Starting phenix.real_space_refine on Wed May 14 12:27:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jnj_36449/05_2025/8jnj_36449_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jnj_36449/05_2025/8jnj_36449.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jnj_36449/05_2025/8jnj_36449.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jnj_36449/05_2025/8jnj_36449.map" model { file = "/net/cci-nas-00/data/ceres_data/8jnj_36449/05_2025/8jnj_36449_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jnj_36449/05_2025/8jnj_36449_neut.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 56 5.16 5 C 7718 2.51 5 N 1948 2.21 5 O 2014 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 11736 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 758, 5868 Classifications: {'peptide': 758} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 38, 'TRANS': 719} Chain breaks: 3 Unresolved non-hydrogen bonds: 137 Unresolved non-hydrogen angles: 159 Unresolved non-hydrogen dihedrals: 115 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 11, 'ARG:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 89 Chain: "B" Number of atoms: 5868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 758, 5868 Classifications: {'peptide': 758} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 38, 'TRANS': 719} Chain breaks: 3 Unresolved non-hydrogen bonds: 137 Unresolved non-hydrogen angles: 159 Unresolved non-hydrogen dihedrals: 115 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 11, 'ARG:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 89 Time building chain proxies: 7.61, per 1000 atoms: 0.65 Number of scatterers: 11736 At special positions: 0 Unit cell: (102.625, 109.193, 117.403, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 56 16.00 O 2014 8.00 N 1948 7.00 C 7718 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.68 Conformation dependent library (CDL) restraints added in 1.5 seconds 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2864 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 9 sheets defined 63.5% alpha, 9.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.42 Creating SS restraints... Processing helix chain 'A' and resid 370 through 381 Processing helix chain 'A' and resid 393 through 408 Processing helix chain 'A' and resid 415 through 424 Processing helix chain 'A' and resid 504 through 510 removed outlier: 3.544A pdb=" N GLU A 508 " --> pdb=" O LEU A 504 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LYS A 509 " --> pdb=" O LYS A 505 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE A 510 " --> pdb=" O LEU A 506 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 504 through 510' Processing helix chain 'A' and resid 568 through 582 Processing helix chain 'A' and resid 584 through 591 removed outlier: 3.539A pdb=" N LEU A 591 " --> pdb=" O GLU A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 607 Processing helix chain 'A' and resid 623 through 638 removed outlier: 4.228A pdb=" N ALA A 627 " --> pdb=" O LEU A 623 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N HIS A 628 " --> pdb=" O ARG A 624 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 693 Processing helix chain 'A' and resid 695 through 702 removed outlier: 3.626A pdb=" N PHE A 700 " --> pdb=" O TYR A 696 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 734 removed outlier: 3.799A pdb=" N LEU A 709 " --> pdb=" O ASP A 705 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE A 713 " --> pdb=" O LEU A 709 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N PHE A 717 " --> pdb=" O ILE A 713 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA A 718 " --> pdb=" O PHE A 714 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER A 721 " --> pdb=" O PHE A 717 " (cutoff:3.500A) Proline residue: A 722 - end of helix Processing helix chain 'A' and resid 739 through 758 Processing helix chain 'A' and resid 768 through 785 removed outlier: 3.565A pdb=" N ALA A 777 " --> pdb=" O VAL A 773 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER A 780 " --> pdb=" O GLU A 776 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N PHE A 781 " --> pdb=" O ALA A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 810 removed outlier: 3.658A pdb=" N ILE A 796 " --> pdb=" O GLY A 792 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N PHE A 802 " --> pdb=" O PHE A 798 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 818 removed outlier: 4.028A pdb=" N PHE A 814 " --> pdb=" O GLU A 811 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU A 815 " --> pdb=" O GLY A 812 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N VAL A 816 " --> pdb=" O SER A 813 " (cutoff:3.500A) Processing helix chain 'A' and resid 820 through 850 removed outlier: 3.547A pdb=" N ILE A 826 " --> pdb=" O PHE A 822 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER A 832 " --> pdb=" O ALA A 828 " (cutoff:3.500A) Processing helix chain 'A' and resid 899 through 924 removed outlier: 3.607A pdb=" N PHE A 912 " --> pdb=" O MET A 908 " (cutoff:3.500A) Processing helix chain 'A' and resid 928 through 935 removed outlier: 4.050A pdb=" N VAL A 934 " --> pdb=" O ARG A 930 " (cutoff:3.500A) Processing helix chain 'A' and resid 938 through 954 removed outlier: 3.592A pdb=" N ILE A 942 " --> pdb=" O PHE A 938 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE A 954 " --> pdb=" O VAL A 950 " (cutoff:3.500A) Processing helix chain 'A' and resid 990 through 997 removed outlier: 3.501A pdb=" N MET A 994 " --> pdb=" O PRO A 990 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 997 through 1020 Processing helix chain 'A' and resid 1021 through 1025 Processing helix chain 'A' and resid 1032 through 1047 Processing helix chain 'A' and resid 1057 through 1068 removed outlier: 3.604A pdb=" N LEU A1068 " --> pdb=" O HIS A1064 " (cutoff:3.500A) Processing helix chain 'A' and resid 1090 through 1102 Processing helix chain 'A' and resid 1103 through 1105 No H-bonds generated for 'chain 'A' and resid 1103 through 1105' Processing helix chain 'A' and resid 1106 through 1111 removed outlier: 3.636A pdb=" N LEU A1110 " --> pdb=" O ILE A1106 " (cutoff:3.500A) Processing helix chain 'A' and resid 1114 through 1129 removed outlier: 3.575A pdb=" N LEU A1118 " --> pdb=" O PRO A1114 " (cutoff:3.500A) Processing helix chain 'A' and resid 1133 through 1142 Processing helix chain 'A' and resid 1145 through 1149 removed outlier: 3.512A pdb=" N HIS A1149 " --> pdb=" O PRO A1146 " (cutoff:3.500A) Processing helix chain 'A' and resid 1152 through 1157 Processing helix chain 'A' and resid 1159 through 1183 removed outlier: 3.773A pdb=" N LEU A1177 " --> pdb=" O CYS A1173 " (cutoff:3.500A) Processing helix chain 'A' and resid 1185 through 1187 No H-bonds generated for 'chain 'A' and resid 1185 through 1187' Processing helix chain 'A' and resid 1188 through 1194 Processing helix chain 'A' and resid 1195 through 1208 removed outlier: 3.892A pdb=" N LEU A1204 " --> pdb=" O ARG A1200 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N THR A1205 " --> pdb=" O MET A1201 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ARG A1206 " --> pdb=" O VAL A1202 " (cutoff:3.500A) Processing helix chain 'A' and resid 1209 through 1217 removed outlier: 3.504A pdb=" N CYS A1215 " --> pdb=" O ARG A1211 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 381 Processing helix chain 'B' and resid 393 through 408 Processing helix chain 'B' and resid 415 through 424 Processing helix chain 'B' and resid 504 through 510 removed outlier: 3.544A pdb=" N GLU B 508 " --> pdb=" O LEU B 504 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LYS B 509 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE B 510 " --> pdb=" O LEU B 506 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 504 through 510' Processing helix chain 'B' and resid 568 through 582 Processing helix chain 'B' and resid 584 through 591 removed outlier: 3.538A pdb=" N LEU B 591 " --> pdb=" O GLU B 587 " (cutoff:3.500A) Processing helix chain 'B' and resid 594 through 607 Processing helix chain 'B' and resid 623 through 638 removed outlier: 4.228A pdb=" N ALA B 627 " --> pdb=" O LEU B 623 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N HIS B 628 " --> pdb=" O ARG B 624 " (cutoff:3.500A) Processing helix chain 'B' and resid 682 through 693 Processing helix chain 'B' and resid 695 through 702 removed outlier: 3.626A pdb=" N PHE B 700 " --> pdb=" O TYR B 696 " (cutoff:3.500A) Processing helix chain 'B' and resid 705 through 734 removed outlier: 3.798A pdb=" N LEU B 709 " --> pdb=" O ASP B 705 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE B 713 " --> pdb=" O LEU B 709 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N PHE B 717 " --> pdb=" O ILE B 713 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA B 718 " --> pdb=" O PHE B 714 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER B 721 " --> pdb=" O PHE B 717 " (cutoff:3.500A) Proline residue: B 722 - end of helix Processing helix chain 'B' and resid 739 through 758 Processing helix chain 'B' and resid 768 through 785 removed outlier: 3.565A pdb=" N ALA B 777 " --> pdb=" O VAL B 773 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER B 780 " --> pdb=" O GLU B 776 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N PHE B 781 " --> pdb=" O ALA B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 788 through 810 removed outlier: 3.658A pdb=" N ILE B 796 " --> pdb=" O GLY B 792 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N PHE B 802 " --> pdb=" O PHE B 798 " (cutoff:3.500A) Processing helix chain 'B' and resid 811 through 818 removed outlier: 4.028A pdb=" N PHE B 814 " --> pdb=" O GLU B 811 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU B 815 " --> pdb=" O GLY B 812 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N VAL B 816 " --> pdb=" O SER B 813 " (cutoff:3.500A) Processing helix chain 'B' and resid 820 through 850 removed outlier: 3.548A pdb=" N ILE B 826 " --> pdb=" O PHE B 822 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER B 832 " --> pdb=" O ALA B 828 " (cutoff:3.500A) Processing helix chain 'B' and resid 899 through 924 removed outlier: 3.606A pdb=" N PHE B 912 " --> pdb=" O MET B 908 " (cutoff:3.500A) Processing helix chain 'B' and resid 928 through 935 removed outlier: 4.050A pdb=" N VAL B 934 " --> pdb=" O ARG B 930 " (cutoff:3.500A) Processing helix chain 'B' and resid 938 through 954 removed outlier: 3.592A pdb=" N ILE B 942 " --> pdb=" O PHE B 938 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE B 954 " --> pdb=" O VAL B 950 " (cutoff:3.500A) Processing helix chain 'B' and resid 990 through 997 removed outlier: 3.501A pdb=" N MET B 994 " --> pdb=" O PRO B 990 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 997 through 1020 Processing helix chain 'B' and resid 1021 through 1025 Processing helix chain 'B' and resid 1032 through 1047 Processing helix chain 'B' and resid 1057 through 1068 removed outlier: 3.604A pdb=" N LEU B1068 " --> pdb=" O HIS B1064 " (cutoff:3.500A) Processing helix chain 'B' and resid 1090 through 1102 Processing helix chain 'B' and resid 1103 through 1105 No H-bonds generated for 'chain 'B' and resid 1103 through 1105' Processing helix chain 'B' and resid 1106 through 1111 removed outlier: 3.636A pdb=" N LEU B1110 " --> pdb=" O ILE B1106 " (cutoff:3.500A) Processing helix chain 'B' and resid 1114 through 1129 removed outlier: 3.575A pdb=" N LEU B1118 " --> pdb=" O PRO B1114 " (cutoff:3.500A) Processing helix chain 'B' and resid 1133 through 1142 Processing helix chain 'B' and resid 1145 through 1149 removed outlier: 3.513A pdb=" N HIS B1149 " --> pdb=" O PRO B1146 " (cutoff:3.500A) Processing helix chain 'B' and resid 1152 through 1157 Processing helix chain 'B' and resid 1159 through 1183 removed outlier: 3.773A pdb=" N LEU B1177 " --> pdb=" O CYS B1173 " (cutoff:3.500A) Processing helix chain 'B' and resid 1185 through 1187 No H-bonds generated for 'chain 'B' and resid 1185 through 1187' Processing helix chain 'B' and resid 1188 through 1194 Processing helix chain 'B' and resid 1195 through 1208 removed outlier: 3.892A pdb=" N LEU B1204 " --> pdb=" O ARG B1200 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N THR B1205 " --> pdb=" O MET B1201 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ARG B1206 " --> pdb=" O VAL B1202 " (cutoff:3.500A) Processing helix chain 'B' and resid 1209 through 1217 removed outlier: 3.503A pdb=" N CYS B1215 " --> pdb=" O ARG B1211 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 359 through 360 removed outlier: 3.685A pdb=" N ARG A 359 " --> pdb=" O GLU A 354 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N THR A 343 " --> pdb=" O VAL A 353 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N LEU A 327 " --> pdb=" O THR A 343 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ARG A 345 " --> pdb=" O VAL A 325 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N VAL A 325 " --> pdb=" O ARG A 345 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N GLU A 326 " --> pdb=" O VAL A 519 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N VAL A 521 " --> pdb=" O GLU A 326 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ASN A 328 " --> pdb=" O VAL A 521 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N CYS A 523 " --> pdb=" O ASN A 328 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N LEU A 330 " --> pdb=" O CYS A 523 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N ALA A 516 " --> pdb=" O VAL A 553 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N PHE A 555 " --> pdb=" O ALA A 516 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N ARG A 554 " --> pdb=" O LEU A 537 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ALA A 384 " --> pdb=" O PHE A 534 " (cutoff:3.500A) removed outlier: 8.438A pdb=" N ARG A 536 " --> pdb=" O ALA A 384 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N LEU A 386 " --> pdb=" O ARG A 536 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ARG A 538 " --> pdb=" O LEU A 386 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ASP A 388 " --> pdb=" O ARG A 538 " (cutoff:3.500A) removed outlier: 10.440A pdb=" N ALA A 540 " --> pdb=" O ASP A 388 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 359 through 360 removed outlier: 3.685A pdb=" N ARG A 359 " --> pdb=" O GLU A 354 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N THR A 343 " --> pdb=" O VAL A 353 " (cutoff:3.500A) removed outlier: 8.494A pdb=" N SER A 428 " --> pdb=" O PRO A 338 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N TRP A 340 " --> pdb=" O SER A 428 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 368 through 369 Processing sheet with id=AA4, first strand: chain 'A' and resid 765 through 766 Processing sheet with id=AA5, first strand: chain 'A' and resid 1069 through 1071 removed outlier: 3.502A pdb=" N GLU A1085 " --> pdb=" O VAL A1070 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 359 through 360 removed outlier: 3.685A pdb=" N ARG B 359 " --> pdb=" O GLU B 354 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N THR B 343 " --> pdb=" O VAL B 353 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N LEU B 327 " --> pdb=" O THR B 343 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ARG B 345 " --> pdb=" O VAL B 325 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N VAL B 325 " --> pdb=" O ARG B 345 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N GLU B 326 " --> pdb=" O VAL B 519 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N VAL B 521 " --> pdb=" O GLU B 326 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ASN B 328 " --> pdb=" O VAL B 521 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N CYS B 523 " --> pdb=" O ASN B 328 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N LEU B 330 " --> pdb=" O CYS B 523 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N ALA B 516 " --> pdb=" O VAL B 553 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N PHE B 555 " --> pdb=" O ALA B 516 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N ARG B 554 " --> pdb=" O LEU B 537 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ALA B 384 " --> pdb=" O PHE B 534 " (cutoff:3.500A) removed outlier: 8.438A pdb=" N ARG B 536 " --> pdb=" O ALA B 384 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N LEU B 386 " --> pdb=" O ARG B 536 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ARG B 538 " --> pdb=" O LEU B 386 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N ASP B 388 " --> pdb=" O ARG B 538 " (cutoff:3.500A) removed outlier: 10.440A pdb=" N ALA B 540 " --> pdb=" O ASP B 388 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 359 through 360 removed outlier: 3.685A pdb=" N ARG B 359 " --> pdb=" O GLU B 354 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N THR B 343 " --> pdb=" O VAL B 353 " (cutoff:3.500A) removed outlier: 8.495A pdb=" N SER B 428 " --> pdb=" O PRO B 338 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N TRP B 340 " --> pdb=" O SER B 428 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 765 through 766 Processing sheet with id=AA9, first strand: chain 'B' and resid 1069 through 1071 removed outlier: 3.501A pdb=" N GLU B1085 " --> pdb=" O VAL B1070 " (cutoff:3.500A) 670 hydrogen bonds defined for protein. 1944 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: 3.55 Time building geometry restraints manager: 3.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3722 1.34 - 1.46: 2252 1.46 - 1.57: 5938 1.57 - 1.69: 0 1.69 - 1.81: 96 Bond restraints: 12008 Sorted by residual: bond pdb=" CB VAL B1004 " pdb=" CG2 VAL B1004 " ideal model delta sigma weight residual 1.521 1.493 0.028 3.30e-02 9.18e+02 7.14e-01 bond pdb=" CB VAL A1004 " pdb=" CG2 VAL A1004 " ideal model delta sigma weight residual 1.521 1.493 0.028 3.30e-02 9.18e+02 7.14e-01 bond pdb=" CB TRP A 795 " pdb=" CG TRP A 795 " ideal model delta sigma weight residual 1.498 1.474 0.024 3.10e-02 1.04e+03 5.95e-01 bond pdb=" CB TRP B 795 " pdb=" CG TRP B 795 " ideal model delta sigma weight residual 1.498 1.474 0.024 3.10e-02 1.04e+03 5.95e-01 bond pdb=" CB PRO A1190 " pdb=" CG PRO A1190 " ideal model delta sigma weight residual 1.492 1.455 0.037 5.00e-02 4.00e+02 5.46e-01 ... (remaining 12003 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.47: 16083 1.47 - 2.94: 197 2.94 - 4.40: 50 4.40 - 5.87: 14 5.87 - 7.34: 2 Bond angle restraints: 16346 Sorted by residual: angle pdb=" C PHE B 349 " pdb=" CA PHE B 349 " pdb=" CB PHE B 349 " ideal model delta sigma weight residual 116.34 111.58 4.76 1.40e+00 5.10e-01 1.16e+01 angle pdb=" C PHE A 349 " pdb=" CA PHE A 349 " pdb=" CB PHE A 349 " ideal model delta sigma weight residual 116.34 111.61 4.73 1.40e+00 5.10e-01 1.14e+01 angle pdb=" N VAL B1197 " pdb=" CA VAL B1197 " pdb=" C VAL B1197 " ideal model delta sigma weight residual 112.35 109.78 2.57 1.20e+00 6.94e-01 4.58e+00 angle pdb=" N VAL A1197 " pdb=" CA VAL A1197 " pdb=" C VAL A1197 " ideal model delta sigma weight residual 112.35 109.79 2.56 1.20e+00 6.94e-01 4.55e+00 angle pdb=" CA LEU B 376 " pdb=" CB LEU B 376 " pdb=" CG LEU B 376 " ideal model delta sigma weight residual 116.30 123.64 -7.34 3.50e+00 8.16e-02 4.40e+00 ... (remaining 16341 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 6784 17.89 - 35.78: 280 35.78 - 53.67: 50 53.67 - 71.56: 12 71.56 - 89.45: 4 Dihedral angle restraints: 7130 sinusoidal: 2732 harmonic: 4398 Sorted by residual: dihedral pdb=" CA ILE A1194 " pdb=" C ILE A1194 " pdb=" N LEU A1195 " pdb=" CA LEU A1195 " ideal model delta harmonic sigma weight residual 180.00 159.89 20.11 0 5.00e+00 4.00e-02 1.62e+01 dihedral pdb=" CA ILE B1194 " pdb=" C ILE B1194 " pdb=" N LEU B1195 " pdb=" CA LEU B1195 " ideal model delta harmonic sigma weight residual 180.00 159.90 20.10 0 5.00e+00 4.00e-02 1.62e+01 dihedral pdb=" CA TRP B 346 " pdb=" C TRP B 346 " pdb=" N ILE B 347 " pdb=" CA ILE B 347 " ideal model delta harmonic sigma weight residual 180.00 161.80 18.20 0 5.00e+00 4.00e-02 1.33e+01 ... (remaining 7127 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1011 0.027 - 0.053: 643 0.053 - 0.080: 174 0.080 - 0.107: 95 0.107 - 0.133: 41 Chirality restraints: 1964 Sorted by residual: chirality pdb=" CA ILE B 510 " pdb=" N ILE B 510 " pdb=" C ILE B 510 " pdb=" CB ILE B 510 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.44e-01 chirality pdb=" CA ILE A 510 " pdb=" N ILE A 510 " pdb=" C ILE A 510 " pdb=" CB ILE A 510 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.44e-01 chirality pdb=" CA VAL B 551 " pdb=" N VAL B 551 " pdb=" C VAL B 551 " pdb=" CB VAL B 551 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.38e-01 ... (remaining 1961 not shown) Planarity restraints: 2040 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A1060 " 0.141 9.50e-02 1.11e+02 6.33e-02 2.46e+00 pdb=" NE ARG A1060 " -0.008 2.00e-02 2.50e+03 pdb=" CZ ARG A1060 " -0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG A1060 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A1060 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B1060 " -0.140 9.50e-02 1.11e+02 6.30e-02 2.44e+00 pdb=" NE ARG B1060 " 0.008 2.00e-02 2.50e+03 pdb=" CZ ARG B1060 " 0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG B1060 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG B1060 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B1189 " 0.023 5.00e-02 4.00e+02 3.44e-02 1.90e+00 pdb=" N PRO B1190 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO B1190 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO B1190 " 0.020 5.00e-02 4.00e+02 ... (remaining 2037 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 3322 2.81 - 3.34: 11701 3.34 - 3.86: 18953 3.86 - 4.38: 23062 4.38 - 4.90: 39675 Nonbonded interactions: 96713 Sorted by model distance: nonbonded pdb=" O LEU B 730 " pdb=" OG1 THR B 734 " model vdw 2.292 3.040 nonbonded pdb=" O LEU A 730 " pdb=" OG1 THR A 734 " model vdw 2.292 3.040 nonbonded pdb=" OG SER B 832 " pdb=" OG SER B1129 " model vdw 2.307 3.040 nonbonded pdb=" OG SER A 832 " pdb=" OG SER A1129 " model vdw 2.308 3.040 nonbonded pdb=" O MET B1181 " pdb=" OG SER B1186 " model vdw 2.308 3.040 ... (remaining 96708 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.840 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: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 28.380 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12008 Z= 0.156 Angle : 0.492 7.339 16346 Z= 0.255 Chirality : 0.041 0.133 1964 Planarity : 0.004 0.063 2040 Dihedral : 10.552 89.452 4266 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.45 % Allowed : 4.50 % Favored : 94.05 % 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: -0.38 (0.21), residues: 1500 helix: -0.49 (0.17), residues: 880 sheet: -0.28 (0.55), residues: 92 loop : 0.57 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 346 HIS 0.006 0.001 HIS A 586 PHE 0.013 0.001 PHE B1189 TYR 0.007 0.001 TYR B1154 ARG 0.002 0.000 ARG B 637 Details of bonding type rmsd hydrogen bonds : bond 0.25784 ( 662) hydrogen bonds : angle 8.61920 ( 1944) covalent geometry : bond 0.00378 (12008) covalent geometry : angle 0.49206 (16346) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 209 time to evaluate : 1.288 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 322 GLU cc_start: 0.6966 (tp30) cc_final: 0.6494 (mp0) REVERT: A 377 ARG cc_start: 0.7526 (ttt-90) cc_final: 0.7260 (mtp180) REVERT: A 378 ARG cc_start: 0.7759 (ttm110) cc_final: 0.7516 (ttm110) REVERT: A 580 MET cc_start: 0.8451 (mmm) cc_final: 0.8121 (mmm) REVERT: A 582 ASP cc_start: 0.7506 (t70) cc_final: 0.7118 (t70) REVERT: A 749 LEU cc_start: 0.8163 (tp) cc_final: 0.7925 (tp) REVERT: A 833 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8054 (mp) REVERT: B 377 ARG cc_start: 0.7510 (ttt-90) cc_final: 0.7263 (mtp180) REVERT: B 378 ARG cc_start: 0.7775 (ttm110) cc_final: 0.7532 (ttm110) REVERT: B 580 MET cc_start: 0.8483 (mmm) cc_final: 0.8144 (mmm) REVERT: B 582 ASP cc_start: 0.7503 (t70) cc_final: 0.7116 (t70) REVERT: B 749 LEU cc_start: 0.8151 (tp) cc_final: 0.7917 (tp) REVERT: B 833 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8121 (mp) outliers start: 18 outliers final: 10 residues processed: 221 average time/residue: 0.2518 time to fit residues: 78.7125 Evaluate side-chains 169 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 157 time to evaluate : 1.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 544 ASP Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 927 PHE Chi-restraints excluded: chain A residue 1152 VAL Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 544 ASP Chi-restraints excluded: chain B residue 833 LEU Chi-restraints excluded: chain B residue 927 PHE Chi-restraints excluded: chain B residue 1152 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 126 optimal weight: 0.9980 chunk 113 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 76 optimal weight: 0.1980 chunk 60 optimal weight: 2.9990 chunk 117 optimal weight: 0.1980 chunk 45 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 87 optimal weight: 4.9990 chunk 136 optimal weight: 0.0370 overall best weight: 0.4258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 628 HIS B 628 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.155083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.116718 restraints weight = 13206.545| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 1.90 r_work: 0.3159 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12008 Z= 0.131 Angle : 0.550 6.367 16346 Z= 0.281 Chirality : 0.041 0.142 1964 Planarity : 0.004 0.051 2040 Dihedral : 5.163 55.842 1632 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.85 % Allowed : 7.96 % Favored : 90.19 % 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: 0.80 (0.22), residues: 1500 helix: 0.76 (0.18), residues: 888 sheet: -0.01 (0.57), residues: 92 loop : 0.49 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 346 HIS 0.006 0.001 HIS B 586 PHE 0.016 0.001 PHE A1122 TYR 0.011 0.001 TYR A 590 ARG 0.004 0.000 ARG A 631 Details of bonding type rmsd hydrogen bonds : bond 0.04642 ( 662) hydrogen bonds : angle 4.79831 ( 1944) covalent geometry : bond 0.00288 (12008) covalent geometry : angle 0.55015 (16346) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 172 time to evaluate : 1.395 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 377 ARG cc_start: 0.7069 (ttt-90) cc_final: 0.6868 (mtp180) REVERT: A 378 ARG cc_start: 0.7540 (ttm110) cc_final: 0.7228 (ttm110) REVERT: A 633 MET cc_start: 0.7035 (mmm) cc_final: 0.6544 (tpp) REVERT: A 636 LYS cc_start: 0.7258 (mmtm) cc_final: 0.6822 (tmtt) REVERT: A 1011 GLU cc_start: 0.8090 (tp30) cc_final: 0.7575 (tt0) REVERT: B 377 ARG cc_start: 0.7065 (ttt-90) cc_final: 0.6863 (mtp180) REVERT: B 378 ARG cc_start: 0.7537 (ttm110) cc_final: 0.7224 (ttm110) REVERT: B 582 ASP cc_start: 0.7463 (t70) cc_final: 0.7121 (t70) REVERT: B 633 MET cc_start: 0.7040 (mmm) cc_final: 0.6423 (tpp) REVERT: B 636 LYS cc_start: 0.7237 (mmtm) cc_final: 0.6817 (tmtt) REVERT: B 1011 GLU cc_start: 0.8097 (tp30) cc_final: 0.7553 (tt0) outliers start: 23 outliers final: 12 residues processed: 184 average time/residue: 0.2585 time to fit residues: 67.7100 Evaluate side-chains 163 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 151 time to evaluate : 1.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 609 SER Chi-restraints excluded: chain A residue 927 PHE Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1152 VAL Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 609 SER Chi-restraints excluded: chain B residue 927 PHE Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1152 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 65 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 8 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 13 optimal weight: 3.9990 chunk 149 optimal weight: 4.9990 chunk 83 optimal weight: 0.9990 chunk 104 optimal weight: 0.6980 chunk 14 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.151732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.111848 restraints weight = 13565.764| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 2.03 r_work: 0.3104 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12008 Z= 0.150 Angle : 0.538 6.476 16346 Z= 0.271 Chirality : 0.042 0.144 1964 Planarity : 0.004 0.054 2040 Dihedral : 4.677 55.265 1620 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.09 % Allowed : 8.92 % Favored : 88.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.22), residues: 1500 helix: 0.98 (0.17), residues: 880 sheet: -0.09 (0.59), residues: 88 loop : 0.57 (0.28), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 346 HIS 0.006 0.001 HIS B 586 PHE 0.018 0.001 PHE B1189 TYR 0.011 0.001 TYR A 590 ARG 0.003 0.000 ARG B 631 Details of bonding type rmsd hydrogen bonds : bond 0.04108 ( 662) hydrogen bonds : angle 4.42947 ( 1944) covalent geometry : bond 0.00359 (12008) covalent geometry : angle 0.53794 (16346) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 156 time to evaluate : 1.382 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 322 GLU cc_start: 0.6699 (tp30) cc_final: 0.5799 (mp0) REVERT: A 378 ARG cc_start: 0.7470 (ttm110) cc_final: 0.7166 (ttm110) REVERT: A 580 MET cc_start: 0.7858 (mmm) cc_final: 0.7599 (mmm) REVERT: A 633 MET cc_start: 0.6903 (mmm) cc_final: 0.6505 (tpp) REVERT: A 1011 GLU cc_start: 0.8065 (tp30) cc_final: 0.7507 (tt0) REVERT: A 1182 SER cc_start: 0.8299 (OUTLIER) cc_final: 0.7708 (t) REVERT: B 322 GLU cc_start: 0.6740 (tp30) cc_final: 0.5832 (mp0) REVERT: B 378 ARG cc_start: 0.7445 (ttm110) cc_final: 0.7138 (ttm110) REVERT: B 580 MET cc_start: 0.7886 (mmm) cc_final: 0.7627 (mmm) REVERT: B 633 MET cc_start: 0.6894 (mmm) cc_final: 0.6386 (tpp) REVERT: B 1011 GLU cc_start: 0.8093 (tp30) cc_final: 0.7531 (tt0) REVERT: B 1182 SER cc_start: 0.8264 (OUTLIER) cc_final: 0.7707 (t) outliers start: 26 outliers final: 13 residues processed: 174 average time/residue: 0.2496 time to fit residues: 61.8306 Evaluate side-chains 155 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 140 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 609 SER Chi-restraints excluded: chain A residue 927 PHE Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1152 VAL Chi-restraints excluded: chain A residue 1182 SER Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 609 SER Chi-restraints excluded: chain B residue 927 PHE Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1152 VAL Chi-restraints excluded: chain B residue 1182 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 101 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 58 optimal weight: 0.2980 chunk 127 optimal weight: 7.9990 chunk 116 optimal weight: 0.5980 chunk 109 optimal weight: 0.5980 chunk 9 optimal weight: 8.9990 chunk 5 optimal weight: 3.9990 chunk 142 optimal weight: 0.5980 chunk 90 optimal weight: 0.9980 chunk 75 optimal weight: 5.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.153953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.114548 restraints weight = 13422.071| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 2.02 r_work: 0.3126 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12008 Z= 0.126 Angle : 0.514 6.436 16346 Z= 0.259 Chirality : 0.041 0.140 1964 Planarity : 0.004 0.051 2040 Dihedral : 4.611 58.395 1620 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.41 % Allowed : 9.97 % Favored : 87.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.22), residues: 1500 helix: 1.13 (0.18), residues: 882 sheet: -0.04 (0.58), residues: 86 loop : 0.52 (0.28), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 346 HIS 0.004 0.001 HIS A 586 PHE 0.017 0.001 PHE B1189 TYR 0.010 0.001 TYR B 569 ARG 0.003 0.000 ARG B 377 Details of bonding type rmsd hydrogen bonds : bond 0.03667 ( 662) hydrogen bonds : angle 4.22267 ( 1944) covalent geometry : bond 0.00294 (12008) covalent geometry : angle 0.51441 (16346) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 161 time to evaluate : 1.354 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 322 GLU cc_start: 0.6700 (tp30) cc_final: 0.5849 (mp0) REVERT: A 378 ARG cc_start: 0.7441 (ttm110) cc_final: 0.7169 (ttm110) REVERT: A 580 MET cc_start: 0.7835 (mmm) cc_final: 0.7505 (mmm) REVERT: A 616 GLU cc_start: 0.8037 (mm-30) cc_final: 0.7788 (mm-30) REVERT: A 633 MET cc_start: 0.6806 (mmm) cc_final: 0.6393 (tpp) REVERT: A 702 ASP cc_start: 0.7834 (m-30) cc_final: 0.7550 (m-30) REVERT: A 916 PHE cc_start: 0.8512 (t80) cc_final: 0.8073 (t80) REVERT: A 1011 GLU cc_start: 0.8025 (tp30) cc_final: 0.7420 (tt0) REVERT: A 1071 MET cc_start: 0.8671 (mmm) cc_final: 0.8317 (mmm) REVERT: A 1182 SER cc_start: 0.8258 (OUTLIER) cc_final: 0.7789 (t) REVERT: B 322 GLU cc_start: 0.6704 (tp30) cc_final: 0.5841 (mp0) REVERT: B 378 ARG cc_start: 0.7432 (ttm110) cc_final: 0.7157 (ttm110) REVERT: B 580 MET cc_start: 0.7869 (mmm) cc_final: 0.7560 (mmm) REVERT: B 633 MET cc_start: 0.6691 (mmm) cc_final: 0.6226 (tpp) REVERT: B 636 LYS cc_start: 0.7105 (mmtm) cc_final: 0.6656 (tmtt) REVERT: B 702 ASP cc_start: 0.7832 (m-30) cc_final: 0.7555 (m-30) REVERT: B 916 PHE cc_start: 0.8492 (t80) cc_final: 0.8049 (t80) REVERT: B 1011 GLU cc_start: 0.8036 (tp30) cc_final: 0.7419 (tt0) REVERT: B 1071 MET cc_start: 0.8649 (mmm) cc_final: 0.8290 (mmm) outliers start: 30 outliers final: 23 residues processed: 184 average time/residue: 0.2282 time to fit residues: 61.2470 Evaluate side-chains 178 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 154 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 609 SER Chi-restraints excluded: chain A residue 756 LEU Chi-restraints excluded: chain A residue 807 MET Chi-restraints excluded: chain A residue 927 PHE Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1152 VAL Chi-restraints excluded: chain A residue 1182 SER Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 523 CYS Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 609 SER Chi-restraints excluded: chain B residue 756 LEU Chi-restraints excluded: chain B residue 807 MET Chi-restraints excluded: chain B residue 927 PHE Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1152 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 40 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 79 optimal weight: 0.1980 chunk 60 optimal weight: 0.0980 chunk 63 optimal weight: 1.9990 chunk 68 optimal weight: 0.4980 chunk 5 optimal weight: 3.9990 chunk 55 optimal weight: 0.7980 chunk 148 optimal weight: 0.9980 chunk 130 optimal weight: 0.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.164330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.129347 restraints weight = 13022.668| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 1.69 r_work: 0.3127 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12008 Z= 0.114 Angle : 0.491 6.502 16346 Z= 0.248 Chirality : 0.040 0.135 1964 Planarity : 0.003 0.046 2040 Dihedral : 4.520 58.921 1620 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.41 % Allowed : 10.37 % Favored : 87.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.22), residues: 1500 helix: 1.16 (0.17), residues: 904 sheet: -0.18 (0.50), residues: 110 loop : 0.61 (0.29), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 346 HIS 0.004 0.001 HIS A 586 PHE 0.016 0.001 PHE B1189 TYR 0.010 0.001 TYR A 569 ARG 0.003 0.000 ARG A 377 Details of bonding type rmsd hydrogen bonds : bond 0.03403 ( 662) hydrogen bonds : angle 4.04398 ( 1944) covalent geometry : bond 0.00264 (12008) covalent geometry : angle 0.49134 (16346) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 169 time to evaluate : 1.353 Fit side-chains REVERT: A 322 GLU cc_start: 0.6785 (tp30) cc_final: 0.5936 (mp0) REVERT: A 580 MET cc_start: 0.8125 (mmm) cc_final: 0.7774 (mmm) REVERT: A 616 GLU cc_start: 0.8075 (mm-30) cc_final: 0.7772 (mm-30) REVERT: A 631 ARG cc_start: 0.6816 (mpt180) cc_final: 0.6306 (mpt180) REVERT: A 633 MET cc_start: 0.7011 (mmm) cc_final: 0.6739 (tpp) REVERT: A 702 ASP cc_start: 0.7872 (m-30) cc_final: 0.7632 (t0) REVERT: A 916 PHE cc_start: 0.8578 (t80) cc_final: 0.8138 (t80) REVERT: A 1011 GLU cc_start: 0.8066 (tp30) cc_final: 0.7564 (tt0) REVERT: B 322 GLU cc_start: 0.6768 (tp30) cc_final: 0.5919 (mp0) REVERT: B 378 ARG cc_start: 0.7623 (ttm110) cc_final: 0.7399 (ttm110) REVERT: B 580 MET cc_start: 0.8114 (mmm) cc_final: 0.7767 (mmm) REVERT: B 616 GLU cc_start: 0.8086 (mm-30) cc_final: 0.7768 (mm-30) REVERT: B 631 ARG cc_start: 0.6851 (mpt180) cc_final: 0.6568 (mpt180) REVERT: B 633 MET cc_start: 0.6806 (mmm) cc_final: 0.6464 (tpp) REVERT: B 636 LYS cc_start: 0.7142 (mmtm) cc_final: 0.6805 (tmtt) REVERT: B 916 PHE cc_start: 0.8577 (t80) cc_final: 0.8132 (t80) REVERT: B 1011 GLU cc_start: 0.8070 (tp30) cc_final: 0.7558 (tt0) REVERT: B 1182 SER cc_start: 0.8359 (OUTLIER) cc_final: 0.7849 (t) outliers start: 30 outliers final: 19 residues processed: 189 average time/residue: 0.2310 time to fit residues: 64.0110 Evaluate side-chains 180 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 160 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 609 SER Chi-restraints excluded: chain A residue 756 LEU Chi-restraints excluded: chain A residue 807 MET Chi-restraints excluded: chain A residue 927 PHE Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1152 VAL Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 523 CYS Chi-restraints excluded: chain B residue 609 SER Chi-restraints excluded: chain B residue 756 LEU Chi-restraints excluded: chain B residue 807 MET Chi-restraints excluded: chain B residue 927 PHE Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1152 VAL Chi-restraints excluded: chain B residue 1182 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 129 optimal weight: 0.9980 chunk 43 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 122 optimal weight: 0.7980 chunk 38 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 chunk 123 optimal weight: 0.6980 chunk 119 optimal weight: 0.5980 chunk 105 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.163011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.127816 restraints weight = 13254.468| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 1.72 r_work: 0.3104 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12008 Z= 0.139 Angle : 0.516 6.492 16346 Z= 0.259 Chirality : 0.041 0.159 1964 Planarity : 0.004 0.049 2040 Dihedral : 4.423 57.040 1618 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.33 % Allowed : 11.50 % Favored : 86.17 % 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: 1.34 (0.22), residues: 1500 helix: 1.23 (0.17), residues: 894 sheet: 0.17 (0.58), residues: 86 loop : 0.65 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 346 HIS 0.005 0.001 HIS A 586 PHE 0.018 0.001 PHE A1189 TYR 0.010 0.001 TYR B 569 ARG 0.003 0.000 ARG B 793 Details of bonding type rmsd hydrogen bonds : bond 0.03513 ( 662) hydrogen bonds : angle 4.06077 ( 1944) covalent geometry : bond 0.00333 (12008) covalent geometry : angle 0.51583 (16346) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 160 time to evaluate : 1.190 Fit side-chains REVERT: A 580 MET cc_start: 0.8197 (mmm) cc_final: 0.7800 (mmm) REVERT: A 631 ARG cc_start: 0.6891 (mpt180) cc_final: 0.6380 (mpt180) REVERT: A 633 MET cc_start: 0.7033 (mmm) cc_final: 0.6765 (tpp) REVERT: A 636 LYS cc_start: 0.7216 (mmtm) cc_final: 0.6786 (tmtt) REVERT: A 916 PHE cc_start: 0.8613 (t80) cc_final: 0.8157 (t80) REVERT: A 1011 GLU cc_start: 0.8099 (tp30) cc_final: 0.7604 (tt0) REVERT: A 1071 MET cc_start: 0.8751 (mmm) cc_final: 0.8502 (mmm) REVERT: A 1182 SER cc_start: 0.8504 (OUTLIER) cc_final: 0.8235 (t) REVERT: B 378 ARG cc_start: 0.7558 (ttm110) cc_final: 0.7331 (ttm110) REVERT: B 580 MET cc_start: 0.8194 (mmm) cc_final: 0.7814 (mmm) REVERT: B 631 ARG cc_start: 0.6789 (mpt180) cc_final: 0.6238 (mpt180) REVERT: B 633 MET cc_start: 0.6794 (mmm) cc_final: 0.6498 (tpp) REVERT: B 636 LYS cc_start: 0.7189 (mmtm) cc_final: 0.6861 (tmtt) REVERT: B 916 PHE cc_start: 0.8620 (t80) cc_final: 0.8159 (t80) REVERT: B 1011 GLU cc_start: 0.8112 (tp30) cc_final: 0.7600 (tt0) REVERT: B 1071 MET cc_start: 0.8743 (mmm) cc_final: 0.8497 (mmm) REVERT: B 1182 SER cc_start: 0.8456 (OUTLIER) cc_final: 0.8169 (t) outliers start: 29 outliers final: 23 residues processed: 179 average time/residue: 0.2176 time to fit residues: 57.1017 Evaluate side-chains 180 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 155 time to evaluate : 1.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 609 SER Chi-restraints excluded: chain A residue 756 LEU Chi-restraints excluded: chain A residue 807 MET Chi-restraints excluded: chain A residue 927 PHE Chi-restraints excluded: chain A residue 978 TRP Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1152 VAL Chi-restraints excluded: chain A residue 1172 LEU Chi-restraints excluded: chain A residue 1182 SER Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 523 CYS Chi-restraints excluded: chain B residue 609 SER Chi-restraints excluded: chain B residue 756 LEU Chi-restraints excluded: chain B residue 807 MET Chi-restraints excluded: chain B residue 927 PHE Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 978 TRP Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1152 VAL Chi-restraints excluded: chain B residue 1182 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 6 optimal weight: 9.9990 chunk 83 optimal weight: 0.9990 chunk 104 optimal weight: 0.7980 chunk 56 optimal weight: 4.9990 chunk 142 optimal weight: 0.8980 chunk 93 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 110 optimal weight: 0.5980 chunk 73 optimal weight: 0.6980 chunk 61 optimal weight: 8.9990 chunk 129 optimal weight: 0.3980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.163798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.128525 restraints weight = 13255.877| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 1.72 r_work: 0.3117 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12008 Z= 0.126 Angle : 0.502 6.507 16346 Z= 0.253 Chirality : 0.041 0.162 1964 Planarity : 0.003 0.047 2040 Dihedral : 4.371 55.495 1618 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.01 % Allowed : 11.98 % Favored : 86.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.22), residues: 1500 helix: 1.33 (0.17), residues: 894 sheet: 0.11 (0.50), residues: 110 loop : 0.69 (0.29), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 346 HIS 0.005 0.001 HIS A 586 PHE 0.017 0.001 PHE B1189 TYR 0.009 0.001 TYR B 569 ARG 0.003 0.000 ARG A 793 Details of bonding type rmsd hydrogen bonds : bond 0.03396 ( 662) hydrogen bonds : angle 4.00424 ( 1944) covalent geometry : bond 0.00298 (12008) covalent geometry : angle 0.50208 (16346) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 158 time to evaluate : 1.253 Fit side-chains REVERT: A 580 MET cc_start: 0.8211 (mmm) cc_final: 0.7819 (mmm) REVERT: A 631 ARG cc_start: 0.6797 (mpt180) cc_final: 0.6203 (mpt180) REVERT: A 636 LYS cc_start: 0.7196 (mmtm) cc_final: 0.6829 (tmtt) REVERT: A 916 PHE cc_start: 0.8560 (t80) cc_final: 0.8099 (t80) REVERT: A 1011 GLU cc_start: 0.8083 (tp30) cc_final: 0.7598 (tt0) REVERT: B 378 ARG cc_start: 0.7535 (ttm110) cc_final: 0.7325 (ttm110) REVERT: B 580 MET cc_start: 0.8226 (mmm) cc_final: 0.7856 (mmm) REVERT: B 631 ARG cc_start: 0.6756 (mpt180) cc_final: 0.6147 (mpt180) REVERT: B 633 MET cc_start: 0.6796 (mmm) cc_final: 0.6455 (tpp) REVERT: B 636 LYS cc_start: 0.7256 (mmtm) cc_final: 0.6936 (tmtt) REVERT: B 916 PHE cc_start: 0.8580 (t80) cc_final: 0.8121 (t80) REVERT: B 1011 GLU cc_start: 0.8102 (tp30) cc_final: 0.7616 (tt0) REVERT: B 1182 SER cc_start: 0.8497 (OUTLIER) cc_final: 0.8246 (t) outliers start: 25 outliers final: 19 residues processed: 175 average time/residue: 0.2338 time to fit residues: 59.8137 Evaluate side-chains 172 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 152 time to evaluate : 1.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 756 LEU Chi-restraints excluded: chain A residue 807 MET Chi-restraints excluded: chain A residue 927 PHE Chi-restraints excluded: chain A residue 978 TRP Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1152 VAL Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 542 GLU Chi-restraints excluded: chain B residue 609 SER Chi-restraints excluded: chain B residue 756 LEU Chi-restraints excluded: chain B residue 807 MET Chi-restraints excluded: chain B residue 927 PHE Chi-restraints excluded: chain B residue 978 TRP Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1152 VAL Chi-restraints excluded: chain B residue 1182 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 3 optimal weight: 5.9990 chunk 131 optimal weight: 4.9990 chunk 89 optimal weight: 0.8980 chunk 1 optimal weight: 0.7980 chunk 88 optimal weight: 5.9990 chunk 11 optimal weight: 9.9990 chunk 134 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 133 optimal weight: 0.0570 chunk 119 optimal weight: 0.9980 overall best weight: 0.7498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.159959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.122901 restraints weight = 13355.394| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 1.84 r_work: 0.3100 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12008 Z= 0.134 Angle : 0.506 6.518 16346 Z= 0.255 Chirality : 0.041 0.158 1964 Planarity : 0.003 0.048 2040 Dihedral : 4.348 53.974 1618 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.17 % Allowed : 12.62 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.22), residues: 1500 helix: 1.32 (0.17), residues: 894 sheet: 0.37 (0.59), residues: 86 loop : 0.67 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 346 HIS 0.005 0.001 HIS A 586 PHE 0.018 0.001 PHE B1189 TYR 0.009 0.001 TYR B 569 ARG 0.003 0.000 ARG A 793 Details of bonding type rmsd hydrogen bonds : bond 0.03422 ( 662) hydrogen bonds : angle 4.00408 ( 1944) covalent geometry : bond 0.00318 (12008) covalent geometry : angle 0.50588 (16346) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 160 time to evaluate : 1.215 Fit side-chains REVERT: A 580 MET cc_start: 0.8183 (mmm) cc_final: 0.7803 (mmm) REVERT: A 636 LYS cc_start: 0.7188 (mmtm) cc_final: 0.6841 (tmtt) REVERT: A 916 PHE cc_start: 0.8569 (t80) cc_final: 0.8116 (t80) REVERT: A 1011 GLU cc_start: 0.8097 (tp30) cc_final: 0.7581 (tt0) REVERT: A 1182 SER cc_start: 0.8515 (OUTLIER) cc_final: 0.8294 (t) REVERT: B 328 ASN cc_start: 0.7043 (p0) cc_final: 0.6786 (p0) REVERT: B 378 ARG cc_start: 0.7499 (ttm110) cc_final: 0.7265 (ttm110) REVERT: B 580 MET cc_start: 0.8187 (mmm) cc_final: 0.7820 (mmm) REVERT: B 631 ARG cc_start: 0.6704 (mpt180) cc_final: 0.6075 (mpt180) REVERT: B 633 MET cc_start: 0.6739 (mmm) cc_final: 0.6415 (tpp) REVERT: B 636 LYS cc_start: 0.7261 (mmtm) cc_final: 0.6943 (tmtt) REVERT: B 916 PHE cc_start: 0.8581 (t80) cc_final: 0.8128 (t80) REVERT: B 1011 GLU cc_start: 0.8122 (tp30) cc_final: 0.7591 (tt0) REVERT: B 1182 SER cc_start: 0.8531 (OUTLIER) cc_final: 0.8299 (t) outliers start: 27 outliers final: 23 residues processed: 178 average time/residue: 0.2236 time to fit residues: 58.0109 Evaluate side-chains 180 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 155 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 609 SER Chi-restraints excluded: chain A residue 756 LEU Chi-restraints excluded: chain A residue 807 MET Chi-restraints excluded: chain A residue 927 PHE Chi-restraints excluded: chain A residue 978 TRP Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1152 VAL Chi-restraints excluded: chain A residue 1172 LEU Chi-restraints excluded: chain A residue 1182 SER Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 523 CYS Chi-restraints excluded: chain B residue 542 GLU Chi-restraints excluded: chain B residue 609 SER Chi-restraints excluded: chain B residue 756 LEU Chi-restraints excluded: chain B residue 807 MET Chi-restraints excluded: chain B residue 927 PHE Chi-restraints excluded: chain B residue 978 TRP Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1152 VAL Chi-restraints excluded: chain B residue 1182 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 107 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 chunk 68 optimal weight: 0.1980 chunk 10 optimal weight: 3.9990 chunk 130 optimal weight: 0.6980 chunk 8 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 7 optimal weight: 0.7980 chunk 126 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.165838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.130952 restraints weight = 13037.870| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 1.72 r_work: 0.3121 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12008 Z= 0.127 Angle : 0.505 6.500 16346 Z= 0.254 Chirality : 0.041 0.174 1964 Planarity : 0.003 0.047 2040 Dihedral : 4.329 53.069 1618 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.01 % Allowed : 12.94 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.22), residues: 1500 helix: 1.35 (0.17), residues: 894 sheet: 0.38 (0.59), residues: 86 loop : 0.74 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 346 HIS 0.005 0.001 HIS A 586 PHE 0.018 0.001 PHE B1189 TYR 0.009 0.001 TYR B 569 ARG 0.003 0.000 ARG A 793 Details of bonding type rmsd hydrogen bonds : bond 0.03384 ( 662) hydrogen bonds : angle 3.98604 ( 1944) covalent geometry : bond 0.00301 (12008) covalent geometry : angle 0.50458 (16346) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 164 time to evaluate : 1.226 Fit side-chains REVERT: A 539 GLU cc_start: 0.7398 (mp0) cc_final: 0.6894 (pm20) REVERT: A 580 MET cc_start: 0.8176 (mmm) cc_final: 0.7810 (mmm) REVERT: A 636 LYS cc_start: 0.7243 (mmtm) cc_final: 0.6923 (tmtt) REVERT: A 916 PHE cc_start: 0.8554 (t80) cc_final: 0.8105 (t80) REVERT: A 1011 GLU cc_start: 0.8081 (tp30) cc_final: 0.7584 (tt0) REVERT: A 1182 SER cc_start: 0.8492 (OUTLIER) cc_final: 0.8285 (t) REVERT: B 328 ASN cc_start: 0.7015 (p0) cc_final: 0.6753 (p0) REVERT: B 580 MET cc_start: 0.8183 (mmm) cc_final: 0.7828 (mmm) REVERT: B 631 ARG cc_start: 0.6719 (mpt180) cc_final: 0.6322 (mpt180) REVERT: B 633 MET cc_start: 0.6770 (mmm) cc_final: 0.6456 (tpp) REVERT: B 636 LYS cc_start: 0.7310 (mmtm) cc_final: 0.7020 (tmtt) REVERT: B 916 PHE cc_start: 0.8564 (t80) cc_final: 0.8114 (t80) REVERT: B 1011 GLU cc_start: 0.8092 (tp30) cc_final: 0.7588 (tt0) REVERT: B 1182 SER cc_start: 0.8512 (OUTLIER) cc_final: 0.8300 (t) outliers start: 25 outliers final: 23 residues processed: 182 average time/residue: 0.2235 time to fit residues: 59.2861 Evaluate side-chains 181 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 156 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 609 SER Chi-restraints excluded: chain A residue 756 LEU Chi-restraints excluded: chain A residue 807 MET Chi-restraints excluded: chain A residue 927 PHE Chi-restraints excluded: chain A residue 978 TRP Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1152 VAL Chi-restraints excluded: chain A residue 1172 LEU Chi-restraints excluded: chain A residue 1182 SER Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 523 CYS Chi-restraints excluded: chain B residue 542 GLU Chi-restraints excluded: chain B residue 609 SER Chi-restraints excluded: chain B residue 756 LEU Chi-restraints excluded: chain B residue 807 MET Chi-restraints excluded: chain B residue 927 PHE Chi-restraints excluded: chain B residue 978 TRP Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1152 VAL Chi-restraints excluded: chain B residue 1182 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 94 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 145 optimal weight: 2.9990 chunk 52 optimal weight: 0.5980 chunk 42 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 102 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 chunk 4 optimal weight: 5.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.162613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.125722 restraints weight = 13059.754| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 1.90 r_work: 0.3124 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 12008 Z= 0.149 Angle : 0.523 6.542 16346 Z= 0.265 Chirality : 0.042 0.190 1964 Planarity : 0.004 0.049 2040 Dihedral : 4.341 51.847 1618 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.09 % Allowed : 13.02 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.22), residues: 1500 helix: 1.27 (0.17), residues: 892 sheet: 0.38 (0.59), residues: 86 loop : 0.71 (0.28), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 346 HIS 0.005 0.001 HIS A 586 PHE 0.018 0.001 PHE B1189 TYR 0.009 0.001 TYR A 569 ARG 0.006 0.000 ARG B 378 Details of bonding type rmsd hydrogen bonds : bond 0.03519 ( 662) hydrogen bonds : angle 4.04942 ( 1944) covalent geometry : bond 0.00357 (12008) covalent geometry : angle 0.52331 (16346) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 157 time to evaluate : 1.192 Fit side-chains REVERT: A 539 GLU cc_start: 0.7446 (mp0) cc_final: 0.6940 (pm20) REVERT: A 580 MET cc_start: 0.8160 (mmm) cc_final: 0.7760 (mmm) REVERT: A 636 LYS cc_start: 0.7321 (mmtm) cc_final: 0.6976 (tmtt) REVERT: A 916 PHE cc_start: 0.8572 (t80) cc_final: 0.8121 (t80) REVERT: A 1011 GLU cc_start: 0.8136 (tp30) cc_final: 0.7590 (tt0) REVERT: A 1182 SER cc_start: 0.8481 (OUTLIER) cc_final: 0.8279 (t) REVERT: B 378 ARG cc_start: 0.7025 (mtp-110) cc_final: 0.6646 (ptp-110) REVERT: B 580 MET cc_start: 0.8138 (mmm) cc_final: 0.7773 (mmm) REVERT: B 633 MET cc_start: 0.6721 (mmm) cc_final: 0.6380 (tpp) REVERT: B 636 LYS cc_start: 0.7285 (mmtm) cc_final: 0.6972 (tmtt) REVERT: B 916 PHE cc_start: 0.8581 (t80) cc_final: 0.8128 (t80) REVERT: B 1011 GLU cc_start: 0.8146 (tp30) cc_final: 0.7595 (tt0) REVERT: B 1182 SER cc_start: 0.8495 (OUTLIER) cc_final: 0.8280 (t) outliers start: 26 outliers final: 23 residues processed: 175 average time/residue: 0.2238 time to fit residues: 56.8262 Evaluate side-chains 179 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 154 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 609 SER Chi-restraints excluded: chain A residue 756 LEU Chi-restraints excluded: chain A residue 807 MET Chi-restraints excluded: chain A residue 927 PHE Chi-restraints excluded: chain A residue 978 TRP Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1152 VAL Chi-restraints excluded: chain A residue 1172 LEU Chi-restraints excluded: chain A residue 1182 SER Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 523 CYS Chi-restraints excluded: chain B residue 542 GLU Chi-restraints excluded: chain B residue 609 SER Chi-restraints excluded: chain B residue 756 LEU Chi-restraints excluded: chain B residue 807 MET Chi-restraints excluded: chain B residue 927 PHE Chi-restraints excluded: chain B residue 978 TRP Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1152 VAL Chi-restraints excluded: chain B residue 1182 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 58 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 129 optimal weight: 0.0870 chunk 100 optimal weight: 3.9990 chunk 101 optimal weight: 0.9990 chunk 69 optimal weight: 0.0470 chunk 75 optimal weight: 6.9990 chunk 109 optimal weight: 0.5980 chunk 26 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 127 optimal weight: 0.6980 overall best weight: 0.4256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.167822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.133033 restraints weight = 12974.462| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 1.72 r_work: 0.3140 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.2644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 12008 Z= 0.107 Angle : 0.491 6.479 16346 Z= 0.248 Chirality : 0.040 0.170 1964 Planarity : 0.003 0.043 2040 Dihedral : 4.224 50.706 1618 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.01 % Allowed : 12.94 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.22), residues: 1500 helix: 1.48 (0.17), residues: 890 sheet: 0.08 (0.50), residues: 112 loop : 0.77 (0.29), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 346 HIS 0.004 0.001 HIS A 586 PHE 0.016 0.001 PHE B1189 TYR 0.010 0.001 TYR A 569 ARG 0.003 0.000 ARG A 793 Details of bonding type rmsd hydrogen bonds : bond 0.03209 ( 662) hydrogen bonds : angle 3.93630 ( 1944) covalent geometry : bond 0.00239 (12008) covalent geometry : angle 0.49084 (16346) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5669.97 seconds wall clock time: 99 minutes 28.15 seconds (5968.15 seconds total)