 750 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 77 through 79 removed outlier: 5.826A pdb=" N TYR C 122 " --> pdb=" O LEU C 272 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N LEU C 272 " --> pdb=" O TYR C 122 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 106 through 110 removed outlier: 5.886A pdb=" N ARG C 290 " --> pdb=" O ILE C 188 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ILE C 188 " --> pdb=" O ARG C 290 " (cutoff:3.500A) 322 hydrogen bonds defined for protein. 891 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.52 Time building geometry restraints manager: 3.42 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: 3462 1.34 - 1.46: 1988 1.46 - 1.57: 5723 1.57 - 1.69: 6 1.69 - 1.81: 89 Bond restraints: 11268 Sorted by residual: bond pdb=" O2B ACP A1101 " pdb=" PB ACP A1101 " ideal model delta sigma weight residual 1.507 1.609 -0.102 2.00e-02 2.50e+03 2.62e+01 bond pdb=" O3A ACP A1101 " pdb=" PB ACP A1101 " ideal model delta sigma weight residual 1.698 1.606 0.092 2.00e-02 2.50e+03 2.10e+01 bond pdb=" C4 ACP A1101 " pdb=" C5 ACP A1101 " ideal model delta sigma weight residual 1.386 1.463 -0.077 2.00e-02 2.50e+03 1.50e+01 bond pdb=" O3G ACP A1101 " pdb=" PG ACP A1101 " ideal model delta sigma weight residual 1.532 1.606 -0.074 2.00e-02 2.50e+03 1.37e+01 bond pdb=" O2G ACP A1101 " pdb=" PG ACP A1101 " ideal model delta sigma weight residual 1.537 1.608 -0.071 2.00e-02 2.50e+03 1.27e+01 ... (remaining 11263 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.32: 15070 2.32 - 4.64: 190 4.64 - 6.96: 12 6.96 - 9.27: 3 9.27 - 11.59: 3 Bond angle restraints: 15278 Sorted by residual: angle pdb=" N LYS A 880 " pdb=" CA LYS A 880 " pdb=" C LYS A 880 " ideal model delta sigma weight residual 111.82 107.26 4.56 1.16e+00 7.43e-01 1.54e+01 angle pdb=" O1B ACP A1101 " pdb=" PB ACP A1101 " pdb=" O2B ACP A1101 " ideal model delta sigma weight residual 119.60 108.01 11.59 3.00e+00 1.11e-01 1.49e+01 angle pdb=" C3B ACP A1101 " pdb=" PB ACP A1101 " pdb=" O3A ACP A1101 " ideal model delta sigma weight residual 98.05 109.14 -11.09 3.00e+00 1.11e-01 1.37e+01 angle pdb=" C ILE A1044 " pdb=" N TRP A1045 " pdb=" CA TRP A1045 " ideal model delta sigma weight residual 120.44 124.65 -4.21 1.30e+00 5.92e-01 1.05e+01 angle pdb=" C2 ACP A1101 " pdb=" N3 ACP A1101 " pdb=" C4 ACP A1101 " ideal model delta sigma weight residual 111.73 121.24 -9.51 3.00e+00 1.11e-01 1.00e+01 ... (remaining 15273 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.42: 6355 23.42 - 46.85: 347 46.85 - 70.27: 32 70.27 - 93.69: 22 93.69 - 117.11: 13 Dihedral angle restraints: 6769 sinusoidal: 2800 harmonic: 3969 Sorted by residual: dihedral pdb=" CA TRP A1045 " pdb=" C TRP A1045 " pdb=" N PRO A1046 " pdb=" CA PRO A1046 " ideal model delta harmonic sigma weight residual 180.00 -155.77 -24.23 0 5.00e+00 4.00e-02 2.35e+01 dihedral pdb=" CA PHE A 347 " pdb=" C PHE A 347 " pdb=" N MET A 348 " pdb=" CA MET A 348 " ideal model delta harmonic sigma weight residual 180.00 158.71 21.29 0 5.00e+00 4.00e-02 1.81e+01 dihedral pdb=" C2 NAG B 2 " pdb=" C3 NAG B 2 " pdb=" C4 NAG B 2 " pdb=" O4 NAG B 2 " ideal model delta sinusoidal sigma weight residual 175.11 58.00 117.11 1 3.00e+01 1.11e-03 1.55e+01 ... (remaining 6766 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 1632 0.086 - 0.173: 86 0.173 - 0.259: 4 0.259 - 0.346: 0 0.346 - 0.432: 1 Chirality restraints: 1723 Sorted by residual: chirality pdb=" C1 NAG B 2 " pdb=" O3 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.29 -0.11 2.00e-02 2.50e+03 2.77e+01 chirality pdb=" C1 NAG B 1 " pdb=" ND2 ASN C 180 " pdb=" C2 NAG B 1 " pdb=" O5 NAG B 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.97 -0.43 2.00e-01 2.50e+01 4.67e+00 chirality pdb=" C2 NAG C 403 " pdb=" C1 NAG C 403 " pdb=" C3 NAG C 403 " pdb=" N2 NAG C 403 " both_signs ideal model delta sigma weight residual False -2.49 -2.25 -0.24 2.00e-01 2.50e+01 1.45e+00 ... (remaining 1720 not shown) Planarity restraints: 1922 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 2 " -0.320 2.00e-02 2.50e+03 2.71e-01 9.21e+02 pdb=" C7 NAG B 2 " 0.081 2.00e-02 2.50e+03 pdb=" C8 NAG B 2 " -0.183 2.00e-02 2.50e+03 pdb=" N2 NAG B 2 " 0.472 2.00e-02 2.50e+03 pdb=" O7 NAG B 2 " -0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 404 " -0.309 2.00e-02 2.50e+03 2.65e-01 8.81e+02 pdb=" C7 NAG C 404 " 0.068 2.00e-02 2.50e+03 pdb=" C8 NAG C 404 " -0.001 2.00e-02 2.50e+03 pdb=" N2 NAG C 404 " 0.455 2.00e-02 2.50e+03 pdb=" O7 NAG C 404 " -0.213 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 403 " -0.304 2.00e-02 2.50e+03 2.61e-01 8.49e+02 pdb=" C7 NAG C 403 " 0.078 2.00e-02 2.50e+03 pdb=" C8 NAG C 403 " -0.177 2.00e-02 2.50e+03 pdb=" N2 NAG C 403 " 0.455 2.00e-02 2.50e+03 pdb=" O7 NAG C 403 " -0.051 2.00e-02 2.50e+03 ... (remaining 1919 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 165 2.52 - 3.12: 10645 3.12 - 3.71: 15519 3.71 - 4.31: 23834 4.31 - 4.90: 38303 Nonbonded interactions: 88466 Sorted by model distance: nonbonded pdb=" OG SER A1063 " pdb=" OG1 THR A1066 " model vdw 1.928 3.040 nonbonded pdb=" OH TYR A 879 " pdb=" OE1 GLU A 966 " model vdw 1.943 3.040 nonbonded pdb=" O ASP A 409 " pdb=" OG1 THR A 413 " model vdw 1.949 3.040 nonbonded pdb=" OD1 ASP A 904 " pdb=" N ALA A 905 " model vdw 1.968 3.120 nonbonded pdb=" OG1 THR A 553 " pdb=" O ASP A 557 " model vdw 1.989 3.040 ... (remaining 88461 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 27.220 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.768 11276 Z= 0.761 Angle : 0.667 11.592 15296 Z= 0.371 Chirality : 0.042 0.432 1723 Planarity : 0.012 0.271 1919 Dihedral : 15.681 117.114 4198 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 53.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.61 % Favored : 85.39 % Rotamer: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -7.27 (0.14), residues: 1342 helix: -5.21 (0.07), residues: 500 sheet: -4.22 (0.32), residues: 166 loop : -4.75 (0.17), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1020 HIS 0.005 0.001 HIS A 864 PHE 0.016 0.001 PHE A 978 TYR 0.011 0.001 TYR A1054 ARG 0.003 0.000 ARG C 309 Details of bonding type rmsd link_NAG-ASN : bond 0.00582 ( 3) link_NAG-ASN : angle 3.90877 ( 9) hydrogen bonds : bond 0.29450 ( 322) hydrogen bonds : angle 12.64686 ( 891) SS BOND : bond 0.00272 ( 3) SS BOND : angle 1.09567 ( 6) link_BETA1-3 : bond 0.00386 ( 1) link_BETA1-3 : angle 1.46149 ( 3) covalent geometry : bond 0.00496 (11268) covalent geometry : angle 0.66015 (15278) Misc. bond : bond 0.76832 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 225 time to evaluate : 1.263 Fit side-chains REVERT: A 58 LYS cc_start: 0.9049 (tttm) cc_final: 0.8752 (tppt) REVERT: A 159 LEU cc_start: 0.9556 (mt) cc_final: 0.9299 (mt) REVERT: A 266 MET cc_start: 0.8505 (mmt) cc_final: 0.8214 (mmt) REVERT: A 431 TYR cc_start: 0.8498 (t80) cc_final: 0.8199 (t80) REVERT: A 678 MET cc_start: 0.9372 (tmm) cc_final: 0.9054 (tmm) REVERT: A 885 ILE cc_start: 0.9515 (tp) cc_final: 0.9233 (tp) REVERT: A 970 PHE cc_start: 0.9076 (m-10) cc_final: 0.8808 (m-80) REVERT: C 158 GLU cc_start: 0.7925 (mm-30) cc_final: 0.7616 (tp30) REVERT: C 310 MET cc_start: 0.8209 (tmm) cc_final: 0.7100 (tmm) outliers start: 0 outliers final: 0 residues processed: 225 average time/residue: 0.2374 time to fit residues: 77.7737 Evaluate side-chains 160 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 1.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 113 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 34 optimal weight: 5.9990 chunk 68 optimal weight: 6.9990 chunk 54 optimal weight: 0.7980 chunk 105 optimal weight: 2.9990 chunk 40 optimal weight: 10.0000 chunk 63 optimal weight: 6.9990 chunk 78 optimal weight: 0.0470 chunk 121 optimal weight: 0.7980 overall best weight: 0.9282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 275 GLN A 641 ASN A 794 GLN A 862 HIS A 892 GLN A 928 GLN ** A 929 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1089 ASN C 130 ASN ** C 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 302 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.113596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.085488 restraints weight = 19021.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.087338 restraints weight = 11994.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.087863 restraints weight = 8765.392| |-----------------------------------------------------------------------------| r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.1919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11276 Z= 0.173 Angle : 0.767 10.512 15296 Z= 0.391 Chirality : 0.049 0.269 1723 Planarity : 0.005 0.035 1919 Dihedral : 11.435 109.873 1580 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 14.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.24 % Favored : 90.76 % Rotamer: Outliers : 1.33 % Allowed : 11.46 % Favored : 87.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.23 (0.18), residues: 1342 helix: -3.45 (0.16), residues: 525 sheet: -3.46 (0.33), residues: 182 loop : -3.45 (0.21), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 376 HIS 0.012 0.001 HIS C 302 PHE 0.018 0.002 PHE A 915 TYR 0.014 0.002 TYR A 608 ARG 0.017 0.001 ARG A 723 Details of bonding type rmsd link_NAG-ASN : bond 0.00304 ( 3) link_NAG-ASN : angle 3.62478 ( 9) hydrogen bonds : bond 0.05967 ( 322) hydrogen bonds : angle 6.73752 ( 891) SS BOND : bond 0.00480 ( 3) SS BOND : angle 1.26702 ( 6) link_BETA1-3 : bond 0.00423 ( 1) link_BETA1-3 : angle 3.49625 ( 3) covalent geometry : bond 0.00387 (11268) covalent geometry : angle 0.76058 (15278) Misc. bond : bond 0.00164 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 224 time to evaluate : 1.361 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 LYS cc_start: 0.8950 (tttm) cc_final: 0.8540 (tppt) REVERT: A 118 ASN cc_start: 0.8793 (t0) cc_final: 0.8539 (t0) REVERT: A 159 LEU cc_start: 0.9495 (mt) cc_final: 0.9228 (mt) REVERT: A 365 MET cc_start: 0.9043 (tpp) cc_final: 0.8796 (mmm) REVERT: A 419 MET cc_start: 0.8689 (mmp) cc_final: 0.8214 (mmp) REVERT: A 714 ARG cc_start: 0.7923 (mtp180) cc_final: 0.7670 (mmm-85) REVERT: A 885 ILE cc_start: 0.9527 (tp) cc_final: 0.9284 (tp) REVERT: A 992 ASN cc_start: 0.8551 (p0) cc_final: 0.7391 (t0) REVERT: C 130 ASN cc_start: 0.8867 (OUTLIER) cc_final: 0.8548 (p0) REVERT: C 310 MET cc_start: 0.8150 (tmm) cc_final: 0.7308 (tmm) outliers start: 16 outliers final: 9 residues processed: 231 average time/residue: 0.2124 time to fit residues: 72.2213 Evaluate side-chains 182 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 172 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 600 PHE Chi-restraints excluded: chain A residue 750 ILE Chi-restraints excluded: chain A residue 822 SER Chi-restraints excluded: chain A residue 898 SER Chi-restraints excluded: chain C residue 126 ASN Chi-restraints excluded: chain C residue 130 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 33 optimal weight: 3.9990 chunk 25 optimal weight: 10.0000 chunk 111 optimal weight: 3.9990 chunk 11 optimal weight: 5.9990 chunk 14 optimal weight: 9.9990 chunk 22 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 chunk 70 optimal weight: 0.0370 chunk 57 optimal weight: 10.0000 chunk 100 optimal weight: 0.7980 chunk 95 optimal weight: 4.9990 overall best weight: 2.5664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN A 584 HIS A 716 HIS ** A 929 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 35 GLN C 211 ASN C 216 ASN C 302 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.111631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.084147 restraints weight = 19416.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.086235 restraints weight = 14367.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.086683 restraints weight = 9431.255| |-----------------------------------------------------------------------------| r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 11276 Z= 0.216 Angle : 0.726 9.047 15296 Z= 0.367 Chirality : 0.048 0.283 1723 Planarity : 0.004 0.037 1919 Dihedral : 9.739 106.649 1580 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.72 % Favored : 91.28 % Rotamer: Outliers : 3.32 % Allowed : 15.37 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.31 (0.20), residues: 1342 helix: -2.59 (0.18), residues: 534 sheet: -2.97 (0.35), residues: 180 loop : -3.02 (0.23), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 323 HIS 0.010 0.001 HIS C 302 PHE 0.016 0.002 PHE C 214 TYR 0.024 0.001 TYR A 608 ARG 0.005 0.000 ARG A 133 Details of bonding type rmsd link_NAG-ASN : bond 0.00232 ( 3) link_NAG-ASN : angle 3.33131 ( 9) hydrogen bonds : bond 0.04716 ( 322) hydrogen bonds : angle 6.00033 ( 891) SS BOND : bond 0.00395 ( 3) SS BOND : angle 1.37873 ( 6) link_BETA1-3 : bond 0.00913 ( 1) link_BETA1-3 : angle 3.45297 ( 3) covalent geometry : bond 0.00508 (11268) covalent geometry : angle 0.71938 (15278) Misc. bond : bond 0.00054 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 191 time to evaluate : 1.198 Fit side-chains revert: symmetry clash REVERT: A 58 LYS cc_start: 0.9008 (tttm) cc_final: 0.8585 (tppt) REVERT: A 118 ASN cc_start: 0.8833 (t0) cc_final: 0.8500 (t0) REVERT: A 266 MET cc_start: 0.8855 (mmm) cc_final: 0.8583 (mmm) REVERT: A 270 MET cc_start: 0.9135 (tmm) cc_final: 0.8929 (ppp) REVERT: A 365 MET cc_start: 0.9277 (tpp) cc_final: 0.9032 (mmm) REVERT: A 419 MET cc_start: 0.8692 (mmp) cc_final: 0.8263 (mmp) REVERT: A 431 TYR cc_start: 0.8364 (t80) cc_final: 0.8156 (t80) REVERT: A 616 ILE cc_start: 0.9539 (pt) cc_final: 0.9229 (mt) REVERT: A 678 MET cc_start: 0.9199 (tmm) cc_final: 0.8716 (tmm) REVERT: A 781 LYS cc_start: 0.8940 (mtpt) cc_final: 0.8534 (mtpt) REVERT: A 877 PHE cc_start: 0.9035 (OUTLIER) cc_final: 0.8157 (t80) REVERT: A 992 ASN cc_start: 0.8597 (p0) cc_final: 0.7400 (t0) REVERT: C 74 ASN cc_start: 0.8018 (t0) cc_final: 0.7567 (t0) REVERT: C 75 ILE cc_start: 0.8926 (OUTLIER) cc_final: 0.8701 (mm) REVERT: C 176 ASN cc_start: 0.8757 (t0) cc_final: 0.8523 (t0) REVERT: C 310 MET cc_start: 0.8345 (tmm) cc_final: 0.7268 (tmm) outliers start: 40 outliers final: 26 residues processed: 216 average time/residue: 0.1907 time to fit residues: 62.1500 Evaluate side-chains 200 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 172 time to evaluate : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 114 HIS Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 600 PHE Chi-restraints excluded: chain A residue 646 THR Chi-restraints excluded: chain A residue 750 ILE Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 822 SER Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 877 PHE Chi-restraints excluded: chain A residue 898 SER Chi-restraints excluded: chain A residue 1077 SER Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 126 ASN Chi-restraints excluded: chain C residue 295 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 15 optimal weight: 9.9990 chunk 99 optimal weight: 1.9990 chunk 31 optimal weight: 0.0770 chunk 105 optimal weight: 0.6980 chunk 118 optimal weight: 6.9990 chunk 32 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 41 optimal weight: 9.9990 chunk 103 optimal weight: 7.9990 chunk 80 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 overall best weight: 1.1542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 ASN A 929 HIS C 302 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.115027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.087231 restraints weight = 19057.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.089244 restraints weight = 10685.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.089725 restraints weight = 7395.737| |-----------------------------------------------------------------------------| r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11276 Z= 0.141 Angle : 0.654 9.089 15296 Z= 0.333 Chirality : 0.045 0.251 1723 Planarity : 0.004 0.039 1919 Dihedral : 8.450 105.811 1580 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % Rotamer: Outliers : 3.41 % Allowed : 17.19 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.58 (0.21), residues: 1342 helix: -1.86 (0.21), residues: 521 sheet: -2.65 (0.35), residues: 187 loop : -2.70 (0.23), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 323 HIS 0.014 0.001 HIS C 302 PHE 0.015 0.001 PHE A1075 TYR 0.030 0.001 TYR C 134 ARG 0.003 0.000 ARG A 940 Details of bonding type rmsd link_NAG-ASN : bond 0.00265 ( 3) link_NAG-ASN : angle 3.20406 ( 9) hydrogen bonds : bond 0.03928 ( 322) hydrogen bonds : angle 5.53530 ( 891) SS BOND : bond 0.00282 ( 3) SS BOND : angle 1.02841 ( 6) link_BETA1-3 : bond 0.00740 ( 1) link_BETA1-3 : angle 2.98310 ( 3) covalent geometry : bond 0.00326 (11268) covalent geometry : angle 0.64773 (15278) Misc. bond : bond 0.00039 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 219 time to evaluate : 1.198 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 LYS cc_start: 0.8996 (tttm) cc_final: 0.8601 (tppt) REVERT: A 118 ASN cc_start: 0.8747 (t0) cc_final: 0.8360 (t0) REVERT: A 212 GLU cc_start: 0.7551 (pp20) cc_final: 0.7092 (pp20) REVERT: A 266 MET cc_start: 0.8693 (mmm) cc_final: 0.8425 (mmm) REVERT: A 498 GLU cc_start: 0.9021 (pt0) cc_final: 0.8522 (pm20) REVERT: A 630 GLU cc_start: 0.9054 (tm-30) cc_final: 0.8680 (tm-30) REVERT: A 698 LEU cc_start: 0.9336 (mt) cc_final: 0.9047 (mp) REVERT: A 877 PHE cc_start: 0.9153 (OUTLIER) cc_final: 0.8320 (t80) REVERT: A 992 ASN cc_start: 0.8577 (p0) cc_final: 0.7480 (t0) REVERT: C 74 ASN cc_start: 0.7947 (t0) cc_final: 0.7381 (t0) REVERT: C 75 ILE cc_start: 0.8883 (OUTLIER) cc_final: 0.8678 (mm) REVERT: C 176 ASN cc_start: 0.8757 (t0) cc_final: 0.8543 (t0) REVERT: C 310 MET cc_start: 0.8293 (tmm) cc_final: 0.7270 (tmm) REVERT: C 329 TYR cc_start: 0.9028 (OUTLIER) cc_final: 0.8609 (m-10) outliers start: 41 outliers final: 22 residues processed: 246 average time/residue: 0.1931 time to fit residues: 71.1893 Evaluate side-chains 214 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 189 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 114 HIS Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 600 PHE Chi-restraints excluded: chain A residue 646 THR Chi-restraints excluded: chain A residue 711 LYS Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 822 SER Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 877 PHE Chi-restraints excluded: chain A residue 898 SER Chi-restraints excluded: chain A residue 1077 SER Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 126 ASN Chi-restraints excluded: chain C residue 256 ASP Chi-restraints excluded: chain C residue 329 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 28 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 chunk 98 optimal weight: 0.0470 chunk 8 optimal weight: 8.9990 chunk 129 optimal weight: 0.5980 chunk 128 optimal weight: 4.9990 chunk 49 optimal weight: 8.9990 chunk 6 optimal weight: 3.9990 chunk 133 optimal weight: 6.9990 chunk 70 optimal weight: 10.0000 chunk 92 optimal weight: 0.8980 overall best weight: 1.5082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 ASN A 517 ASN A 664 HIS C 302 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.115020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.086905 restraints weight = 19126.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.088523 restraints weight = 13874.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.089875 restraints weight = 8975.404| |-----------------------------------------------------------------------------| r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.3323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 11276 Z= 0.151 Angle : 0.652 9.085 15296 Z= 0.329 Chirality : 0.046 0.264 1723 Planarity : 0.004 0.040 1919 Dihedral : 8.088 103.039 1580 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.90 % Favored : 92.10 % Rotamer: Outliers : 3.82 % Allowed : 19.85 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.17 (0.22), residues: 1342 helix: -1.44 (0.22), residues: 523 sheet: -2.35 (0.36), residues: 187 loop : -2.57 (0.23), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 323 HIS 0.008 0.001 HIS C 302 PHE 0.015 0.001 PHE A1075 TYR 0.025 0.001 TYR A 431 ARG 0.005 0.000 ARG A 940 Details of bonding type rmsd link_NAG-ASN : bond 0.00190 ( 3) link_NAG-ASN : angle 3.08567 ( 9) hydrogen bonds : bond 0.03747 ( 322) hydrogen bonds : angle 5.28331 ( 891) SS BOND : bond 0.00318 ( 3) SS BOND : angle 1.02945 ( 6) link_BETA1-3 : bond 0.00794 ( 1) link_BETA1-3 : angle 2.86016 ( 3) covalent geometry : bond 0.00355 (11268) covalent geometry : angle 0.64696 (15278) Misc. bond : bond 0.00010 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 202 time to evaluate : 1.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 LYS cc_start: 0.9012 (tttm) cc_final: 0.8578 (tppt) REVERT: A 118 ASN cc_start: 0.8753 (t0) cc_final: 0.8334 (t0) REVERT: A 212 GLU cc_start: 0.7490 (pp20) cc_final: 0.7087 (pp20) REVERT: A 266 MET cc_start: 0.8637 (mmm) cc_final: 0.8424 (mmm) REVERT: A 498 GLU cc_start: 0.8985 (pt0) cc_final: 0.8422 (pm20) REVERT: A 523 GLU cc_start: 0.7812 (mm-30) cc_final: 0.7532 (mm-30) REVERT: A 696 GLU cc_start: 0.7103 (tm-30) cc_final: 0.6813 (tm-30) REVERT: A 877 PHE cc_start: 0.8999 (OUTLIER) cc_final: 0.8179 (t80) REVERT: A 940 ARG cc_start: 0.7809 (ttp-110) cc_final: 0.7484 (ttp-110) REVERT: A 992 ASN cc_start: 0.8665 (p0) cc_final: 0.7616 (t0) REVERT: C 74 ASN cc_start: 0.8085 (t0) cc_final: 0.7538 (t0) REVERT: C 215 ARG cc_start: 0.8562 (mmm160) cc_final: 0.8130 (mmt180) REVERT: C 310 MET cc_start: 0.8336 (tmm) cc_final: 0.7232 (tmm) REVERT: C 329 TYR cc_start: 0.8965 (OUTLIER) cc_final: 0.8391 (m-10) outliers start: 46 outliers final: 33 residues processed: 231 average time/residue: 0.1989 time to fit residues: 68.1165 Evaluate side-chains 216 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 181 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 114 HIS Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 600 PHE Chi-restraints excluded: chain A residue 646 THR Chi-restraints excluded: chain A residue 691 PHE Chi-restraints excluded: chain A residue 752 ASP Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 822 SER Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 877 PHE Chi-restraints excluded: chain A residue 898 SER Chi-restraints excluded: chain A residue 1077 SER Chi-restraints excluded: chain C residue 126 ASN Chi-restraints excluded: chain C residue 256 ASP Chi-restraints excluded: chain C residue 292 TRP Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 302 HIS Chi-restraints excluded: chain C residue 329 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 2 optimal weight: 0.5980 chunk 113 optimal weight: 10.0000 chunk 85 optimal weight: 5.9990 chunk 16 optimal weight: 7.9990 chunk 5 optimal weight: 0.4980 chunk 112 optimal weight: 0.6980 chunk 126 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 90 optimal weight: 3.9990 chunk 47 optimal weight: 8.9990 chunk 56 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 664 HIS ** C 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 302 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.115763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.088072 restraints weight = 19252.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.088827 restraints weight = 12950.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.089782 restraints weight = 9187.921| |-----------------------------------------------------------------------------| r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.3538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11276 Z= 0.126 Angle : 0.633 9.143 15296 Z= 0.319 Chirality : 0.044 0.245 1723 Planarity : 0.004 0.040 1919 Dihedral : 7.839 101.361 1580 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 3.74 % Allowed : 19.77 % Favored : 76.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.92 (0.22), residues: 1342 helix: -1.16 (0.22), residues: 522 sheet: -2.28 (0.36), residues: 191 loop : -2.47 (0.24), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 207 HIS 0.006 0.001 HIS C 302 PHE 0.015 0.001 PHE A 462 TYR 0.019 0.001 TYR A 431 ARG 0.003 0.000 ARG A 206 Details of bonding type rmsd link_NAG-ASN : bond 0.00212 ( 3) link_NAG-ASN : angle 3.07704 ( 9) hydrogen bonds : bond 0.03541 ( 322) hydrogen bonds : angle 5.16420 ( 891) SS BOND : bond 0.00279 ( 3) SS BOND : angle 0.88500 ( 6) link_BETA1-3 : bond 0.00808 ( 1) link_BETA1-3 : angle 2.83437 ( 3) covalent geometry : bond 0.00293 (11268) covalent geometry : angle 0.62722 (15278) Misc. bond : bond 0.00029 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 202 time to evaluate : 1.300 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 LYS cc_start: 0.9019 (tttm) cc_final: 0.8646 (tppt) REVERT: A 118 ASN cc_start: 0.8738 (t0) cc_final: 0.8268 (t0) REVERT: A 212 GLU cc_start: 0.7455 (pp20) cc_final: 0.7056 (pp20) REVERT: A 309 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8791 (mp) REVERT: A 498 GLU cc_start: 0.8823 (pt0) cc_final: 0.8322 (pm20) REVERT: A 523 GLU cc_start: 0.7815 (mm-30) cc_final: 0.7543 (mm-30) REVERT: A 678 MET cc_start: 0.9025 (tmm) cc_final: 0.8519 (tmm) REVERT: A 696 GLU cc_start: 0.7117 (tm-30) cc_final: 0.6721 (tm-30) REVERT: A 781 LYS cc_start: 0.8821 (mtpt) cc_final: 0.8280 (mtpp) REVERT: A 877 PHE cc_start: 0.8992 (OUTLIER) cc_final: 0.8163 (t80) REVERT: A 940 ARG cc_start: 0.7870 (ttp-110) cc_final: 0.7531 (ttp-110) REVERT: A 992 ASN cc_start: 0.8714 (p0) cc_final: 0.7816 (t0) REVERT: A 1053 MET cc_start: 0.8453 (mtp) cc_final: 0.8199 (mtp) REVERT: A 1076 ILE cc_start: 0.9485 (mt) cc_final: 0.9276 (mm) REVERT: C 74 ASN cc_start: 0.8122 (t0) cc_final: 0.7849 (t0) REVERT: C 255 GLU cc_start: 0.8833 (mm-30) cc_final: 0.8587 (mm-30) REVERT: C 310 MET cc_start: 0.8257 (tmm) cc_final: 0.7117 (tmm) REVERT: C 329 TYR cc_start: 0.8879 (OUTLIER) cc_final: 0.7996 (m-10) outliers start: 45 outliers final: 31 residues processed: 229 average time/residue: 0.2099 time to fit residues: 71.7677 Evaluate side-chains 225 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 191 time to evaluate : 1.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 114 HIS Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 600 PHE Chi-restraints excluded: chain A residue 646 THR Chi-restraints excluded: chain A residue 691 PHE Chi-restraints excluded: chain A residue 711 LYS Chi-restraints excluded: chain A residue 752 ASP Chi-restraints excluded: chain A residue 822 SER Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 877 PHE Chi-restraints excluded: chain A residue 898 SER Chi-restraints excluded: chain A residue 1077 SER Chi-restraints excluded: chain A residue 1087 LEU Chi-restraints excluded: chain C residue 126 ASN Chi-restraints excluded: chain C residue 242 MET Chi-restraints excluded: chain C residue 256 ASP Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 292 TRP Chi-restraints excluded: chain C residue 302 HIS Chi-restraints excluded: chain C residue 329 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 27 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 72 optimal weight: 5.9990 chunk 109 optimal weight: 7.9990 chunk 52 optimal weight: 5.9990 chunk 104 optimal weight: 3.9990 chunk 115 optimal weight: 9.9990 chunk 55 optimal weight: 7.9990 chunk 9 optimal weight: 5.9990 chunk 98 optimal weight: 0.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 ASN A 314 GLN ** A 888 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1051 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 302 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.112598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.084291 restraints weight = 19619.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.085955 restraints weight = 12941.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.086637 restraints weight = 8758.357| |-----------------------------------------------------------------------------| r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.3497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 11276 Z= 0.223 Angle : 0.714 11.580 15296 Z= 0.350 Chirality : 0.047 0.234 1723 Planarity : 0.004 0.039 1919 Dihedral : 7.793 98.845 1580 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.27 % Favored : 91.73 % Rotamer: Outliers : 4.40 % Allowed : 19.93 % Favored : 75.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.92 (0.22), residues: 1342 helix: -1.19 (0.22), residues: 538 sheet: -2.31 (0.35), residues: 194 loop : -2.45 (0.24), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 207 HIS 0.009 0.001 HIS C 302 PHE 0.020 0.002 PHE A1075 TYR 0.022 0.002 TYR A 431 ARG 0.004 0.000 ARG A 206 Details of bonding type rmsd link_NAG-ASN : bond 0.00294 ( 3) link_NAG-ASN : angle 3.21945 ( 9) hydrogen bonds : bond 0.03815 ( 322) hydrogen bonds : angle 5.25844 ( 891) SS BOND : bond 0.00359 ( 3) SS BOND : angle 1.20390 ( 6) link_BETA1-3 : bond 0.00814 ( 1) link_BETA1-3 : angle 3.44652 ( 3) covalent geometry : bond 0.00523 (11268) covalent geometry : angle 0.70853 (15278) Misc. bond : bond 0.00004 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 186 time to evaluate : 1.387 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 LYS cc_start: 0.9044 (tttm) cc_final: 0.8690 (tppt) REVERT: A 94 PRO cc_start: 0.9343 (Cg_exo) cc_final: 0.9131 (Cg_endo) REVERT: A 118 ASN cc_start: 0.8772 (t0) cc_final: 0.8351 (t0) REVERT: A 212 GLU cc_start: 0.7436 (pp20) cc_final: 0.7100 (pp20) REVERT: A 258 TYR cc_start: 0.8256 (m-10) cc_final: 0.8006 (m-10) REVERT: A 523 GLU cc_start: 0.7768 (mm-30) cc_final: 0.7512 (mm-30) REVERT: A 678 MET cc_start: 0.9113 (tmm) cc_final: 0.8892 (tmm) REVERT: A 696 GLU cc_start: 0.7014 (tm-30) cc_final: 0.6668 (tm-30) REVERT: A 781 LYS cc_start: 0.8932 (mtpt) cc_final: 0.8501 (mtpp) REVERT: A 877 PHE cc_start: 0.9095 (OUTLIER) cc_final: 0.8222 (t80) REVERT: A 935 LEU cc_start: 0.9357 (OUTLIER) cc_final: 0.9038 (tt) REVERT: A 940 ARG cc_start: 0.7901 (ttp-110) cc_final: 0.7568 (ttp-110) REVERT: A 992 ASN cc_start: 0.8736 (p0) cc_final: 0.7905 (t0) REVERT: C 74 ASN cc_start: 0.8269 (t0) cc_final: 0.7902 (t0) REVERT: C 261 MET cc_start: 0.8885 (OUTLIER) cc_final: 0.7893 (tpp) REVERT: C 310 MET cc_start: 0.8389 (tmm) cc_final: 0.7729 (tmm) REVERT: C 329 TYR cc_start: 0.8881 (OUTLIER) cc_final: 0.8128 (m-10) outliers start: 53 outliers final: 44 residues processed: 220 average time/residue: 0.2121 time to fit residues: 69.8588 Evaluate side-chains 221 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 173 time to evaluate : 1.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 114 HIS Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 600 PHE Chi-restraints excluded: chain A residue 646 THR Chi-restraints excluded: chain A residue 691 PHE Chi-restraints excluded: chain A residue 711 LYS Chi-restraints excluded: chain A residue 752 ASP Chi-restraints excluded: chain A residue 814 ILE Chi-restraints excluded: chain A residue 822 SER Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 877 PHE Chi-restraints excluded: chain A residue 898 SER Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 1006 THR Chi-restraints excluded: chain A residue 1008 THR Chi-restraints excluded: chain A residue 1077 SER Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 126 ASN Chi-restraints excluded: chain C residue 242 MET Chi-restraints excluded: chain C residue 256 ASP Chi-restraints excluded: chain C residue 261 MET Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 302 HIS Chi-restraints excluded: chain C residue 329 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 125 optimal weight: 0.9980 chunk 115 optimal weight: 5.9990 chunk 23 optimal weight: 0.8980 chunk 117 optimal weight: 5.9990 chunk 56 optimal weight: 6.9990 chunk 18 optimal weight: 8.9990 chunk 54 optimal weight: 10.0000 chunk 8 optimal weight: 8.9990 chunk 63 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 chunk 80 optimal weight: 0.8980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 664 HIS ** A 888 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 302 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.115645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.087792 restraints weight = 19143.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.089607 restraints weight = 14265.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.090248 restraints weight = 9329.538| |-----------------------------------------------------------------------------| r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.3720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11276 Z= 0.134 Angle : 0.673 11.274 15296 Z= 0.328 Chirality : 0.045 0.245 1723 Planarity : 0.004 0.040 1919 Dihedral : 7.788 98.381 1580 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 3.49 % Allowed : 21.84 % Favored : 74.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.72 (0.22), residues: 1342 helix: -1.01 (0.23), residues: 526 sheet: -2.18 (0.36), residues: 193 loop : -2.34 (0.24), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 207 HIS 0.005 0.001 HIS A 470 PHE 0.016 0.001 PHE A 462 TYR 0.031 0.001 TYR A 431 ARG 0.005 0.000 ARG A 206 Details of bonding type rmsd link_NAG-ASN : bond 0.00206 ( 3) link_NAG-ASN : angle 2.95064 ( 9) hydrogen bonds : bond 0.03505 ( 322) hydrogen bonds : angle 5.07042 ( 891) SS BOND : bond 0.00326 ( 3) SS BOND : angle 0.91386 ( 6) link_BETA1-3 : bond 0.00784 ( 1) link_BETA1-3 : angle 3.16015 ( 3) covalent geometry : bond 0.00314 (11268) covalent geometry : angle 0.66779 (15278) Misc. bond : bond 0.00037 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 191 time to evaluate : 1.311 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 LYS cc_start: 0.9047 (tttm) cc_final: 0.8700 (tppt) REVERT: A 118 ASN cc_start: 0.8774 (t0) cc_final: 0.8278 (t0) REVERT: A 212 GLU cc_start: 0.7426 (pp20) cc_final: 0.7080 (pp20) REVERT: A 498 GLU cc_start: 0.8772 (pt0) cc_final: 0.8418 (pm20) REVERT: A 523 GLU cc_start: 0.7772 (mm-30) cc_final: 0.7527 (mm-30) REVERT: A 678 MET cc_start: 0.9071 (tmm) cc_final: 0.8830 (tmm) REVERT: A 696 GLU cc_start: 0.6985 (tm-30) cc_final: 0.6531 (tm-30) REVERT: A 781 LYS cc_start: 0.8951 (mtpt) cc_final: 0.8343 (mttp) REVERT: A 877 PHE cc_start: 0.9067 (OUTLIER) cc_final: 0.8077 (t80) REVERT: A 935 LEU cc_start: 0.9312 (OUTLIER) cc_final: 0.9001 (tt) REVERT: A 938 ASP cc_start: 0.8405 (t0) cc_final: 0.7527 (t0) REVERT: A 940 ARG cc_start: 0.7865 (ttp-110) cc_final: 0.7605 (ttp-110) REVERT: A 942 TYR cc_start: 0.7450 (m-80) cc_final: 0.7041 (m-80) REVERT: A 992 ASN cc_start: 0.8722 (p0) cc_final: 0.7922 (t0) REVERT: C 74 ASN cc_start: 0.8296 (t0) cc_final: 0.7938 (t0) REVERT: C 310 MET cc_start: 0.8326 (tmm) cc_final: 0.8055 (tmm) REVERT: C 329 TYR cc_start: 0.8853 (OUTLIER) cc_final: 0.8014 (m-10) outliers start: 42 outliers final: 34 residues processed: 215 average time/residue: 0.2154 time to fit residues: 68.4072 Evaluate side-chains 215 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 178 time to evaluate : 1.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 114 HIS Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 600 PHE Chi-restraints excluded: chain A residue 646 THR Chi-restraints excluded: chain A residue 691 PHE Chi-restraints excluded: chain A residue 711 LYS Chi-restraints excluded: chain A residue 752 ASP Chi-restraints excluded: chain A residue 822 SER Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 877 PHE Chi-restraints excluded: chain A residue 898 SER Chi-restraints excluded: chain A residue 925 LEU Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 1008 THR Chi-restraints excluded: chain A residue 1064 VAL Chi-restraints excluded: chain A residue 1077 SER Chi-restraints excluded: chain A residue 1087 LEU Chi-restraints excluded: chain C residue 126 ASN Chi-restraints excluded: chain C residue 242 MET Chi-restraints excluded: chain C residue 256 ASP Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 329 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 57 optimal weight: 10.0000 chunk 114 optimal weight: 0.0670 chunk 79 optimal weight: 2.9990 chunk 1 optimal weight: 8.9990 chunk 117 optimal weight: 3.9990 chunk 121 optimal weight: 9.9990 chunk 72 optimal weight: 4.9990 chunk 64 optimal weight: 0.9990 chunk 101 optimal weight: 5.9990 chunk 37 optimal weight: 0.5980 chunk 25 optimal weight: 0.0370 overall best weight: 0.9400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN A 664 HIS A 888 GLN ** C 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.116805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.089467 restraints weight = 18990.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.091359 restraints weight = 13694.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.091902 restraints weight = 9015.195| |-----------------------------------------------------------------------------| r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.3959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 11276 Z= 0.126 Angle : 0.655 13.448 15296 Z= 0.318 Chirality : 0.044 0.248 1723 Planarity : 0.003 0.040 1919 Dihedral : 7.605 97.587 1580 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 3.24 % Allowed : 21.93 % Favored : 74.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.53 (0.23), residues: 1342 helix: -0.86 (0.23), residues: 525 sheet: -2.02 (0.37), residues: 186 loop : -2.26 (0.25), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 207 HIS 0.006 0.001 HIS C 302 PHE 0.027 0.001 PHE A1075 TYR 0.020 0.001 TYR C 273 ARG 0.005 0.000 ARG A 206 Details of bonding type rmsd link_NAG-ASN : bond 0.00236 ( 3) link_NAG-ASN : angle 3.04396 ( 9) hydrogen bonds : bond 0.03373 ( 322) hydrogen bonds : angle 4.94293 ( 891) SS BOND : bond 0.00288 ( 3) SS BOND : angle 0.82159 ( 6) link_BETA1-3 : bond 0.00722 ( 1) link_BETA1-3 : angle 2.98212 ( 3) covalent geometry : bond 0.00294 (11268) covalent geometry : angle 0.65001 (15278) Misc. bond : bond 0.00033 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 191 time to evaluate : 1.380 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 LYS cc_start: 0.9037 (tttm) cc_final: 0.8712 (tppt) REVERT: A 114 HIS cc_start: 0.8261 (OUTLIER) cc_final: 0.7984 (t-90) REVERT: A 118 ASN cc_start: 0.8702 (t0) cc_final: 0.8215 (t0) REVERT: A 212 GLU cc_start: 0.7427 (pp20) cc_final: 0.7130 (pp20) REVERT: A 523 GLU cc_start: 0.7743 (mm-30) cc_final: 0.7499 (mm-30) REVERT: A 678 MET cc_start: 0.9006 (tmm) cc_final: 0.8745 (tmm) REVERT: A 696 GLU cc_start: 0.7038 (tm-30) cc_final: 0.6661 (tm-30) REVERT: A 781 LYS cc_start: 0.8872 (mtpt) cc_final: 0.8364 (mttp) REVERT: A 877 PHE cc_start: 0.9045 (OUTLIER) cc_final: 0.8094 (t80) REVERT: A 935 LEU cc_start: 0.9283 (OUTLIER) cc_final: 0.8974 (tt) REVERT: A 938 ASP cc_start: 0.8378 (t0) cc_final: 0.7384 (t0) REVERT: A 940 ARG cc_start: 0.7924 (ttp-110) cc_final: 0.7713 (ttp-110) REVERT: A 942 TYR cc_start: 0.7345 (m-80) cc_final: 0.6958 (m-80) REVERT: A 992 ASN cc_start: 0.8754 (p0) cc_final: 0.7974 (t0) REVERT: C 74 ASN cc_start: 0.8291 (t0) cc_final: 0.8041 (t0) REVERT: C 178 MET cc_start: 0.7839 (tpp) cc_final: 0.7459 (tpt) REVERT: C 310 MET cc_start: 0.8341 (tmm) cc_final: 0.8057 (tmm) REVERT: C 329 TYR cc_start: 0.8795 (OUTLIER) cc_final: 0.7968 (m-10) outliers start: 39 outliers final: 31 residues processed: 214 average time/residue: 0.2061 time to fit residues: 65.5240 Evaluate side-chains 213 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 178 time to evaluate : 1.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 114 HIS Chi-restraints excluded: chain A residue 129 GLU Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 600 PHE Chi-restraints excluded: chain A residue 646 THR Chi-restraints excluded: chain A residue 691 PHE Chi-restraints excluded: chain A residue 711 LYS Chi-restraints excluded: chain A residue 752 ASP Chi-restraints excluded: chain A residue 822 SER Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 877 PHE Chi-restraints excluded: chain A residue 898 SER Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 1008 THR Chi-restraints excluded: chain A residue 1077 SER Chi-restraints excluded: chain A residue 1087 LEU Chi-restraints excluded: chain C residue 126 ASN Chi-restraints excluded: chain C residue 242 MET Chi-restraints excluded: chain C residue 256 ASP Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 329 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 93 optimal weight: 0.5980 chunk 86 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 12 optimal weight: 0.0870 chunk 117 optimal weight: 4.9990 chunk 114 optimal weight: 0.0370 chunk 119 optimal weight: 7.9990 chunk 49 optimal weight: 8.9990 chunk 30 optimal weight: 10.0000 chunk 15 optimal weight: 2.9990 chunk 47 optimal weight: 7.9990 overall best weight: 1.3440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 664 HIS ** A 888 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.116510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.088553 restraints weight = 19148.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.090151 restraints weight = 14363.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.090860 restraints weight = 9526.498| |-----------------------------------------------------------------------------| r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.4006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11276 Z= 0.144 Angle : 0.682 12.937 15296 Z= 0.330 Chirality : 0.045 0.245 1723 Planarity : 0.004 0.041 1919 Dihedral : 7.549 96.453 1580 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 2.91 % Allowed : 22.51 % Favored : 74.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.52 (0.23), residues: 1342 helix: -0.80 (0.23), residues: 541 sheet: -2.05 (0.36), residues: 200 loop : -2.31 (0.25), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 207 HIS 0.004 0.001 HIS A 470 PHE 0.015 0.001 PHE A 462 TYR 0.017 0.001 TYR A 318 ARG 0.009 0.000 ARG A 206 Details of bonding type rmsd link_NAG-ASN : bond 0.00165 ( 3) link_NAG-ASN : angle 3.07303 ( 9) hydrogen bonds : bond 0.03510 ( 322) hydrogen bonds : angle 4.96330 ( 891) SS BOND : bond 0.00292 ( 3) SS BOND : angle 0.88310 ( 6) link_BETA1-3 : bond 0.00786 ( 1) link_BETA1-3 : angle 2.99495 ( 3) covalent geometry : bond 0.00341 (11268) covalent geometry : angle 0.67658 (15278) Misc. bond : bond 0.00020 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 183 time to evaluate : 1.150 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 LYS cc_start: 0.9064 (tttm) cc_final: 0.8719 (tppt) REVERT: A 118 ASN cc_start: 0.8713 (t0) cc_final: 0.8203 (t0) REVERT: A 523 GLU cc_start: 0.7759 (mm-30) cc_final: 0.7519 (mm-30) REVERT: A 678 MET cc_start: 0.8987 (tmm) cc_final: 0.8782 (tmm) REVERT: A 696 GLU cc_start: 0.6890 (tm-30) cc_final: 0.6430 (tm-30) REVERT: A 751 ILE cc_start: 0.9236 (mt) cc_final: 0.9016 (mm) REVERT: A 877 PHE cc_start: 0.9031 (OUTLIER) cc_final: 0.8135 (t80) REVERT: A 935 LEU cc_start: 0.9294 (OUTLIER) cc_final: 0.8980 (tt) REVERT: A 938 ASP cc_start: 0.8382 (t0) cc_final: 0.7339 (t0) REVERT: A 940 ARG cc_start: 0.7947 (ttp-110) cc_final: 0.7714 (ttp-110) REVERT: A 942 TYR cc_start: 0.7397 (m-80) cc_final: 0.7010 (m-80) REVERT: A 992 ASN cc_start: 0.8755 (p0) cc_final: 0.8005 (t0) REVERT: C 74 ASN cc_start: 0.8344 (t0) cc_final: 0.8069 (t0) REVERT: C 178 MET cc_start: 0.7872 (tpp) cc_final: 0.7469 (tpt) REVERT: C 310 MET cc_start: 0.8371 (tmm) cc_final: 0.8089 (tmm) REVERT: C 329 TYR cc_start: 0.8790 (OUTLIER) cc_final: 0.8001 (m-10) outliers start: 35 outliers final: 30 residues processed: 203 average time/residue: 0.1927 time to fit residues: 57.8761 Evaluate side-chains 209 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 176 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 114 HIS Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 600 PHE Chi-restraints excluded: chain A residue 646 THR Chi-restraints excluded: chain A residue 691 PHE Chi-restraints excluded: chain A residue 711 LYS Chi-restraints excluded: chain A residue 752 ASP Chi-restraints excluded: chain A residue 822 SER Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 877 PHE Chi-restraints excluded: chain A residue 898 SER Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 1008 THR Chi-restraints excluded: chain A residue 1077 SER Chi-restraints excluded: chain A residue 1087 LEU Chi-restraints excluded: chain C residue 126 ASN Chi-restraints excluded: chain C residue 256 ASP Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 329 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 67 optimal weight: 5.9990 chunk 18 optimal weight: 7.9990 chunk 39 optimal weight: 9.9990 chunk 80 optimal weight: 3.9990 chunk 122 optimal weight: 0.0010 chunk 74 optimal weight: 2.9990 chunk 25 optimal weight: 9.9990 chunk 128 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 72 optimal weight: 0.8980 overall best weight: 1.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 ASN A 213 GLN A 664 HIS ** A 888 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.116135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.088204 restraints weight = 19086.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.089872 restraints weight = 14235.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.090525 restraints weight = 9465.415| |-----------------------------------------------------------------------------| r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.4082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11276 Z= 0.154 Angle : 0.682 12.670 15296 Z= 0.334 Chirality : 0.045 0.243 1723 Planarity : 0.004 0.052 1919 Dihedral : 7.524 96.056 1580 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 3.07 % Allowed : 22.59 % Favored : 74.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.47 (0.23), residues: 1342 helix: -0.75 (0.23), residues: 539 sheet: -1.94 (0.36), residues: 200 loop : -2.33 (0.25), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 207 HIS 0.010 0.001 HIS C 302 PHE 0.042 0.001 PHE A 462 TYR 0.028 0.001 TYR A 722 ARG 0.012 0.000 ARG A 723 Details of bonding type rmsd link_NAG-ASN : bond 0.00170 ( 3) link_NAG-ASN : angle 3.12522 ( 9) hydrogen bonds : bond 0.03421 ( 322) hydrogen bonds : angle 4.94640 ( 891) SS BOND : bond 0.00312 ( 3) SS BOND : angle 0.90891 ( 6) link_BETA1-3 : bond 0.00617 ( 1) link_BETA1-3 : angle 3.06606 ( 3) covalent geometry : bond 0.00364 (11268) covalent geometry : angle 0.67703 (15278) Misc. bond : bond 0.00023 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3303.01 seconds wall clock time: 58 minutes 40.58 seconds (3520.58 seconds total)