Starting phenix.real_space_refine on Sat Jul 20 14:16:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bsp_30163/07_2024/7bsp_30163_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bsp_30163/07_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_30163/07_2024/7bsp_30163.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bsp_30163/07_2024/7bsp_30163.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bsp_30163/07_2024/7bsp_30163_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bsp_30163/07_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 Residue "A ARG 135": "NH1" <-> "NH2" Residue "A GLU 212": "OE1" <-> "OE2" Residue "A ARG 237": "NH1" <-> "NH2" Residue "A ARG 332": "NH1" <-> "NH2" Residue "A GLU 383": "OE1" <-> "OE2" Residue "A GLU 387": "OE1" <-> "OE2" Residue "A GLU 423": "OE1" <-> "OE2" Residue "A GLU 488": "OE1" <-> "OE2" Residue "A ARG 521": "NH1" <-> "NH2" Residue "A GLU 528": "OE1" <-> "OE2" Residue "A GLU 530": "OE1" <-> "OE2" Residue "A GLU 555": "OE1" <-> "OE2" Residue "A GLU 579": "OE1" <-> "OE2" Residue "A GLU 586": "OE1" <-> "OE2" Residue "A GLU 602": "OE1" <-> "OE2" Residue "A GLU 609": "OE1" <-> "OE2" Residue "A GLU 649": "OE1" <-> "OE2" Residue "A GLU 658": "OE1" <-> "OE2" Residue "A GLU 699": "OE1" <-> "OE2" Residue "A ARG 839": "NH1" <-> "NH2" Residue "A GLU 966": "OE1" <-> "OE2" Residue "A GLU 985": "OE1" <-> "OE2" Residue "A PHE 1017": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1052": "NH1" <-> "NH2" Residue "A GLU 1081": "OE1" <-> "OE2" Residue "C ARG 27": "NH1" <-> "NH2" Residue "C ARG 76": "NH1" <-> "NH2" Residue "C GLU 86": "OE1" <-> "OE2" Residue "C ARG 132": "NH1" <-> "NH2" Residue "C ARG 270": "NH1" <-> "NH2" Residue "C ARG 309": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 6.84, per 1000 atoms: 0.62 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 - 3.50 Amino acid : False - 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: 4.54 Conformation dependent library (CDL) restraints added in 1.9 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: 1.33 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: 3.46 Time building geometry restraints manager: 4.95 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: 99.90 - 107.13: 299 107.13 - 114.35: 6699 114.35 - 121.58: 5750 121.58 - 128.81: 2462 128.81 - 136.03: 68 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 2.440 nonbonded pdb=" OH TYR A 879 " pdb=" OE1 GLU A 966 " model vdw 1.943 2.440 nonbonded pdb=" O ASP A 409 " pdb=" OG1 THR A 413 " model vdw 1.949 2.440 nonbonded pdb=" OD1 ASP A 904 " pdb=" N ALA A 905 " model vdw 1.968 2.520 nonbonded pdb=" OG1 THR A 553 " pdb=" O ASP A 557 " model vdw 1.989 2.440 ... (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 ========== 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: 0.880 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: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 32.450 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.830 ------------------------------------------------------------------------------- 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 : 1.266 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: 0.2188 time to fit residues: 70.6749 Evaluate side-chains 160 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 160 time to evaluate : 1.230 ------------------------------------------------------------------------------- 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: 0.9990 chunk 56 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 68 optimal weight: 7.9990 chunk 54 optimal weight: 0.9980 chunk 105 optimal weight: 2.9990 chunk 40 optimal weight: 9.9990 chunk 63 optimal weight: 6.9990 chunk 78 optimal weight: 0.4980 chunk 121 optimal weight: 10.0000 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 641 ASN A 716 HIS A 794 GLN A 862 HIS A 892 GLN ** A 929 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1089 ASN C 130 ASN ** C 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 302 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 11268 Z= 0.259 Angle : 0.738 10.178 15278 Z= 0.376 Chirality : 0.048 0.311 1723 Planarity : 0.005 0.035 1919 Dihedral : 11.206 107.934 1580 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 15.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.54 % Favored : 90.46 % Rotamer: Outliers : 1.99 % Allowed : 11.46 % Favored : 86.54 % 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: -5.36 (0.18), residues: 1342 helix: -3.58 (0.15), residues: 533 sheet: -3.45 (0.33), residues: 183 loop : -3.50 (0.21), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 376 HIS 0.012 0.001 HIS C 302 PHE 0.021 0.002 PHE A1036 TYR 0.014 0.002 TYR A 108 ARG 0.005 0.000 ARG A 133 *********************** 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 244 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 220 time to evaluate : 1.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 LYS cc_start: 0.9001 (tttm) cc_final: 0.8572 (tppt) REVERT: A 117 ASP cc_start: 0.8448 (m-30) cc_final: 0.8044 (t0) REVERT: A 118 ASN cc_start: 0.8828 (t0) cc_final: 0.8593 (t0) REVERT: A 154 THR cc_start: 0.9048 (OUTLIER) cc_final: 0.8836 (m) REVERT: A 365 MET cc_start: 0.9118 (tpp) cc_final: 0.8822 (mmm) REVERT: A 419 MET cc_start: 0.8642 (mmp) cc_final: 0.8388 (mmp) REVERT: A 650 ASP cc_start: 0.8391 (t0) cc_final: 0.8040 (t0) REVERT: A 714 ARG cc_start: 0.7998 (mtp180) cc_final: 0.7555 (mmm-85) REVERT: A 781 LYS cc_start: 0.8874 (mtpt) cc_final: 0.8603 (ttpt) REVERT: A 885 ILE cc_start: 0.9385 (tp) cc_final: 0.9115 (tp) REVERT: A 992 ASN cc_start: 0.8371 (p0) cc_final: 0.7428 (t0) REVERT: C 130 ASN cc_start: 0.8879 (OUTLIER) cc_final: 0.8476 (p0) REVERT: C 310 MET cc_start: 0.8102 (tmm) cc_final: 0.7230 (tmm) outliers start: 24 outliers final: 15 residues processed: 231 average time/residue: 0.2095 time to fit residues: 70.4262 Evaluate side-chains 194 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 177 time to evaluate : 1.136 ------------------------------------------------------------------------------- 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 100 THR Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 539 ASN Chi-restraints excluded: chain A residue 600 PHE Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 713 ASP 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: 9.9990 chunk 37 optimal weight: 1.9990 chunk 101 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 121 optimal weight: 20.0000 chunk 131 optimal weight: 7.9990 chunk 108 optimal weight: 5.9990 chunk 120 optimal weight: 0.6980 chunk 41 optimal weight: 10.0000 chunk 97 optimal weight: 4.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 130 ASN A 213 GLN A 584 HIS A 929 HIS ** C 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 216 ASN C 302 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11268 Z= 0.276 Angle : 0.688 9.077 15278 Z= 0.347 Chirality : 0.047 0.275 1723 Planarity : 0.004 0.039 1919 Dihedral : 9.257 104.112 1580 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 14.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.17 % Favored : 90.83 % Rotamer: Outliers : 3.41 % Allowed : 15.61 % Favored : 80.98 % 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: -4.27 (0.20), residues: 1342 helix: -2.56 (0.18), residues: 536 sheet: -2.90 (0.35), residues: 182 loop : -3.00 (0.23), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 323 HIS 0.010 0.001 HIS C 302 PHE 0.016 0.002 PHE C 214 TYR 0.019 0.001 TYR A 771 ARG 0.007 0.000 ARG A 516 *********************** 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 240 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 199 time to evaluate : 1.274 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 LYS cc_start: 0.9009 (tttm) cc_final: 0.8609 (tppt) REVERT: A 117 ASP cc_start: 0.8480 (m-30) cc_final: 0.8085 (t0) REVERT: A 118 ASN cc_start: 0.8873 (t0) cc_final: 0.8563 (t0) REVERT: A 419 MET cc_start: 0.8644 (mmp) cc_final: 0.8277 (mmp) REVERT: A 431 TYR cc_start: 0.8350 (t80) cc_final: 0.8130 (t80) REVERT: A 498 GLU cc_start: 0.9030 (pt0) cc_final: 0.8564 (pm20) REVERT: A 517 ASN cc_start: 0.8455 (t0) cc_final: 0.8218 (t0) REVERT: A 616 ILE cc_start: 0.9498 (pt) cc_final: 0.9199 (mt) REVERT: A 643 ILE cc_start: 0.9467 (mt) cc_final: 0.9267 (mm) REVERT: A 678 MET cc_start: 0.9108 (tmm) cc_final: 0.8638 (tmm) REVERT: A 714 ARG cc_start: 0.7806 (mtp180) cc_final: 0.7518 (mmm-85) REVERT: A 877 PHE cc_start: 0.9111 (OUTLIER) cc_final: 0.8233 (t80) REVERT: A 992 ASN cc_start: 0.8415 (p0) cc_final: 0.7501 (t0) REVERT: C 74 ASN cc_start: 0.7945 (t0) cc_final: 0.7478 (t0) REVERT: C 75 ILE cc_start: 0.8919 (mt) cc_final: 0.8718 (mm) REVERT: C 176 ASN cc_start: 0.8776 (t0) cc_final: 0.8515 (t0) REVERT: C 261 MET cc_start: 0.8633 (mmp) cc_final: 0.7844 (tpp) REVERT: C 310 MET cc_start: 0.8213 (tmm) cc_final: 0.7230 (tmm) outliers start: 41 outliers final: 30 residues processed: 218 average time/residue: 0.1997 time to fit residues: 64.8195 Evaluate side-chains 211 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 180 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 145 ASP 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 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 539 ASN Chi-restraints excluded: chain A residue 600 PHE Chi-restraints excluded: chain A residue 620 MET Chi-restraints excluded: chain A residue 646 THR Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 713 ASP 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 829 VAL Chi-restraints excluded: chain A residue 877 PHE Chi-restraints excluded: chain A residue 895 CYS 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: 9.9990 chunk 13 optimal weight: 10.0000 chunk 58 optimal weight: 7.9990 chunk 81 optimal weight: 0.6980 chunk 122 optimal weight: 3.9990 chunk 129 optimal weight: 2.9990 chunk 115 optimal weight: 10.0000 chunk 34 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 ASN ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.2811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 11268 Z= 0.299 Angle : 0.676 9.602 15278 Z= 0.341 Chirality : 0.046 0.248 1723 Planarity : 0.004 0.042 1919 Dihedral : 8.370 103.049 1580 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.61 % Favored : 90.39 % Rotamer: Outliers : 4.73 % Allowed : 16.36 % Favored : 78.90 % 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: -3.75 (0.21), residues: 1342 helix: -2.07 (0.20), residues: 538 sheet: -2.59 (0.36), residues: 182 loop : -2.78 (0.23), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 313 HIS 0.014 0.001 HIS C 302 PHE 0.013 0.002 PHE A 462 TYR 0.019 0.002 TYR A 771 ARG 0.004 0.000 ARG A 516 *********************** 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 246 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 189 time to evaluate : 1.257 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 45 ILE cc_start: 0.8382 (tt) cc_final: 0.8096 (mm) REVERT: A 58 LYS cc_start: 0.9052 (tttm) cc_final: 0.8634 (tppt) REVERT: A 117 ASP cc_start: 0.8161 (m-30) cc_final: 0.7719 (t0) REVERT: A 118 ASN cc_start: 0.8850 (t0) cc_final: 0.8505 (t0) REVERT: A 498 GLU cc_start: 0.9063 (pt0) cc_final: 0.8526 (pm20) REVERT: A 616 ILE cc_start: 0.9449 (pt) cc_final: 0.9170 (mt) REVERT: A 678 MET cc_start: 0.9165 (tmm) cc_final: 0.8912 (tmm) REVERT: A 696 GLU cc_start: 0.7128 (tm-30) cc_final: 0.6721 (tm-30) REVERT: A 714 ARG cc_start: 0.7778 (mtp180) cc_final: 0.7523 (mmm-85) REVERT: A 877 PHE cc_start: 0.9135 (OUTLIER) cc_final: 0.8238 (t80) REVERT: A 885 ILE cc_start: 0.9254 (tp) cc_final: 0.8931 (tp) REVERT: A 992 ASN cc_start: 0.8492 (p0) cc_final: 0.7565 (t0) REVERT: C 74 ASN cc_start: 0.7992 (t0) cc_final: 0.7393 (t0) REVERT: C 176 ASN cc_start: 0.8851 (t0) cc_final: 0.8594 (t0) REVERT: C 261 MET cc_start: 0.8569 (mmp) cc_final: 0.7809 (tpp) REVERT: C 310 MET cc_start: 0.8269 (tmm) cc_final: 0.7243 (tmm) REVERT: C 329 TYR cc_start: 0.8911 (OUTLIER) cc_final: 0.8359 (m-10) outliers start: 57 outliers final: 39 residues processed: 224 average time/residue: 0.1996 time to fit residues: 66.6613 Evaluate side-chains 219 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 178 time to evaluate : 1.245 ------------------------------------------------------------------------------- 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 86 THR Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 114 HIS Chi-restraints excluded: chain A residue 145 ASP 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 235 VAL Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 264 THR 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 484 THR Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 539 ASN Chi-restraints excluded: chain A residue 600 PHE Chi-restraints excluded: chain A residue 620 MET Chi-restraints excluded: chain A residue 646 THR Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 711 LYS Chi-restraints excluded: chain A residue 713 ASP Chi-restraints excluded: chain A residue 750 ILE Chi-restraints excluded: chain A residue 752 ASP Chi-restraints excluded: chain A residue 761 ASN Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 877 PHE Chi-restraints excluded: chain A residue 895 CYS Chi-restraints excluded: chain A residue 898 SER Chi-restraints excluded: chain A residue 1004 VAL 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 Chi-restraints excluded: chain C residue 329 TYR Chi-restraints excluded: chain C residue 338 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 73 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 96 optimal weight: 0.9980 chunk 53 optimal weight: 9.9990 chunk 110 optimal weight: 0.9990 chunk 89 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 66 optimal weight: 9.9990 chunk 116 optimal weight: 4.9990 chunk 32 optimal weight: 0.6980 chunk 43 optimal weight: 6.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 929 HIS ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.3135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11268 Z= 0.189 Angle : 0.632 9.123 15278 Z= 0.316 Chirality : 0.045 0.265 1723 Planarity : 0.004 0.041 1919 Dihedral : 8.080 101.751 1580 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.68 % Favored : 92.32 % Rotamer: Outliers : 2.91 % Allowed : 19.19 % Favored : 77.91 % 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: -3.25 (0.21), residues: 1342 helix: -1.54 (0.21), residues: 531 sheet: -2.33 (0.37), residues: 182 loop : -2.61 (0.24), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 313 HIS 0.006 0.001 HIS C 302 PHE 0.016 0.001 PHE A 462 TYR 0.023 0.001 TYR A 431 ARG 0.004 0.000 ARG A 940 *********************** 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 237 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 202 time to evaluate : 1.336 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 45 ILE cc_start: 0.8446 (tt) cc_final: 0.8242 (mm) REVERT: A 58 LYS cc_start: 0.9013 (tttm) cc_final: 0.8686 (tppt) REVERT: A 117 ASP cc_start: 0.8117 (m-30) cc_final: 0.7727 (t0) REVERT: A 118 ASN cc_start: 0.8773 (t0) cc_final: 0.8383 (t0) REVERT: A 212 GLU cc_start: 0.7504 (pp20) cc_final: 0.7079 (pp20) REVERT: A 498 GLU cc_start: 0.8962 (pt0) cc_final: 0.8418 (pm20) REVERT: A 616 ILE cc_start: 0.9329 (pt) cc_final: 0.9102 (mt) REVERT: A 696 GLU cc_start: 0.7238 (tm-30) cc_final: 0.6944 (tm-30) REVERT: A 714 ARG cc_start: 0.7755 (mtp180) cc_final: 0.7476 (mmm-85) REVERT: A 877 PHE cc_start: 0.9101 (OUTLIER) cc_final: 0.8174 (t80) REVERT: A 885 ILE cc_start: 0.9188 (tp) cc_final: 0.8844 (tp) REVERT: A 992 ASN cc_start: 0.8392 (p0) cc_final: 0.7633 (t0) REVERT: C 74 ASN cc_start: 0.8011 (t0) cc_final: 0.7762 (t0) REVERT: C 176 ASN cc_start: 0.8794 (t0) cc_final: 0.8534 (t0) REVERT: C 242 MET cc_start: 0.8671 (pmm) cc_final: 0.8431 (pmm) REVERT: C 310 MET cc_start: 0.8219 (tmm) cc_final: 0.7146 (tmm) REVERT: C 329 TYR cc_start: 0.8815 (OUTLIER) cc_final: 0.8165 (m-10) outliers start: 35 outliers final: 26 residues processed: 225 average time/residue: 0.1912 time to fit residues: 64.5708 Evaluate side-chains 211 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 183 time to evaluate : 1.238 ------------------------------------------------------------------------------- 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 86 THR Chi-restraints excluded: chain A residue 114 HIS Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 152 ASP 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 539 ASN Chi-restraints excluded: chain A residue 600 PHE Chi-restraints excluded: chain A residue 620 MET Chi-restraints excluded: chain A residue 646 THR Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 691 PHE Chi-restraints excluded: chain A residue 713 ASP Chi-restraints excluded: chain A residue 814 ILE Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 877 PHE Chi-restraints excluded: chain A residue 898 SER Chi-restraints excluded: chain A residue 1077 SER Chi-restraints excluded: chain C residue 126 ASN Chi-restraints excluded: chain C residue 256 ASP Chi-restraints excluded: chain C residue 292 TRP Chi-restraints excluded: chain C residue 302 HIS Chi-restraints excluded: chain C residue 329 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 116 optimal weight: 3.9990 chunk 25 optimal weight: 6.9990 chunk 76 optimal weight: 7.9990 chunk 31 optimal weight: 5.9990 chunk 129 optimal weight: 7.9990 chunk 107 optimal weight: 6.9990 chunk 60 optimal weight: 7.9990 chunk 10 optimal weight: 10.0000 chunk 42 optimal weight: 9.9990 chunk 68 optimal weight: 3.9990 chunk 124 optimal weight: 0.9980 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN ** A 888 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: 0.8563 moved from start: 0.3026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.091 11268 Z= 0.490 Angle : 0.770 9.089 15278 Z= 0.383 Chirality : 0.050 0.245 1723 Planarity : 0.004 0.042 1919 Dihedral : 8.090 98.359 1580 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 16.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.58 % Favored : 89.42 % Rotamer: Outliers : 5.48 % Allowed : 19.35 % 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: -3.44 (0.21), residues: 1342 helix: -1.69 (0.20), residues: 546 sheet: -2.36 (0.37), residues: 183 loop : -2.78 (0.24), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 313 HIS 0.011 0.002 HIS C 302 PHE 0.014 0.002 PHE A1075 TYR 0.035 0.002 TYR C 134 ARG 0.004 0.001 ARG A 940 *********************** 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: 66 poor density : 174 time to evaluate : 1.176 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 LYS cc_start: 0.9081 (tttm) cc_final: 0.8738 (tppt) REVERT: A 117 ASP cc_start: 0.8423 (m-30) cc_final: 0.8107 (t0) REVERT: A 118 ASN cc_start: 0.8867 (t0) cc_final: 0.8507 (t0) REVERT: A 212 GLU cc_start: 0.7428 (pp20) cc_final: 0.7042 (pp20) REVERT: A 523 GLU cc_start: 0.7850 (mm-30) cc_final: 0.7598 (mm-30) REVERT: A 678 MET cc_start: 0.9122 (tmm) cc_final: 0.8741 (tmm) REVERT: A 696 GLU cc_start: 0.7180 (tm-30) cc_final: 0.6910 (tm-30) REVERT: A 877 PHE cc_start: 0.9180 (OUTLIER) cc_final: 0.8290 (t80) REVERT: A 885 ILE cc_start: 0.9204 (tp) cc_final: 0.8900 (tp) REVERT: A 897 PHE cc_start: 0.9076 (OUTLIER) cc_final: 0.8593 (m-10) REVERT: A 935 LEU cc_start: 0.9439 (OUTLIER) cc_final: 0.9037 (tt) REVERT: A 992 ASN cc_start: 0.8608 (p0) cc_final: 0.7702 (t0) REVERT: C 74 ASN cc_start: 0.8152 (t0) cc_final: 0.7812 (t0) REVERT: C 310 MET cc_start: 0.8378 (tmm) cc_final: 0.7752 (tmm) REVERT: C 329 TYR cc_start: 0.8888 (OUTLIER) cc_final: 0.8401 (m-10) outliers start: 66 outliers final: 48 residues processed: 219 average time/residue: 0.1848 time to fit residues: 60.9922 Evaluate side-chains 216 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 164 time to evaluate : 1.151 ------------------------------------------------------------------------------- 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 86 THR Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 114 HIS Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 264 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 484 THR Chi-restraints excluded: chain A residue 539 ASN Chi-restraints excluded: chain A residue 600 PHE Chi-restraints excluded: chain A residue 620 MET Chi-restraints excluded: chain A residue 646 THR Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 691 PHE Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 711 LYS Chi-restraints excluded: chain A residue 713 ASP Chi-restraints excluded: chain A residue 752 ASP Chi-restraints excluded: chain A residue 761 ASN Chi-restraints excluded: chain A residue 812 LEU 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 895 CYS 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 1004 VAL Chi-restraints excluded: chain A residue 1077 SER Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 126 ASN Chi-restraints excluded: chain C residue 256 ASP Chi-restraints excluded: chain C residue 268 THR 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: 10.0000 chunk 73 optimal weight: 0.9980 chunk 94 optimal weight: 0.8980 chunk 109 optimal weight: 8.9990 chunk 72 optimal weight: 4.9990 chunk 129 optimal weight: 0.4980 chunk 80 optimal weight: 0.5980 chunk 78 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 664 HIS C 35 GLN ** 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: 0.3396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11268 Z= 0.183 Angle : 0.645 11.161 15278 Z= 0.317 Chirality : 0.044 0.247 1723 Planarity : 0.004 0.041 1919 Dihedral : 7.836 98.466 1580 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 3.24 % Allowed : 22.09 % Favored : 74.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.90 (0.22), residues: 1342 helix: -1.17 (0.22), residues: 530 sheet: -2.14 (0.37), residues: 182 loop : -2.50 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 292 HIS 0.014 0.001 HIS C 302 PHE 0.015 0.001 PHE A 462 TYR 0.025 0.001 TYR A 431 ARG 0.005 0.000 ARG A 940 *********************** 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 237 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 198 time to evaluate : 1.059 Fit side-chains revert: symmetry clash REVERT: A 58 LYS cc_start: 0.9013 (tttm) cc_final: 0.8666 (tppt) REVERT: A 114 HIS cc_start: 0.8290 (OUTLIER) cc_final: 0.8079 (t-90) REVERT: A 117 ASP cc_start: 0.8322 (m-30) cc_final: 0.8028 (t0) REVERT: A 118 ASN cc_start: 0.8784 (t0) cc_final: 0.8426 (t0) REVERT: A 168 ASP cc_start: 0.8195 (t70) cc_final: 0.7795 (t0) REVERT: A 212 GLU cc_start: 0.7435 (pp20) cc_final: 0.7047 (pp20) REVERT: A 309 LEU cc_start: 0.9162 (OUTLIER) cc_final: 0.8851 (mp) REVERT: A 523 GLU cc_start: 0.7892 (mm-30) cc_final: 0.7644 (mm-30) REVERT: A 696 GLU cc_start: 0.7259 (tm-30) cc_final: 0.6890 (tm-30) REVERT: A 877 PHE cc_start: 0.9113 (OUTLIER) cc_final: 0.8217 (t80) REVERT: A 885 ILE cc_start: 0.9184 (tp) cc_final: 0.8793 (tp) REVERT: A 992 ASN cc_start: 0.8423 (p0) cc_final: 0.7714 (t0) REVERT: C 74 ASN cc_start: 0.8157 (t0) cc_final: 0.7839 (t0) REVERT: C 310 MET cc_start: 0.8248 (tmm) cc_final: 0.7731 (tmm) REVERT: C 329 TYR cc_start: 0.8869 (OUTLIER) cc_final: 0.8172 (m-10) outliers start: 39 outliers final: 29 residues processed: 222 average time/residue: 0.1972 time to fit residues: 65.0094 Evaluate side-chains 213 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 180 time to evaluate : 1.192 ------------------------------------------------------------------------------- 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 145 ASP Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 539 ASN Chi-restraints excluded: chain A residue 600 PHE Chi-restraints excluded: chain A residue 646 THR Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 691 PHE Chi-restraints excluded: chain A residue 713 ASP Chi-restraints excluded: chain A residue 752 ASP Chi-restraints excluded: chain A residue 754 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 242 MET Chi-restraints excluded: chain C residue 256 ASP Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 292 TRP Chi-restraints excluded: chain C residue 302 HIS Chi-restraints excluded: chain C residue 329 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 77 optimal weight: 7.9990 chunk 38 optimal weight: 6.9990 chunk 25 optimal weight: 0.9990 chunk 82 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 12 optimal weight: 0.9990 chunk 101 optimal weight: 0.9990 chunk 117 optimal weight: 2.9990 chunk 123 optimal weight: 0.9990 chunk 112 optimal weight: 3.9990 overall best weight: 0.9788 ------------------------------------------------------------------------------- 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 302 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.3553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 11268 Z= 0.199 Angle : 0.627 10.510 15278 Z= 0.311 Chirality : 0.044 0.251 1723 Planarity : 0.004 0.041 1919 Dihedral : 7.639 97.434 1580 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.90 % Favored : 92.10 % Rotamer: Outliers : 3.57 % Allowed : 21.35 % 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: -2.71 (0.22), residues: 1342 helix: -0.95 (0.22), residues: 529 sheet: -2.03 (0.37), residues: 183 loop : -2.47 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 313 HIS 0.007 0.001 HIS C 302 PHE 0.015 0.001 PHE A 462 TYR 0.021 0.001 TYR A 431 ARG 0.005 0.000 ARG A 940 *********************** 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 236 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 193 time to evaluate : 1.164 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 LYS cc_start: 0.9057 (tttm) cc_final: 0.8596 (tppt) REVERT: A 117 ASP cc_start: 0.8342 (m-30) cc_final: 0.7868 (t0) REVERT: A 118 ASN cc_start: 0.8784 (t0) cc_final: 0.8373 (t0) REVERT: A 168 ASP cc_start: 0.8149 (t70) cc_final: 0.7736 (t0) REVERT: A 194 ILE cc_start: 0.9040 (pt) cc_final: 0.8809 (mm) REVERT: A 212 GLU cc_start: 0.7375 (pp20) cc_final: 0.7015 (pp20) REVERT: A 309 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8832 (mp) REVERT: A 523 GLU cc_start: 0.7862 (mm-30) cc_final: 0.7614 (mm-30) REVERT: A 678 MET cc_start: 0.9139 (tmm) cc_final: 0.8593 (tmm) REVERT: A 696 GLU cc_start: 0.7260 (tm-30) cc_final: 0.6850 (tm-30) REVERT: A 781 LYS cc_start: 0.8687 (mtmt) cc_final: 0.8389 (mtpp) REVERT: A 877 PHE cc_start: 0.9147 (OUTLIER) cc_final: 0.8155 (t80) REVERT: A 885 ILE cc_start: 0.9175 (tp) cc_final: 0.8748 (tp) REVERT: A 935 LEU cc_start: 0.9338 (OUTLIER) cc_final: 0.8929 (tt) REVERT: A 992 ASN cc_start: 0.8438 (p0) cc_final: 0.7767 (t0) REVERT: C 74 ASN cc_start: 0.8227 (t0) cc_final: 0.7910 (t0) REVERT: C 310 MET cc_start: 0.8274 (tmm) cc_final: 0.7998 (tmm) REVERT: C 329 TYR cc_start: 0.8848 (OUTLIER) cc_final: 0.7912 (m-10) outliers start: 43 outliers final: 32 residues processed: 220 average time/residue: 0.1946 time to fit residues: 64.2173 Evaluate side-chains 214 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 178 time to evaluate : 1.154 ------------------------------------------------------------------------------- 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 86 THR Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 539 ASN Chi-restraints excluded: chain A residue 600 PHE Chi-restraints excluded: chain A residue 620 MET Chi-restraints excluded: chain A residue 646 THR Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 691 PHE Chi-restraints excluded: chain A residue 713 ASP Chi-restraints excluded: chain A residue 752 ASP 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 1077 SER Chi-restraints excluded: chain A residue 1087 LEU Chi-restraints excluded: chain C residue 126 ASN Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 242 MET Chi-restraints excluded: chain C residue 256 ASP Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 329 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 120 optimal weight: 2.9990 chunk 123 optimal weight: 0.0670 chunk 72 optimal weight: 0.7980 chunk 52 optimal weight: 6.9990 chunk 94 optimal weight: 0.0980 chunk 36 optimal weight: 10.0000 chunk 108 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 119 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 chunk 127 optimal weight: 0.0870 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN A 664 HIS A 888 GLN ** C 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.3859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11268 Z= 0.171 Angle : 0.612 10.337 15278 Z= 0.301 Chirality : 0.043 0.254 1723 Planarity : 0.004 0.041 1919 Dihedral : 7.455 96.870 1580 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 3.32 % Allowed : 22.26 % Favored : 74.42 % 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: -2.43 (0.23), residues: 1342 helix: -0.70 (0.23), residues: 530 sheet: -1.80 (0.38), residues: 183 loop : -2.35 (0.24), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 376 HIS 0.004 0.001 HIS A 929 PHE 0.027 0.001 PHE A1075 TYR 0.029 0.001 TYR A 431 ARG 0.006 0.000 ARG A 940 *********************** 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 237 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 197 time to evaluate : 1.220 Fit side-chains revert: symmetry clash REVERT: A 58 LYS cc_start: 0.9096 (tttm) cc_final: 0.8620 (tppt) REVERT: A 117 ASP cc_start: 0.8306 (m-30) cc_final: 0.7814 (t0) REVERT: A 118 ASN cc_start: 0.8765 (t0) cc_final: 0.8331 (t0) REVERT: A 168 ASP cc_start: 0.8028 (t70) cc_final: 0.7606 (t0) REVERT: A 194 ILE cc_start: 0.9004 (pt) cc_final: 0.8761 (mm) REVERT: A 212 GLU cc_start: 0.7438 (pp20) cc_final: 0.7096 (pp20) REVERT: A 523 GLU cc_start: 0.7875 (mm-30) cc_final: 0.7651 (mm-30) REVERT: A 696 GLU cc_start: 0.7337 (tm-30) cc_final: 0.6646 (tm-30) REVERT: A 711 LYS cc_start: 0.9154 (OUTLIER) cc_final: 0.8720 (ttpt) REVERT: A 877 PHE cc_start: 0.9151 (OUTLIER) cc_final: 0.8122 (t80) REVERT: A 885 ILE cc_start: 0.9161 (tp) cc_final: 0.8699 (tp) REVERT: A 935 LEU cc_start: 0.9323 (OUTLIER) cc_final: 0.8923 (tt) REVERT: A 985 GLU cc_start: 0.8043 (tm-30) cc_final: 0.7827 (tm-30) REVERT: A 992 ASN cc_start: 0.8360 (p0) cc_final: 0.7798 (t0) REVERT: C 74 ASN cc_start: 0.8266 (t0) cc_final: 0.8050 (t0) REVERT: C 178 MET cc_start: 0.7780 (tpp) cc_final: 0.7394 (tpt) REVERT: C 256 ASP cc_start: 0.8122 (OUTLIER) cc_final: 0.7835 (t0) REVERT: C 310 MET cc_start: 0.8223 (tmm) cc_final: 0.7963 (tmm) REVERT: C 329 TYR cc_start: 0.8809 (OUTLIER) cc_final: 0.7961 (m-10) outliers start: 40 outliers final: 27 residues processed: 224 average time/residue: 0.1969 time to fit residues: 65.9400 Evaluate side-chains 214 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 182 time to evaluate : 1.235 ------------------------------------------------------------------------------- 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 86 THR Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 539 ASN Chi-restraints excluded: chain A residue 600 PHE Chi-restraints excluded: chain A residue 620 MET Chi-restraints excluded: chain A residue 646 THR Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 691 PHE Chi-restraints excluded: chain A residue 711 LYS Chi-restraints excluded: chain A residue 713 ASP Chi-restraints excluded: chain A residue 752 ASP 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 C residue 44 ILE Chi-restraints excluded: chain C residue 126 ASN Chi-restraints excluded: chain C residue 204 ILE 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: 7.9990 chunk 60 optimal weight: 0.7980 chunk 88 optimal weight: 0.5980 chunk 133 optimal weight: 6.9990 chunk 122 optimal weight: 7.9990 chunk 106 optimal weight: 3.9990 chunk 11 optimal weight: 0.0370 chunk 82 optimal weight: 1.9990 chunk 65 optimal weight: 6.9990 chunk 84 optimal weight: 0.6980 chunk 113 optimal weight: 0.8980 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 ASN A 575 ASN A 664 HIS A 888 GLN ** C 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.4024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 11268 Z= 0.186 Angle : 0.625 10.211 15278 Z= 0.311 Chirality : 0.044 0.252 1723 Planarity : 0.004 0.041 1919 Dihedral : 7.346 96.329 1580 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 2.91 % Allowed : 23.17 % Favored : 73.92 % 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: -2.40 (0.23), residues: 1342 helix: -0.62 (0.23), residues: 538 sheet: -1.79 (0.36), residues: 198 loop : -2.40 (0.24), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 207 HIS 0.012 0.001 HIS C 302 PHE 0.018 0.001 PHE A 970 TYR 0.026 0.001 TYR A 431 ARG 0.006 0.000 ARG A 940 ********************** 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 227 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 192 time to evaluate : 1.345 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 LYS cc_start: 0.9089 (tttm) cc_final: 0.8638 (tppt) REVERT: A 117 ASP cc_start: 0.8309 (m-30) cc_final: 0.7821 (t0) REVERT: A 118 ASN cc_start: 0.8688 (t0) cc_final: 0.8265 (t0) REVERT: A 168 ASP cc_start: 0.8015 (t70) cc_final: 0.7648 (t0) REVERT: A 194 ILE cc_start: 0.8979 (pt) cc_final: 0.8736 (mm) REVERT: A 212 GLU cc_start: 0.7413 (pp20) cc_final: 0.7068 (pp20) REVERT: A 270 MET cc_start: 0.8965 (ppp) cc_final: 0.8626 (ppp) REVERT: A 523 GLU cc_start: 0.7835 (mm-30) cc_final: 0.7600 (mm-30) REVERT: A 678 MET cc_start: 0.8967 (tmm) cc_final: 0.8404 (ttp) REVERT: A 711 LYS cc_start: 0.9165 (OUTLIER) cc_final: 0.8693 (ttpt) REVERT: A 781 LYS cc_start: 0.8675 (mtmt) cc_final: 0.8230 (mttp) REVERT: A 877 PHE cc_start: 0.9137 (OUTLIER) cc_final: 0.8080 (t80) REVERT: A 885 ILE cc_start: 0.9154 (tp) cc_final: 0.8638 (tp) REVERT: A 935 LEU cc_start: 0.9306 (OUTLIER) cc_final: 0.8927 (tt) REVERT: A 985 GLU cc_start: 0.8004 (tm-30) cc_final: 0.7784 (tm-30) REVERT: A 992 ASN cc_start: 0.8369 (p0) cc_final: 0.7867 (t0) REVERT: C 74 ASN cc_start: 0.8302 (t0) cc_final: 0.8089 (t0) REVERT: C 178 MET cc_start: 0.7785 (tpp) cc_final: 0.7399 (tpt) REVERT: C 256 ASP cc_start: 0.8056 (OUTLIER) cc_final: 0.7806 (t0) REVERT: C 302 HIS cc_start: 0.7704 (p-80) cc_final: 0.7404 (p-80) REVERT: C 310 MET cc_start: 0.8235 (tmm) cc_final: 0.7954 (tmm) REVERT: C 329 TYR cc_start: 0.8817 (OUTLIER) cc_final: 0.7918 (m-10) outliers start: 35 outliers final: 28 residues processed: 211 average time/residue: 0.1990 time to fit residues: 63.1535 Evaluate side-chains 212 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 179 time to evaluate : 1.315 ------------------------------------------------------------------------------- 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 86 THR Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 539 ASN Chi-restraints excluded: chain A residue 600 PHE Chi-restraints excluded: chain A residue 620 MET Chi-restraints excluded: chain A residue 646 THR Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 691 PHE Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 711 LYS Chi-restraints excluded: chain A residue 713 ASP Chi-restraints excluded: chain A residue 752 ASP 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 1053 MET Chi-restraints excluded: chain A residue 1087 LEU Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 126 ASN Chi-restraints excluded: chain C residue 204 ILE 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: 1.9990 chunk 98 optimal weight: 0.8980 chunk 15 optimal weight: 0.0030 chunk 29 optimal weight: 0.0870 chunk 106 optimal weight: 6.9990 chunk 44 optimal weight: 7.9990 chunk 109 optimal weight: 0.6980 chunk 13 optimal weight: 3.9990 chunk 19 optimal weight: 0.0870 chunk 93 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 overall best weight: 0.3546 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 HIS A 664 HIS A 888 GLN ** C 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.119051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.091171 restraints weight = 18730.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.092519 restraints weight = 13996.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.093748 restraints weight = 8724.578| |-----------------------------------------------------------------------------| r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.4229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 11268 Z= 0.175 Angle : 0.618 10.099 15278 Z= 0.308 Chirality : 0.043 0.254 1723 Planarity : 0.004 0.041 1919 Dihedral : 7.274 96.248 1580 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.15 % Favored : 92.85 % Rotamer: Outliers : 2.49 % Allowed : 24.25 % Favored : 73.26 % 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: -2.22 (0.23), residues: 1342 helix: -0.47 (0.23), residues: 537 sheet: -1.59 (0.37), residues: 197 loop : -2.36 (0.24), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP C 207 HIS 0.011 0.001 HIS C 302 PHE 0.040 0.001 PHE A 462 TYR 0.029 0.001 TYR A 431 ARG 0.006 0.000 ARG A 940 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2268.68 seconds wall clock time: 41 minutes 40.93 seconds (2500.93 seconds total)