Starting phenix.real_space_refine on Wed Sep 25 19:53:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bsp_30163/09_2024/7bsp_30163_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bsp_30163/09_2024/7bsp_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bsp_30163/09_2024/7bsp_30163.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bsp_30163/09_2024/7bsp_30163.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bsp_30163/09_2024/7bsp_30163_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bsp_30163/09_2024/7bsp_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-5461/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: 6.54, 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: 3.10 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: 1.53 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: 3.99 Time building geometry restraints manager: 3.54 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: 0.800 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: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 28.110 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.610 ------------------------------------------------------------------------------- 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 : 0.005 0.102 11268 Z= 0.317 Angle : 0.660 11.592 15278 Z= 0.370 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 225 time to evaluate : 1.234 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: 0.2248 time to fit residues: 72.8939 Evaluate side-chains 160 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 160 time to evaluate : 1.241 ------------------------------------------------------------------------------- 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: 0.8980 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: 9.9990 overall best weight: 0.9482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 641 ASN A 716 HIS A 794 GLN A 862 HIS A 892 GLN ** A 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 929 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1089 ASN C 130 ASN C 211 ASN C 302 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 11268 Z= 0.238 Angle : 0.754 10.439 15278 Z= 0.386 Chirality : 0.049 0.272 1723 Planarity : 0.005 0.035 1919 Dihedral : 11.152 110.436 1580 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.87 % Favored : 91.13 % Rotamer: Outliers : 1.41 % Allowed : 11.79 % Favored : 86.79 % 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: -5.10 (0.19), residues: 1342 helix: -3.34 (0.16), residues: 526 sheet: -3.42 (0.33), residues: 182 loop : -3.35 (0.22), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 376 HIS 0.013 0.002 HIS C 302 PHE 0.021 0.002 PHE A1036 TYR 0.017 0.002 TYR A 608 ARG 0.009 0.001 ARG A 723 *********************** 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 246 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 229 time to evaluate : 1.293 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 LYS cc_start: 0.8984 (tttm) cc_final: 0.8555 (tppt) REVERT: A 118 ASN cc_start: 0.8831 (t0) cc_final: 0.8541 (t0) REVERT: A 154 THR cc_start: 0.9045 (OUTLIER) cc_final: 0.8825 (m) REVERT: A 159 LEU cc_start: 0.9457 (mt) cc_final: 0.9242 (mt) REVERT: A 348 MET cc_start: 0.9108 (mmm) cc_final: 0.8897 (tpp) REVERT: A 365 MET cc_start: 0.9067 (tpp) cc_final: 0.8848 (mmm) REVERT: A 419 MET cc_start: 0.8650 (mmp) cc_final: 0.8187 (mmp) REVERT: A 616 ILE cc_start: 0.9562 (pt) cc_final: 0.9172 (mt) REVERT: A 714 ARG cc_start: 0.7919 (mtp180) cc_final: 0.7589 (mmm-85) REVERT: A 992 ASN cc_start: 0.8328 (p0) cc_final: 0.7213 (t0) REVERT: C 130 ASN cc_start: 0.8917 (OUTLIER) cc_final: 0.8544 (p0) REVERT: C 310 MET cc_start: 0.8087 (tmm) cc_final: 0.7219 (tmm) outliers start: 17 outliers final: 9 residues processed: 237 average time/residue: 0.2210 time to fit residues: 75.3599 Evaluate side-chains 189 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 178 time to evaluate : 1.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ILE 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 154 THR 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 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 67 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 101 optimal weight: 5.9990 chunk 82 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 121 optimal weight: 0.0270 chunk 131 optimal weight: 5.9990 chunk 108 optimal weight: 4.9990 chunk 120 optimal weight: 4.9990 chunk 41 optimal weight: 8.9990 chunk 97 optimal weight: 5.9990 overall best weight: 3.0046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN A 314 GLN A 584 HIS ** A 929 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 35 GLN C 36 GLN ** C 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 216 ASN C 302 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.2566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 11268 Z= 0.378 Angle : 0.744 9.094 15278 Z= 0.377 Chirality : 0.048 0.282 1723 Planarity : 0.004 0.038 1919 Dihedral : 9.461 105.885 1580 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.02 % Favored : 90.98 % Rotamer: Outliers : 3.24 % Allowed : 15.95 % Favored : 80.81 % 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: -2.60 (0.18), residues: 536 sheet: -3.00 (0.35), residues: 183 loop : -2.98 (0.23), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 323 HIS 0.011 0.001 HIS C 302 PHE 0.014 0.002 PHE A 462 TYR 0.021 0.002 TYR A 608 ARG 0.006 0.000 ARG A 206 *********************** 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 239 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 200 time to evaluate : 1.353 Fit side-chains revert: symmetry clash REVERT: A 58 LYS cc_start: 0.9032 (tttm) cc_final: 0.8621 (tppt) REVERT: A 118 ASN cc_start: 0.8872 (t0) cc_final: 0.8505 (t0) REVERT: A 365 MET cc_start: 0.9339 (tpp) cc_final: 0.9106 (mmm) REVERT: A 419 MET cc_start: 0.8688 (mmp) cc_final: 0.8252 (mmp) REVERT: A 431 TYR cc_start: 0.8366 (t80) cc_final: 0.8140 (t80) REVERT: A 547 MET cc_start: 0.8654 (tmm) cc_final: 0.8373 (tmm) REVERT: A 630 GLU cc_start: 0.8986 (tm-30) cc_final: 0.8653 (tm-30) REVERT: A 678 MET cc_start: 0.9184 (tmm) cc_final: 0.8711 (tmm) REVERT: A 696 GLU cc_start: 0.6876 (tm-30) cc_final: 0.6582 (tm-30) REVERT: A 877 PHE cc_start: 0.9163 (OUTLIER) cc_final: 0.8246 (t80) REVERT: A 992 ASN cc_start: 0.8430 (p0) cc_final: 0.7202 (t0) REVERT: C 74 ASN cc_start: 0.8002 (t0) cc_final: 0.7682 (t0) REVERT: C 310 MET cc_start: 0.8246 (tmm) cc_final: 0.7189 (tmm) outliers start: 39 outliers final: 27 residues processed: 220 average time/residue: 0.2042 time to fit residues: 66.6892 Evaluate side-chains 195 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 167 time to evaluate : 1.256 ------------------------------------------------------------------------------- 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 146 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain A residue 260 VAL 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 761 ASN 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 295 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 120 optimal weight: 3.9990 chunk 91 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 81 optimal weight: 0.9990 chunk 122 optimal weight: 6.9990 chunk 129 optimal weight: 0.6980 chunk 115 optimal weight: 0.7980 chunk 34 optimal weight: 0.8980 chunk 107 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 929 HIS ** C 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 302 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.3184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11268 Z= 0.194 Angle : 0.651 9.513 15278 Z= 0.330 Chirality : 0.045 0.248 1723 Planarity : 0.004 0.039 1919 Dihedral : 8.350 105.640 1580 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 3.41 % Allowed : 17.61 % Favored : 78.99 % 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: -3.47 (0.21), residues: 1342 helix: -1.79 (0.21), residues: 522 sheet: -2.65 (0.35), residues: 189 loop : -2.57 (0.24), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 376 HIS 0.015 0.001 HIS C 302 PHE 0.015 0.001 PHE A 462 TYR 0.018 0.001 TYR A 771 ARG 0.006 0.000 ARG A 625 *********************** 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 256 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 215 time to evaluate : 1.272 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 LYS cc_start: 0.9024 (tttm) cc_final: 0.8511 (tppt) REVERT: A 118 ASN cc_start: 0.8753 (t0) cc_final: 0.8351 (t0) REVERT: A 258 TYR cc_start: 0.8324 (m-80) cc_final: 0.7998 (m-10) REVERT: A 348 MET cc_start: 0.9061 (mmm) cc_final: 0.8804 (tpp) REVERT: A 498 GLU cc_start: 0.8814 (pt0) cc_final: 0.8451 (pm20) REVERT: A 625 ARG cc_start: 0.8649 (OUTLIER) cc_final: 0.8052 (ttt180) REVERT: A 630 GLU cc_start: 0.8948 (tm-30) cc_final: 0.8591 (tm-30) REVERT: A 696 GLU cc_start: 0.7026 (tm-30) cc_final: 0.6656 (tm-30) REVERT: A 877 PHE cc_start: 0.9129 (OUTLIER) cc_final: 0.8209 (t80) REVERT: C 74 ASN cc_start: 0.7801 (t0) cc_final: 0.7223 (t0) REVERT: C 75 ILE cc_start: 0.8879 (OUTLIER) cc_final: 0.8637 (mm) REVERT: C 256 ASP cc_start: 0.8234 (OUTLIER) cc_final: 0.7946 (t0) REVERT: C 310 MET cc_start: 0.8232 (tmm) cc_final: 0.7227 (tmm) REVERT: C 329 TYR cc_start: 0.8994 (OUTLIER) cc_final: 0.8595 (m-10) outliers start: 41 outliers final: 17 residues processed: 245 average time/residue: 0.1888 time to fit residues: 69.3737 Evaluate side-chains 209 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 187 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 77 LEU 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 411 THR 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 625 ARG 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 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 73 optimal weight: 7.9990 chunk 1 optimal weight: 0.0270 chunk 96 optimal weight: 4.9990 chunk 53 optimal weight: 7.9990 chunk 110 optimal weight: 6.9990 chunk 89 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 66 optimal weight: 7.9990 chunk 116 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 43 optimal weight: 10.0000 overall best weight: 2.1842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 ASN A 517 ASN A 664 HIS ** C 142 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 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 0.044 11268 Z= 0.287 Angle : 0.682 10.979 15278 Z= 0.338 Chirality : 0.046 0.238 1723 Planarity : 0.004 0.040 1919 Dihedral : 8.156 102.595 1580 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer: Outliers : 4.15 % Allowed : 19.52 % 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: -3.23 (0.22), residues: 1342 helix: -1.54 (0.21), residues: 525 sheet: -2.42 (0.36), residues: 188 loop : -2.55 (0.24), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 313 HIS 0.010 0.001 HIS C 302 PHE 0.012 0.001 PHE A 462 TYR 0.020 0.001 TYR A 431 ARG 0.005 0.000 ARG A 625 *********************** 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 242 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 192 time to evaluate : 1.139 Fit side-chains revert: symmetry clash REVERT: A 45 ILE cc_start: 0.9223 (tp) cc_final: 0.8996 (tt) REVERT: A 58 LYS cc_start: 0.9046 (tttm) cc_final: 0.8651 (tppt) REVERT: A 118 ASN cc_start: 0.8789 (t0) cc_final: 0.8265 (p0) REVERT: A 348 MET cc_start: 0.9044 (mmm) cc_final: 0.8765 (tpp) REVERT: A 498 GLU cc_start: 0.8893 (pt0) cc_final: 0.8576 (pm20) REVERT: A 523 GLU cc_start: 0.7772 (mm-30) cc_final: 0.7499 (mm-30) REVERT: A 630 GLU cc_start: 0.8944 (tm-30) cc_final: 0.8575 (tm-30) REVERT: A 696 GLU cc_start: 0.6982 (tm-30) cc_final: 0.6701 (tm-30) REVERT: A 781 LYS cc_start: 0.8795 (mtpt) cc_final: 0.8249 (mtpp) REVERT: A 877 PHE cc_start: 0.9160 (OUTLIER) cc_final: 0.8273 (t80) REVERT: A 940 ARG cc_start: 0.7759 (ttp-110) cc_final: 0.7423 (ttp-110) REVERT: A 992 ASN cc_start: 0.8528 (p0) cc_final: 0.7508 (t0) REVERT: C 74 ASN cc_start: 0.7911 (t0) cc_final: 0.7301 (t0) REVERT: C 75 ILE cc_start: 0.8864 (OUTLIER) cc_final: 0.8637 (mm) REVERT: C 310 MET cc_start: 0.8303 (tmm) cc_final: 0.7208 (tmm) REVERT: C 329 TYR cc_start: 0.8964 (OUTLIER) cc_final: 0.8359 (m-10) outliers start: 50 outliers final: 33 residues processed: 224 average time/residue: 0.2048 time to fit residues: 68.9021 Evaluate side-chains 211 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 175 time to evaluate : 1.356 ------------------------------------------------------------------------------- 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 146 VAL 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 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 472 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 754 SER 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 1008 THR Chi-restraints excluded: chain A residue 1077 SER Chi-restraints excluded: chain C residue 66 ILE 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 295 VAL 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 116 optimal weight: 0.9990 chunk 25 optimal weight: 0.2980 chunk 76 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 chunk 129 optimal weight: 6.9990 chunk 107 optimal weight: 4.9990 chunk 60 optimal weight: 5.9990 chunk 10 optimal weight: 20.0000 chunk 42 optimal weight: 8.9990 chunk 68 optimal weight: 0.9990 chunk 124 optimal weight: 5.9990 overall best weight: 2.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 664 HIS ** C 142 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.3413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 11268 Z= 0.293 Angle : 0.692 9.396 15278 Z= 0.341 Chirality : 0.046 0.254 1723 Planarity : 0.004 0.041 1919 Dihedral : 8.011 99.872 1580 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer: Outliers : 4.07 % Allowed : 20.51 % Favored : 75.42 % 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: -3.09 (0.22), residues: 1342 helix: -1.32 (0.22), residues: 526 sheet: -2.32 (0.36), residues: 189 loop : -2.58 (0.24), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 292 HIS 0.005 0.001 HIS C 302 PHE 0.015 0.001 PHE A1075 TYR 0.024 0.002 TYR C 134 ARG 0.003 0.000 ARG A 723 *********************** 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 240 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 191 time to evaluate : 1.354 Fit side-chains revert: symmetry clash REVERT: A 45 ILE cc_start: 0.9190 (tp) cc_final: 0.8983 (tt) REVERT: A 58 LYS cc_start: 0.9039 (tttm) cc_final: 0.8662 (tppt) REVERT: A 94 PRO cc_start: 0.9284 (Cg_exo) cc_final: 0.9076 (Cg_endo) REVERT: A 118 ASN cc_start: 0.8764 (t0) cc_final: 0.8257 (p0) REVERT: A 348 MET cc_start: 0.8977 (mmm) cc_final: 0.8701 (tpp) REVERT: A 498 GLU cc_start: 0.8811 (pt0) cc_final: 0.8416 (pm20) REVERT: A 523 GLU cc_start: 0.7746 (mm-30) cc_final: 0.7498 (mm-30) REVERT: A 630 GLU cc_start: 0.8924 (tm-30) cc_final: 0.8552 (tm-30) REVERT: A 678 MET cc_start: 0.9014 (tmm) cc_final: 0.8580 (tmm) REVERT: A 696 GLU cc_start: 0.7021 (tm-30) cc_final: 0.6715 (tm-30) REVERT: A 781 LYS cc_start: 0.8904 (mtpt) cc_final: 0.8404 (mtpp) REVERT: A 820 ASP cc_start: 0.8668 (m-30) cc_final: 0.8365 (m-30) REVERT: A 877 PHE cc_start: 0.9174 (OUTLIER) cc_final: 0.8257 (t80) REVERT: A 885 ILE cc_start: 0.9236 (tp) cc_final: 0.8861 (tp) REVERT: A 940 ARG cc_start: 0.7759 (ttp-110) cc_final: 0.7423 (ttp-110) REVERT: A 992 ASN cc_start: 0.8584 (p0) cc_final: 0.7541 (t0) REVERT: C 74 ASN cc_start: 0.7996 (t0) cc_final: 0.7465 (t0) REVERT: C 75 ILE cc_start: 0.8891 (OUTLIER) cc_final: 0.8668 (mm) REVERT: C 310 MET cc_start: 0.8321 (tmm) cc_final: 0.7798 (tmm) REVERT: C 329 TYR cc_start: 0.8909 (OUTLIER) cc_final: 0.8195 (m-10) outliers start: 49 outliers final: 37 residues processed: 224 average time/residue: 0.2016 time to fit residues: 67.4570 Evaluate side-chains 217 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 177 time to evaluate : 1.219 ------------------------------------------------------------------------------- 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 114 HIS Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 141 ILE 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 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 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 1008 THR Chi-restraints excluded: chain A residue 1077 SER Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 75 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 14 optimal weight: 5.9990 chunk 73 optimal weight: 6.9990 chunk 94 optimal weight: 0.8980 chunk 109 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 chunk 129 optimal weight: 7.9990 chunk 80 optimal weight: 0.9980 chunk 78 optimal weight: 0.9980 chunk 59 optimal weight: 6.9990 chunk 79 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 664 HIS ** C 142 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.3658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11268 Z= 0.202 Angle : 0.659 9.239 15278 Z= 0.324 Chirality : 0.045 0.247 1723 Planarity : 0.004 0.040 1919 Dihedral : 7.841 99.261 1580 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.68 % Favored : 92.32 % Rotamer: Outliers : 3.65 % Allowed : 20.93 % Favored : 75.42 % 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: -2.81 (0.22), residues: 1342 helix: -1.04 (0.22), residues: 522 sheet: -2.17 (0.36), residues: 189 loop : -2.45 (0.24), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 313 HIS 0.011 0.001 HIS C 302 PHE 0.013 0.001 PHE A 462 TYR 0.021 0.001 TYR C 134 ARG 0.006 0.000 ARG A 625 *********************** 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 246 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 202 time to evaluate : 1.185 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 45 ILE cc_start: 0.9168 (tp) cc_final: 0.8953 (tt) REVERT: A 58 LYS cc_start: 0.9059 (tttm) cc_final: 0.8713 (tppt) REVERT: A 118 ASN cc_start: 0.8734 (t0) cc_final: 0.8266 (t0) REVERT: A 348 MET cc_start: 0.8940 (mmm) cc_final: 0.8685 (tpp) REVERT: A 498 GLU cc_start: 0.8724 (pt0) cc_final: 0.8409 (pm20) REVERT: A 523 GLU cc_start: 0.7742 (mm-30) cc_final: 0.7494 (mm-30) REVERT: A 678 MET cc_start: 0.9036 (tmm) cc_final: 0.8830 (tmm) REVERT: A 696 GLU cc_start: 0.6983 (tm-30) cc_final: 0.6527 (tm-30) REVERT: A 781 LYS cc_start: 0.8943 (mtpt) cc_final: 0.8666 (mtpp) REVERT: A 820 ASP cc_start: 0.8663 (m-30) cc_final: 0.8335 (m-30) REVERT: A 877 PHE cc_start: 0.9165 (OUTLIER) cc_final: 0.8218 (t80) REVERT: A 885 ILE cc_start: 0.9204 (tp) cc_final: 0.8807 (tp) REVERT: A 897 PHE cc_start: 0.8900 (OUTLIER) cc_final: 0.8601 (m-10) REVERT: A 935 LEU cc_start: 0.9369 (OUTLIER) cc_final: 0.8989 (tt) REVERT: A 940 ARG cc_start: 0.7812 (ttp-110) cc_final: 0.7515 (ttp-110) REVERT: A 992 ASN cc_start: 0.8544 (p0) cc_final: 0.7630 (t0) REVERT: A 1053 MET cc_start: 0.8489 (mtp) cc_final: 0.8169 (mtp) REVERT: A 1056 VAL cc_start: 0.8937 (t) cc_final: 0.8688 (p) REVERT: C 74 ASN cc_start: 0.8013 (t0) cc_final: 0.7521 (t0) REVERT: C 75 ILE cc_start: 0.8852 (OUTLIER) cc_final: 0.8641 (mm) REVERT: C 256 ASP cc_start: 0.8154 (OUTLIER) cc_final: 0.7894 (t0) REVERT: C 310 MET cc_start: 0.8277 (tmm) cc_final: 0.8027 (tmm) REVERT: C 329 TYR cc_start: 0.8881 (OUTLIER) cc_final: 0.8083 (m-10) outliers start: 44 outliers final: 32 residues processed: 227 average time/residue: 0.2047 time to fit residues: 68.7653 Evaluate side-chains 224 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 186 time to evaluate : 1.219 ------------------------------------------------------------------------------- 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 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 232 LEU 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 328 THR Chi-restraints excluded: chain A residue 411 THR 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 691 PHE 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 897 PHE Chi-restraints excluded: chain A residue 898 SER Chi-restraints excluded: chain A residue 935 LEU 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 77 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 82 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 63 optimal weight: 6.9990 chunk 12 optimal weight: 3.9990 chunk 101 optimal weight: 0.7980 chunk 117 optimal weight: 6.9990 chunk 123 optimal weight: 0.9980 chunk 112 optimal weight: 3.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 ** C 142 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.3809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11268 Z= 0.218 Angle : 0.657 9.212 15278 Z= 0.321 Chirality : 0.045 0.246 1723 Planarity : 0.004 0.041 1919 Dihedral : 7.683 98.015 1580 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.82 % Favored : 92.18 % Rotamer: Outliers : 3.90 % Allowed : 21.18 % Favored : 74.92 % 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: -2.70 (0.22), residues: 1342 helix: -0.95 (0.22), residues: 529 sheet: -2.05 (0.36), residues: 190 loop : -2.43 (0.24), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 207 HIS 0.006 0.001 HIS A 470 PHE 0.024 0.001 PHE A1075 TYR 0.024 0.001 TYR A 431 ARG 0.005 0.000 ARG A 206 *********************** 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 235 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 188 time to evaluate : 1.246 Fit side-chains revert: symmetry clash REVERT: A 58 LYS cc_start: 0.9071 (tttm) cc_final: 0.8718 (tppt) REVERT: A 114 HIS cc_start: 0.8224 (OUTLIER) cc_final: 0.7953 (t-90) REVERT: A 118 ASN cc_start: 0.8734 (t0) cc_final: 0.8280 (t0) REVERT: A 348 MET cc_start: 0.8929 (mmm) cc_final: 0.8679 (tpp) REVERT: A 498 GLU cc_start: 0.8709 (pt0) cc_final: 0.8348 (pm20) REVERT: A 523 GLU cc_start: 0.7735 (mm-30) cc_final: 0.7499 (mm-30) REVERT: A 678 MET cc_start: 0.9025 (tmm) cc_final: 0.8799 (tmm) REVERT: A 696 GLU cc_start: 0.7045 (tm-30) cc_final: 0.6743 (tm-30) REVERT: A 781 LYS cc_start: 0.8943 (mtpt) cc_final: 0.8376 (mttp) REVERT: A 820 ASP cc_start: 0.8656 (m-30) cc_final: 0.8361 (m-30) REVERT: A 877 PHE cc_start: 0.9161 (OUTLIER) cc_final: 0.8215 (t80) REVERT: A 885 ILE cc_start: 0.9226 (tp) cc_final: 0.8808 (tp) REVERT: A 897 PHE cc_start: 0.8880 (OUTLIER) cc_final: 0.8590 (m-10) REVERT: A 935 LEU cc_start: 0.9348 (OUTLIER) cc_final: 0.8975 (tt) REVERT: A 938 ASP cc_start: 0.8470 (t0) cc_final: 0.7616 (t0) REVERT: A 940 ARG cc_start: 0.7837 (ttp-110) cc_final: 0.7562 (ttp-110) REVERT: A 942 TYR cc_start: 0.7369 (m-80) cc_final: 0.7053 (m-80) REVERT: A 1053 MET cc_start: 0.8525 (mtp) cc_final: 0.8236 (mtp) REVERT: C 74 ASN cc_start: 0.8072 (t0) cc_final: 0.7607 (t0) REVERT: C 75 ILE cc_start: 0.8807 (OUTLIER) cc_final: 0.8581 (mm) REVERT: C 178 MET cc_start: 0.8110 (tpp) cc_final: 0.7653 (tpt) REVERT: C 215 ARG cc_start: 0.8555 (mmm160) cc_final: 0.8321 (mmt-90) REVERT: C 256 ASP cc_start: 0.8148 (OUTLIER) cc_final: 0.7855 (t0) REVERT: C 310 MET cc_start: 0.8299 (tmm) cc_final: 0.8034 (tmm) REVERT: C 329 TYR cc_start: 0.8838 (OUTLIER) cc_final: 0.7972 (m-10) outliers start: 47 outliers final: 33 residues processed: 218 average time/residue: 0.2046 time to fit residues: 67.1110 Evaluate side-chains 218 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 178 time to evaluate : 1.259 ------------------------------------------------------------------------------- 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 127 ILE Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 174 THR 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 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 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 897 PHE Chi-restraints excluded: chain A residue 898 SER Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 1077 SER Chi-restraints excluded: chain A residue 1087 LEU Chi-restraints excluded: chain C residue 75 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 268 THR Chi-restraints excluded: chain C residue 302 HIS 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 120 optimal weight: 0.0030 chunk 123 optimal weight: 0.9980 chunk 72 optimal weight: 0.8980 chunk 52 optimal weight: 0.8980 chunk 94 optimal weight: 0.3980 chunk 36 optimal weight: 6.9990 chunk 108 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 chunk 119 optimal weight: 7.9990 chunk 79 optimal weight: 0.5980 chunk 127 optimal weight: 0.8980 overall best weight: 0.5590 ------------------------------------------------------------------------------- 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 ** C 142 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.3983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11268 Z= 0.182 Angle : 0.649 9.307 15278 Z= 0.318 Chirality : 0.044 0.250 1723 Planarity : 0.004 0.041 1919 Dihedral : 7.596 97.901 1580 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 3.32 % Allowed : 21.51 % Favored : 75.17 % 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 (0.22), residues: 1342 helix: -0.79 (0.23), residues: 523 sheet: -1.93 (0.37), residues: 182 loop : -2.36 (0.24), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 207 HIS 0.018 0.001 HIS C 302 PHE 0.016 0.001 PHE C 304 TYR 0.030 0.001 TYR A 431 ARG 0.006 0.000 ARG A 206 *********************** 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 234 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 194 time to evaluate : 1.241 Fit side-chains revert: symmetry clash REVERT: A 58 LYS cc_start: 0.9064 (tttm) cc_final: 0.8702 (tppt) REVERT: A 114 HIS cc_start: 0.8207 (OUTLIER) cc_final: 0.7946 (t-90) REVERT: A 118 ASN cc_start: 0.8737 (t0) cc_final: 0.8258 (t0) REVERT: A 212 GLU cc_start: 0.7597 (pp20) cc_final: 0.7127 (pp20) REVERT: A 348 MET cc_start: 0.8905 (mmm) cc_final: 0.8669 (tpp) REVERT: A 523 GLU cc_start: 0.7736 (mm-30) cc_final: 0.7494 (mm-30) REVERT: A 678 MET cc_start: 0.8987 (tmm) cc_final: 0.8778 (tmm) REVERT: A 696 GLU cc_start: 0.6969 (tm-30) cc_final: 0.6732 (tm-30) REVERT: A 781 LYS cc_start: 0.8917 (mtpt) cc_final: 0.8487 (mttp) REVERT: A 877 PHE cc_start: 0.9144 (OUTLIER) cc_final: 0.8167 (t80) REVERT: A 885 ILE cc_start: 0.9198 (tp) cc_final: 0.8700 (tp) REVERT: A 935 LEU cc_start: 0.9327 (OUTLIER) cc_final: 0.8968 (tt) REVERT: A 938 ASP cc_start: 0.8354 (t0) cc_final: 0.7431 (t0) REVERT: A 940 ARG cc_start: 0.7759 (ttp-110) cc_final: 0.7551 (ttp-110) REVERT: A 942 TYR cc_start: 0.7246 (m-80) cc_final: 0.6880 (m-80) REVERT: A 1053 MET cc_start: 0.8438 (mtp) cc_final: 0.8164 (mtp) REVERT: C 74 ASN cc_start: 0.8124 (t0) cc_final: 0.7682 (t0) REVERT: C 75 ILE cc_start: 0.8784 (OUTLIER) cc_final: 0.8561 (mm) REVERT: C 178 MET cc_start: 0.8020 (tpp) cc_final: 0.7622 (tpt) REVERT: C 215 ARG cc_start: 0.8519 (mmm160) cc_final: 0.8286 (mmt-90) REVERT: C 256 ASP cc_start: 0.8071 (OUTLIER) cc_final: 0.7811 (t0) REVERT: C 310 MET cc_start: 0.8255 (tmm) cc_final: 0.8001 (tmm) REVERT: C 329 TYR cc_start: 0.8812 (OUTLIER) cc_final: 0.7895 (m-10) outliers start: 40 outliers final: 30 residues processed: 219 average time/residue: 0.2221 time to fit residues: 73.5648 Evaluate side-chains 218 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 182 time to evaluate : 1.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 127 ILE Chi-restraints excluded: chain A residue 129 GLU Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 232 LEU 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 328 THR Chi-restraints excluded: chain A residue 411 THR 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 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 935 LEU 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 75 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 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 77 optimal weight: 3.9990 chunk 60 optimal weight: 8.9990 chunk 88 optimal weight: 4.9990 chunk 133 optimal weight: 6.9990 chunk 122 optimal weight: 4.9990 chunk 106 optimal weight: 0.5980 chunk 11 optimal weight: 7.9990 chunk 82 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 chunk 113 optimal weight: 6.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- 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 ** C 142 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.3923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11268 Z= 0.261 Angle : 0.684 12.462 15278 Z= 0.335 Chirality : 0.045 0.243 1723 Planarity : 0.004 0.041 1919 Dihedral : 7.588 96.386 1580 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 3.32 % Allowed : 21.59 % Favored : 75.08 % 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: -2.59 (0.22), residues: 1342 helix: -0.81 (0.22), residues: 533 sheet: -1.93 (0.36), residues: 191 loop : -2.46 (0.24), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 207 HIS 0.005 0.001 HIS A 470 PHE 0.026 0.001 PHE A1075 TYR 0.020 0.001 TYR A 431 ARG 0.008 0.000 ARG A 206 ********************** 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 232 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 192 time to evaluate : 1.184 Fit side-chains revert: symmetry clash REVERT: A 58 LYS cc_start: 0.9089 (tttm) cc_final: 0.8741 (tppt) REVERT: A 114 HIS cc_start: 0.8198 (OUTLIER) cc_final: 0.7964 (t-90) REVERT: A 118 ASN cc_start: 0.8758 (t0) cc_final: 0.8294 (t0) REVERT: A 212 GLU cc_start: 0.7650 (pp20) cc_final: 0.7214 (pp20) REVERT: A 302 LYS cc_start: 0.9138 (ttmt) cc_final: 0.8852 (mtmt) REVERT: A 348 MET cc_start: 0.8930 (mmm) cc_final: 0.8705 (tpp) REVERT: A 523 GLU cc_start: 0.7745 (mm-30) cc_final: 0.7504 (mm-30) REVERT: A 678 MET cc_start: 0.9025 (tmm) cc_final: 0.8812 (tmm) REVERT: A 696 GLU cc_start: 0.6803 (tm-30) cc_final: 0.6312 (tm-30) REVERT: A 714 ARG cc_start: 0.7599 (mmm-85) cc_final: 0.7282 (mmm-85) REVERT: A 877 PHE cc_start: 0.9186 (OUTLIER) cc_final: 0.8185 (t80) REVERT: A 935 LEU cc_start: 0.9321 (OUTLIER) cc_final: 0.8950 (tt) REVERT: A 938 ASP cc_start: 0.8393 (t0) cc_final: 0.7257 (t0) REVERT: A 940 ARG cc_start: 0.7851 (ttp-110) cc_final: 0.7602 (ttp-110) REVERT: A 942 TYR cc_start: 0.7330 (m-80) cc_final: 0.6971 (m-80) REVERT: A 992 ASN cc_start: 0.8565 (p0) cc_final: 0.7796 (t0) REVERT: A 1053 MET cc_start: 0.8495 (mtp) cc_final: 0.8167 (mtp) REVERT: A 1056 VAL cc_start: 0.8963 (t) cc_final: 0.8736 (p) REVERT: C 74 ASN cc_start: 0.8211 (t0) cc_final: 0.7800 (t0) REVERT: C 75 ILE cc_start: 0.8806 (OUTLIER) cc_final: 0.8579 (mm) REVERT: C 178 MET cc_start: 0.8088 (tpp) cc_final: 0.7608 (tpp) REVERT: C 215 ARG cc_start: 0.8570 (mmm160) cc_final: 0.8341 (mmt-90) REVERT: C 256 ASP cc_start: 0.8164 (OUTLIER) cc_final: 0.7859 (t0) REVERT: C 310 MET cc_start: 0.8322 (tmm) cc_final: 0.8054 (tmm) REVERT: C 329 TYR cc_start: 0.8845 (OUTLIER) cc_final: 0.7979 (m-10) outliers start: 40 outliers final: 31 residues processed: 217 average time/residue: 0.2045 time to fit residues: 65.8113 Evaluate side-chains 225 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 188 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 127 ILE Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 232 LEU 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 328 THR Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 492 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 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 935 LEU 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 75 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 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 32 optimal weight: 0.7980 chunk 98 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 29 optimal weight: 0.7980 chunk 106 optimal weight: 2.9990 chunk 44 optimal weight: 10.0000 chunk 109 optimal weight: 6.9990 chunk 13 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 93 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 664 HIS A 888 GLN ** C 142 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 = 0.3396 r_free = 0.3396 target = 0.117816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.090456 restraints weight = 18847.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.092507 restraints weight = 10525.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.093199 restraints weight = 7266.355| |-----------------------------------------------------------------------------| r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.4134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11268 Z= 0.196 Angle : 0.675 12.664 15278 Z= 0.333 Chirality : 0.044 0.247 1723 Planarity : 0.004 0.052 1919 Dihedral : 7.561 96.656 1580 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 3.16 % Allowed : 22.26 % 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: -2.38 (0.23), residues: 1342 helix: -0.65 (0.23), residues: 526 sheet: -1.83 (0.37), residues: 190 loop : -2.29 (0.24), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 207 HIS 0.005 0.001 HIS C 302 PHE 0.042 0.001 PHE A 462 TYR 0.024 0.001 TYR A 722 ARG 0.011 0.000 ARG A 723 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2281.54 seconds wall clock time: 42 minutes 17.00 seconds (2537.00 seconds total)