Starting phenix.real_space_refine on Sat Oct 11 04:54:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jnj_36449/10_2025/8jnj_36449_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jnj_36449/10_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 { model { file = "/net/cci-nas-00/data/ceres_data/8jnj_36449/10_2025/8jnj_36449_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jnj_36449/10_2025/8jnj_36449_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jnj_36449/10_2025/8jnj_36449.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jnj_36449/10_2025/8jnj_36449.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/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, 'ASP:plan': 3, 'ASN:plan1': 1} 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, 'ASP:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 89 Time building chain proxies: 2.66, per 1000 atoms: 0.23 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: 1.00 Conformation dependent library (CDL) restraints added in 542.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.37 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: 2.11 Time building geometry restraints manager: 1.35 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: 0.01 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: 5.820 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: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 11.910 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.420 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.002 0.000 ARG B 637 TYR 0.007 0.001 TYR B1154 PHE 0.013 0.001 PHE B1189 TRP 0.008 0.001 TRP B 346 HIS 0.006 0.001 HIS A 586 Details of bonding type rmsd covalent geometry : bond 0.00378 (12008) covalent geometry : angle 0.49206 (16346) hydrogen bonds : bond 0.25784 ( 662) hydrogen bonds : angle 8.61920 ( 1944) *********************** 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 : 0.319 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: 0.1154 time to fit residues: 35.9580 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 : 0.417 ------------------------------------------------------------------------------- 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 98 optimal weight: 6.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.2980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.3757 r_free = 0.3757 target = 0.155528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.117430 restraints weight = 13402.230| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 1.92 r_work: 0.3132 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12008 Z= 0.158 Angle : 0.571 6.730 16346 Z= 0.291 Chirality : 0.042 0.150 1964 Planarity : 0.004 0.054 2040 Dihedral : 5.232 55.495 1632 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.49 % Allowed : 7.32 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.75 (0.22), residues: 1500 helix: 0.74 (0.18), residues: 876 sheet: -0.02 (0.57), residues: 92 loop : 0.45 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 631 TYR 0.011 0.002 TYR B 789 PHE 0.017 0.001 PHE A1122 TRP 0.013 0.002 TRP B 360 HIS 0.007 0.001 HIS B 586 Details of bonding type rmsd covalent geometry : bond 0.00373 (12008) covalent geometry : angle 0.57066 (16346) hydrogen bonds : bond 0.04703 ( 662) hydrogen bonds : angle 4.84888 ( 1944) *********************** 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 198 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 167 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 322 GLU cc_start: 0.6840 (tp30) cc_final: 0.5990 (mp0) REVERT: A 377 ARG cc_start: 0.7070 (ttt-90) cc_final: 0.6856 (mtp180) REVERT: A 378 ARG cc_start: 0.7544 (ttm110) cc_final: 0.7231 (ttm110) REVERT: A 580 MET cc_start: 0.8250 (mmm) cc_final: 0.8049 (mmm) REVERT: A 582 ASP cc_start: 0.7498 (t70) cc_final: 0.7138 (t70) REVERT: A 633 MET cc_start: 0.7020 (mmm) cc_final: 0.6540 (tpp) REVERT: A 1011 GLU cc_start: 0.8103 (tp30) cc_final: 0.7568 (tt0) REVERT: B 322 GLU cc_start: 0.6836 (tp30) cc_final: 0.5973 (mp0) REVERT: B 377 ARG cc_start: 0.7067 (ttt-90) cc_final: 0.6854 (mtp180) REVERT: B 378 ARG cc_start: 0.7526 (ttm110) cc_final: 0.7211 (ttm110) REVERT: B 580 MET cc_start: 0.8251 (mmm) cc_final: 0.8044 (mmm) REVERT: B 582 ASP cc_start: 0.7490 (t70) cc_final: 0.7135 (t70) REVERT: B 633 MET cc_start: 0.7029 (mmm) cc_final: 0.6424 (tpp) REVERT: B 1011 GLU cc_start: 0.8130 (tp30) cc_final: 0.7606 (tt0) outliers start: 31 outliers final: 15 residues processed: 182 average time/residue: 0.1118 time to fit residues: 28.8939 Evaluate side-chains 161 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 146 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 352 ASP 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 B residue 343 THR Chi-restraints excluded: chain B residue 352 ASP 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 104 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 72 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 110 optimal weight: 0.5980 chunk 140 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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 = 0.3823 r_free = 0.3823 target = 0.159850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.122461 restraints weight = 13320.567| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 1.94 r_work: 0.3098 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12008 Z= 0.181 Angle : 0.563 6.783 16346 Z= 0.284 Chirality : 0.043 0.148 1964 Planarity : 0.004 0.057 2040 Dihedral : 4.904 54.473 1624 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.17 % Allowed : 9.08 % Favored : 88.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.87 (0.22), residues: 1500 helix: 0.86 (0.17), residues: 878 sheet: -0.05 (0.59), residues: 86 loop : 0.46 (0.28), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 631 TYR 0.010 0.002 TYR A 569 PHE 0.019 0.002 PHE A 585 TRP 0.014 0.002 TRP B 346 HIS 0.007 0.001 HIS B 586 Details of bonding type rmsd covalent geometry : bond 0.00441 (12008) covalent geometry : angle 0.56287 (16346) hydrogen bonds : bond 0.04254 ( 662) hydrogen bonds : angle 4.52839 ( 1944) *********************** 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: 27 poor density : 155 time to evaluate : 0.296 Fit side-chains revert: symmetry clash REVERT: A 322 GLU cc_start: 0.6935 (tp30) cc_final: 0.6005 (mp0) REVERT: A 378 ARG cc_start: 0.7586 (ttm110) cc_final: 0.7276 (ttm110) REVERT: A 580 MET cc_start: 0.8124 (mmm) cc_final: 0.7789 (mmm) REVERT: A 633 MET cc_start: 0.7058 (mmm) cc_final: 0.6664 (tpp) REVERT: A 1011 GLU cc_start: 0.8197 (tp30) cc_final: 0.7671 (tt0) REVERT: A 1182 SER cc_start: 0.8417 (OUTLIER) cc_final: 0.7787 (t) REVERT: B 322 GLU cc_start: 0.6919 (tp30) cc_final: 0.5983 (mp0) REVERT: B 378 ARG cc_start: 0.7574 (ttm110) cc_final: 0.7263 (ttm110) REVERT: B 580 MET cc_start: 0.8124 (mmm) cc_final: 0.7787 (mmm) REVERT: B 633 MET cc_start: 0.7045 (mmm) cc_final: 0.6541 (tpp) REVERT: B 1011 GLU cc_start: 0.8199 (tp30) cc_final: 0.7689 (tt0) REVERT: B 1182 SER cc_start: 0.8415 (OUTLIER) cc_final: 0.7791 (t) outliers start: 27 outliers final: 15 residues processed: 175 average time/residue: 0.1136 time to fit residues: 28.7244 Evaluate side-chains 162 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 145 time to evaluate : 0.434 ------------------------------------------------------------------------------- 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 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 397 VAL 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 27 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 chunk 28 optimal weight: 0.3980 chunk 82 optimal weight: 4.9990 chunk 93 optimal weight: 0.8980 chunk 118 optimal weight: 1.9990 chunk 110 optimal weight: 0.5980 chunk 73 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 = 0.3687 r_free = 0.3687 target = 0.150500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.110804 restraints weight = 13622.928| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 2.02 r_work: 0.3080 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 12008 Z= 0.184 Angle : 0.562 6.633 16346 Z= 0.282 Chirality : 0.043 0.150 1964 Planarity : 0.004 0.056 2040 Dihedral : 4.928 57.428 1624 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.57 % Allowed : 10.53 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.89 (0.22), residues: 1500 helix: 0.85 (0.17), residues: 892 sheet: -0.14 (0.58), residues: 86 loop : 0.54 (0.28), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 793 TYR 0.010 0.001 TYR B 569 PHE 0.019 0.001 PHE A1189 TRP 0.014 0.001 TRP B 346 HIS 0.005 0.001 HIS A 586 Details of bonding type rmsd covalent geometry : bond 0.00451 (12008) covalent geometry : angle 0.56243 (16346) hydrogen bonds : bond 0.03953 ( 662) hydrogen bonds : angle 4.41222 ( 1944) *********************** 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 179 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 147 time to evaluate : 0.465 Fit side-chains revert: symmetry clash REVERT: A 378 ARG cc_start: 0.7507 (ttm110) cc_final: 0.7210 (ttm110) REVERT: A 580 MET cc_start: 0.7844 (mmm) cc_final: 0.7514 (mmm) REVERT: A 616 GLU cc_start: 0.8077 (mm-30) cc_final: 0.7851 (mm-30) REVERT: A 633 MET cc_start: 0.6826 (mmm) cc_final: 0.6407 (tpp) REVERT: A 702 ASP cc_start: 0.7864 (m-30) cc_final: 0.7459 (t0) REVERT: A 1011 GLU cc_start: 0.8117 (tp30) cc_final: 0.7538 (tt0) REVERT: A 1182 SER cc_start: 0.8331 (OUTLIER) cc_final: 0.7799 (t) REVERT: B 378 ARG cc_start: 0.7485 (ttm110) cc_final: 0.7185 (ttm110) REVERT: B 580 MET cc_start: 0.7883 (mmm) cc_final: 0.7554 (mmm) REVERT: B 616 GLU cc_start: 0.8010 (mm-30) cc_final: 0.7782 (mm-30) REVERT: B 633 MET cc_start: 0.6683 (mmm) cc_final: 0.6246 (tpp) REVERT: B 702 ASP cc_start: 0.7861 (m-30) cc_final: 0.7458 (t0) REVERT: B 1011 GLU cc_start: 0.8129 (tp30) cc_final: 0.7550 (tt0) REVERT: B 1182 SER cc_start: 0.8310 (OUTLIER) cc_final: 0.7803 (t) outliers start: 32 outliers final: 23 residues processed: 170 average time/residue: 0.1080 time to fit residues: 26.9052 Evaluate side-chains 164 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 139 time to evaluate : 0.378 ------------------------------------------------------------------------------- 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 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 978 TRP 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 Chi-restraints excluded: chain B residue 1182 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 17 optimal weight: 0.9990 chunk 9 optimal weight: 5.9990 chunk 79 optimal weight: 6.9990 chunk 129 optimal weight: 0.5980 chunk 66 optimal weight: 0.6980 chunk 100 optimal weight: 4.9990 chunk 118 optimal weight: 0.0870 chunk 90 optimal weight: 0.7980 chunk 83 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 112 optimal weight: 0.5980 overall best weight: 0.5558 ------------------------------------------------------------------------------- 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 = 0.3739 r_free = 0.3739 target = 0.154865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.116513 restraints weight = 13382.670| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 1.92 r_work: 0.3140 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.2242 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= 0.119 Angle : 0.501 6.421 16346 Z= 0.253 Chirality : 0.040 0.137 1964 Planarity : 0.004 0.051 2040 Dihedral : 4.743 57.540 1624 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.25 % Allowed : 11.58 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.08 (0.22), residues: 1500 helix: 1.10 (0.18), residues: 894 sheet: -0.23 (0.50), residues: 110 loop : 0.47 (0.29), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 631 TYR 0.010 0.001 TYR B 569 PHE 0.016 0.001 PHE A1189 TRP 0.013 0.001 TRP B 346 HIS 0.005 0.001 HIS B 586 Details of bonding type rmsd covalent geometry : bond 0.00277 (12008) covalent geometry : angle 0.50113 (16346) hydrogen bonds : bond 0.03452 ( 662) hydrogen bonds : angle 4.12179 ( 1944) *********************** 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 193 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 165 time to evaluate : 0.426 Fit side-chains REVERT: A 580 MET cc_start: 0.7939 (mmm) cc_final: 0.7608 (mmm) REVERT: A 616 GLU cc_start: 0.8051 (mm-30) cc_final: 0.7737 (mm-30) REVERT: A 631 ARG cc_start: 0.6677 (mpt180) cc_final: 0.6425 (mpt180) REVERT: A 633 MET cc_start: 0.6950 (mmm) cc_final: 0.6613 (tpp) REVERT: A 636 LYS cc_start: 0.7156 (mmtm) cc_final: 0.6720 (tmtt) REVERT: A 702 ASP cc_start: 0.7911 (m-30) cc_final: 0.7687 (t0) REVERT: A 916 PHE cc_start: 0.8580 (t80) cc_final: 0.8135 (t80) REVERT: A 1011 GLU cc_start: 0.8086 (tp30) cc_final: 0.7516 (tt0) REVERT: B 378 ARG cc_start: 0.7587 (ttm110) cc_final: 0.7326 (ttm110) REVERT: B 580 MET cc_start: 0.7991 (mmm) cc_final: 0.7699 (mmm) REVERT: B 616 GLU cc_start: 0.7999 (mm-30) cc_final: 0.7664 (mm-30) REVERT: B 631 ARG cc_start: 0.6822 (mpt180) cc_final: 0.6545 (mpt180) REVERT: B 633 MET cc_start: 0.6766 (mmm) cc_final: 0.6394 (tpp) REVERT: B 636 LYS cc_start: 0.7138 (mmtm) cc_final: 0.6781 (tmtt) REVERT: B 702 ASP cc_start: 0.7912 (m-30) cc_final: 0.7687 (t0) REVERT: B 916 PHE cc_start: 0.8586 (t80) cc_final: 0.8127 (t80) REVERT: B 1011 GLU cc_start: 0.8099 (tp30) cc_final: 0.7527 (tt0) outliers start: 28 outliers final: 18 residues processed: 184 average time/residue: 0.0972 time to fit residues: 26.0393 Evaluate side-chains 175 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 157 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 21 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 147 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 75 optimal weight: 6.9990 chunk 122 optimal weight: 0.0010 chunk 7 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 111 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 overall best weight: 1.3592 ------------------------------------------------------------------------------- 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 = 0.3684 r_free = 0.3684 target = 0.150188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.110399 restraints weight = 13638.756| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 2.04 r_work: 0.3077 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 12008 Z= 0.202 Angle : 0.577 7.038 16346 Z= 0.289 Chirality : 0.044 0.174 1964 Planarity : 0.004 0.055 2040 Dihedral : 4.606 54.912 1618 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.33 % Allowed : 13.02 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.01 (0.22), residues: 1500 helix: 0.94 (0.17), residues: 892 sheet: 0.02 (0.58), residues: 86 loop : 0.57 (0.28), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 793 TYR 0.010 0.001 TYR A 569 PHE 0.020 0.002 PHE A1189 TRP 0.014 0.002 TRP B 346 HIS 0.006 0.001 HIS B 586 Details of bonding type rmsd covalent geometry : bond 0.00497 (12008) covalent geometry : angle 0.57719 (16346) hydrogen bonds : bond 0.03933 ( 662) hydrogen bonds : angle 4.28344 ( 1944) *********************** 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 183 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 154 time to evaluate : 0.355 Fit side-chains REVERT: A 580 MET cc_start: 0.7925 (mmm) cc_final: 0.7542 (mmm) REVERT: A 633 MET cc_start: 0.6790 (mmm) cc_final: 0.6445 (tpp) REVERT: A 702 ASP cc_start: 0.7957 (m-30) cc_final: 0.7613 (t0) REVERT: A 916 PHE cc_start: 0.8534 (t80) cc_final: 0.7754 (t80) REVERT: A 1011 GLU cc_start: 0.8156 (tp30) cc_final: 0.7566 (tt0) REVERT: A 1071 MET cc_start: 0.8708 (mmm) cc_final: 0.8406 (mmm) REVERT: A 1182 SER cc_start: 0.8291 (OUTLIER) cc_final: 0.7776 (t) REVERT: B 378 ARG cc_start: 0.7522 (ttm110) cc_final: 0.7232 (ttm110) REVERT: B 580 MET cc_start: 0.7896 (mmm) cc_final: 0.7529 (mmm) REVERT: B 616 GLU cc_start: 0.7958 (mm-30) cc_final: 0.7659 (mm-30) REVERT: B 631 ARG cc_start: 0.6587 (mpt180) cc_final: 0.6047 (mpt180) REVERT: B 633 MET cc_start: 0.6555 (mmm) cc_final: 0.6222 (tpp) REVERT: B 636 LYS cc_start: 0.7080 (mmtm) cc_final: 0.6732 (tmtt) REVERT: B 702 ASP cc_start: 0.7966 (m-30) cc_final: 0.7622 (t0) REVERT: B 916 PHE cc_start: 0.8536 (t80) cc_final: 0.7758 (t80) REVERT: B 1011 GLU cc_start: 0.8163 (tp30) cc_final: 0.7571 (tt0) REVERT: B 1071 MET cc_start: 0.8703 (mmm) cc_final: 0.8418 (mmm) REVERT: B 1182 SER cc_start: 0.8285 (OUTLIER) cc_final: 0.7777 (t) outliers start: 29 outliers final: 24 residues processed: 174 average time/residue: 0.1015 time to fit residues: 25.8471 Evaluate side-chains 174 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 148 time to evaluate : 0.337 ------------------------------------------------------------------------------- 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 524 VAL Chi-restraints excluded: chain A residue 609 SER Chi-restraints excluded: chain A residue 697 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 945 LEU 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 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 697 LEU 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 125 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 134 optimal weight: 0.8980 chunk 77 optimal weight: 0.6980 chunk 46 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 99 optimal weight: 7.9990 chunk 132 optimal weight: 0.5980 overall best weight: 1.1982 ------------------------------------------------------------------------------- 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 = 0.3686 r_free = 0.3686 target = 0.150624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.111108 restraints weight = 13575.209| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 2.02 r_work: 0.3085 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12008 Z= 0.183 Angle : 0.558 6.438 16346 Z= 0.280 Chirality : 0.043 0.176 1964 Planarity : 0.004 0.055 2040 Dihedral : 4.595 54.303 1618 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.41 % Allowed : 13.18 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.99 (0.22), residues: 1500 helix: 0.92 (0.17), residues: 892 sheet: 0.05 (0.58), residues: 86 loop : 0.56 (0.28), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 793 TYR 0.010 0.001 TYR B 569 PHE 0.019 0.001 PHE B1189 TRP 0.014 0.001 TRP B 346 HIS 0.006 0.001 HIS A 586 Details of bonding type rmsd covalent geometry : bond 0.00448 (12008) covalent geometry : angle 0.55751 (16346) hydrogen bonds : bond 0.03800 ( 662) hydrogen bonds : angle 4.24102 ( 1944) *********************** 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 181 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 151 time to evaluate : 0.436 Fit side-chains REVERT: A 580 MET cc_start: 0.7894 (mmm) cc_final: 0.7524 (mmm) REVERT: A 633 MET cc_start: 0.6820 (mmm) cc_final: 0.6477 (tpp) REVERT: A 636 LYS cc_start: 0.7097 (mmtm) cc_final: 0.6717 (tmtt) REVERT: A 702 ASP cc_start: 0.7859 (m-30) cc_final: 0.7621 (t0) REVERT: A 908 MET cc_start: 0.7909 (ttm) cc_final: 0.7705 (ttm) REVERT: A 916 PHE cc_start: 0.8527 (t80) cc_final: 0.7751 (t80) REVERT: A 1011 GLU cc_start: 0.8132 (tp30) cc_final: 0.7549 (tt0) REVERT: A 1071 MET cc_start: 0.8715 (mmm) cc_final: 0.8492 (mmm) REVERT: B 378 ARG cc_start: 0.7532 (ttm110) cc_final: 0.7234 (ttm110) REVERT: B 580 MET cc_start: 0.7948 (mmm) cc_final: 0.7584 (mmm) REVERT: B 631 ARG cc_start: 0.6602 (mpt180) cc_final: 0.6005 (mpt180) REVERT: B 633 MET cc_start: 0.6604 (mmm) cc_final: 0.6226 (tpp) REVERT: B 636 LYS cc_start: 0.7178 (mmtm) cc_final: 0.6823 (tmtt) REVERT: B 702 ASP cc_start: 0.7870 (m-30) cc_final: 0.7629 (t0) REVERT: B 908 MET cc_start: 0.7911 (ttm) cc_final: 0.7708 (ttm) REVERT: B 916 PHE cc_start: 0.8527 (t80) cc_final: 0.7755 (t80) REVERT: B 1011 GLU cc_start: 0.8122 (tp30) cc_final: 0.7546 (tt0) REVERT: B 1071 MET cc_start: 0.8704 (mmm) cc_final: 0.8493 (mmm) outliers start: 30 outliers final: 27 residues processed: 170 average time/residue: 0.1059 time to fit residues: 26.0013 Evaluate side-chains 170 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 143 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 697 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 945 LEU 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 524 VAL Chi-restraints excluded: chain B residue 542 GLU Chi-restraints excluded: chain B residue 609 SER Chi-restraints excluded: chain B residue 697 LEU 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 107 optimal weight: 0.5980 chunk 130 optimal weight: 0.9990 chunk 111 optimal weight: 0.7980 chunk 61 optimal weight: 5.9990 chunk 122 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 123 optimal weight: 0.6980 chunk 46 optimal weight: 4.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.3841 r_free = 0.3841 target = 0.161811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.125027 restraints weight = 13113.031| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 1.89 r_work: 0.3129 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.2394 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= 0.140 Angle : 0.525 6.377 16346 Z= 0.264 Chirality : 0.042 0.170 1964 Planarity : 0.004 0.052 2040 Dihedral : 4.529 54.410 1618 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.41 % Allowed : 13.75 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.10 (0.22), residues: 1500 helix: 1.07 (0.17), residues: 896 sheet: -0.07 (0.50), residues: 110 loop : 0.55 (0.29), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 793 TYR 0.009 0.001 TYR A 569 PHE 0.018 0.001 PHE B1189 TRP 0.013 0.001 TRP B 346 HIS 0.005 0.001 HIS A 586 Details of bonding type rmsd covalent geometry : bond 0.00334 (12008) covalent geometry : angle 0.52458 (16346) hydrogen bonds : bond 0.03534 ( 662) hydrogen bonds : angle 4.10306 ( 1944) *********************** 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 181 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 151 time to evaluate : 0.447 Fit side-chains REVERT: A 580 MET cc_start: 0.8048 (mmm) cc_final: 0.7718 (mmm) REVERT: A 633 MET cc_start: 0.6955 (mmm) cc_final: 0.6624 (tpp) REVERT: A 636 LYS cc_start: 0.7211 (mmtm) cc_final: 0.6829 (tmtt) REVERT: A 916 PHE cc_start: 0.8606 (t80) cc_final: 0.8123 (t80) REVERT: A 1011 GLU cc_start: 0.8127 (tp30) cc_final: 0.7556 (tt0) REVERT: B 378 ARG cc_start: 0.7550 (ttm110) cc_final: 0.7267 (ttm110) REVERT: B 580 MET cc_start: 0.8098 (mmm) cc_final: 0.7790 (mmm) REVERT: B 631 ARG cc_start: 0.6699 (mpt180) cc_final: 0.6085 (mpt180) REVERT: B 633 MET cc_start: 0.6722 (mmm) cc_final: 0.6364 (tpp) REVERT: B 636 LYS cc_start: 0.7248 (mmtm) cc_final: 0.6916 (tmtt) REVERT: B 916 PHE cc_start: 0.8610 (t80) cc_final: 0.8122 (t80) REVERT: B 1011 GLU cc_start: 0.8130 (tp30) cc_final: 0.7558 (tt0) REVERT: B 1071 MET cc_start: 0.8729 (mmm) cc_final: 0.8529 (mmm) outliers start: 30 outliers final: 26 residues processed: 175 average time/residue: 0.1091 time to fit residues: 28.0535 Evaluate side-chains 172 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 146 time to evaluate : 0.442 ------------------------------------------------------------------------------- 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 697 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 373 LEU Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 542 GLU Chi-restraints excluded: chain B residue 609 SER Chi-restraints excluded: chain B residue 697 LEU 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 3 optimal weight: 5.9990 chunk 17 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 31 optimal weight: 0.4980 chunk 26 optimal weight: 3.9990 chunk 9 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 140 optimal weight: 0.6980 chunk 77 optimal weight: 0.0270 chunk 111 optimal weight: 1.9990 overall best weight: 0.8240 ------------------------------------------------------------------------------- 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 = 0.3844 r_free = 0.3844 target = 0.162039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.125137 restraints weight = 12974.498| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 1.90 r_work: 0.3131 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.2435 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= 0.144 Angle : 0.531 6.402 16346 Z= 0.268 Chirality : 0.042 0.191 1964 Planarity : 0.004 0.050 2040 Dihedral : 4.506 54.041 1618 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.17 % Allowed : 13.91 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.23 (0.22), residues: 1500 helix: 1.13 (0.17), residues: 892 sheet: 0.15 (0.59), residues: 86 loop : 0.62 (0.28), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 631 TYR 0.010 0.001 TYR A 569 PHE 0.018 0.001 PHE A1189 TRP 0.013 0.001 TRP B 346 HIS 0.005 0.001 HIS A 586 Details of bonding type rmsd covalent geometry : bond 0.00345 (12008) covalent geometry : angle 0.53064 (16346) hydrogen bonds : bond 0.03552 ( 662) hydrogen bonds : angle 4.06467 ( 1944) *********************** 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 184 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 157 time to evaluate : 0.405 Fit side-chains REVERT: A 580 MET cc_start: 0.8099 (mmm) cc_final: 0.7772 (mmm) REVERT: A 631 ARG cc_start: 0.6542 (mpt180) cc_final: 0.6331 (mpt180) REVERT: A 633 MET cc_start: 0.6942 (mmm) cc_final: 0.6613 (tpp) REVERT: A 636 LYS cc_start: 0.7203 (mmtm) cc_final: 0.6828 (tmtt) REVERT: A 916 PHE cc_start: 0.8596 (t80) cc_final: 0.8118 (t80) REVERT: A 1011 GLU cc_start: 0.8133 (tp30) cc_final: 0.7564 (tt0) REVERT: B 580 MET cc_start: 0.8123 (mmm) cc_final: 0.7796 (mmm) REVERT: B 633 MET cc_start: 0.6722 (mmm) cc_final: 0.6365 (tpp) REVERT: B 636 LYS cc_start: 0.7253 (mmtm) cc_final: 0.6942 (tmtt) REVERT: B 916 PHE cc_start: 0.8602 (t80) cc_final: 0.8129 (t80) REVERT: B 1011 GLU cc_start: 0.8132 (tp30) cc_final: 0.7572 (tt0) outliers start: 27 outliers final: 23 residues processed: 176 average time/residue: 0.1105 time to fit residues: 28.3170 Evaluate side-chains 172 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 149 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 397 VAL 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 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 524 VAL 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 54 optimal weight: 0.0970 chunk 35 optimal weight: 0.5980 chunk 110 optimal weight: 0.5980 chunk 136 optimal weight: 0.0270 chunk 126 optimal weight: 0.8980 chunk 135 optimal weight: 5.9990 chunk 143 optimal weight: 1.9990 chunk 108 optimal weight: 0.0370 chunk 96 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 chunk 97 optimal weight: 0.8980 overall best weight: 0.2714 ------------------------------------------------------------------------------- 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 = 0.3749 r_free = 0.3749 target = 0.157874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.119525 restraints weight = 13428.288| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 1.91 r_work: 0.3137 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.2713 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= 0.099 Angle : 0.492 7.943 16346 Z= 0.249 Chirality : 0.040 0.161 1964 Planarity : 0.003 0.040 2040 Dihedral : 4.370 54.781 1618 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.77 % Allowed : 14.39 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.47 (0.22), residues: 1500 helix: 1.40 (0.17), residues: 892 sheet: -0.00 (0.50), residues: 110 loop : 0.64 (0.29), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 378 TYR 0.009 0.001 TYR A 569 PHE 0.015 0.001 PHE B1189 TRP 0.014 0.001 TRP B 346 HIS 0.004 0.001 HIS A 586 Details of bonding type rmsd covalent geometry : bond 0.00212 (12008) covalent geometry : angle 0.49174 (16346) hydrogen bonds : bond 0.03135 ( 662) hydrogen bonds : angle 3.88870 ( 1944) ********************** 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 209 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 187 time to evaluate : 0.446 Fit side-chains REVERT: A 580 MET cc_start: 0.8140 (mmm) cc_final: 0.7939 (mmm) REVERT: A 633 MET cc_start: 0.6947 (mmm) cc_final: 0.6629 (tpp) REVERT: A 636 LYS cc_start: 0.7158 (mmtm) cc_final: 0.6836 (tmtt) REVERT: A 916 PHE cc_start: 0.8486 (t80) cc_final: 0.8073 (t80) REVERT: A 949 LEU cc_start: 0.8177 (mt) cc_final: 0.7942 (mt) REVERT: B 378 ARG cc_start: 0.7001 (mtp-110) cc_final: 0.6705 (ptp-110) REVERT: B 580 MET cc_start: 0.8130 (mmm) cc_final: 0.7895 (mmm) REVERT: B 631 ARG cc_start: 0.6659 (mpt180) cc_final: 0.6152 (mpt180) REVERT: B 633 MET cc_start: 0.6716 (mmm) cc_final: 0.6398 (tpp) REVERT: B 636 LYS cc_start: 0.7269 (mmtm) cc_final: 0.7024 (tmtt) REVERT: B 916 PHE cc_start: 0.8489 (t80) cc_final: 0.8074 (t80) REVERT: B 949 LEU cc_start: 0.8187 (mt) cc_final: 0.7950 (mt) REVERT: B 1089 GLN cc_start: 0.8081 (pm20) cc_final: 0.7787 (pm20) outliers start: 22 outliers final: 18 residues processed: 202 average time/residue: 0.1020 time to fit residues: 30.2602 Evaluate side-chains 184 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 166 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 542 GLU 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 1152 VAL Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 523 CYS Chi-restraints excluded: chain B residue 542 GLU 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 1152 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 80 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 129 optimal weight: 0.6980 chunk 112 optimal weight: 0.6980 chunk 127 optimal weight: 0.4980 chunk 25 optimal weight: 3.9990 chunk 116 optimal weight: 0.7980 chunk 9 optimal weight: 6.9990 chunk 28 optimal weight: 0.9980 chunk 110 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3869 r_free = 0.3869 target = 0.166268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.131415 restraints weight = 13169.183| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 1.70 r_work: 0.3140 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.2719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12008 Z= 0.133 Angle : 0.534 9.017 16346 Z= 0.267 Chirality : 0.042 0.173 1964 Planarity : 0.004 0.043 2040 Dihedral : 4.373 54.056 1618 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.61 % Allowed : 15.43 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.39 (0.22), residues: 1500 helix: 1.31 (0.17), residues: 892 sheet: -0.13 (0.49), residues: 112 loop : 0.69 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 345 TYR 0.009 0.001 TYR A 569 PHE 0.018 0.001 PHE B1189 TRP 0.014 0.001 TRP B 346 HIS 0.005 0.001 HIS A 586 Details of bonding type rmsd covalent geometry : bond 0.00316 (12008) covalent geometry : angle 0.53380 (16346) hydrogen bonds : bond 0.03407 ( 662) hydrogen bonds : angle 3.95547 ( 1944) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2834.19 seconds wall clock time: 49 minutes 17.30 seconds (2957.30 seconds total)