Starting phenix.real_space_refine on Sat Jul 20 19:05:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jnj_36449/07_2024/8jnj_36449_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jnj_36449/07_2024/8jnj_36449.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jnj_36449/07_2024/8jnj_36449.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jnj_36449/07_2024/8jnj_36449.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jnj_36449/07_2024/8jnj_36449_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jnj_36449/07_2024/8jnj_36449_neut.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 56 5.16 5 C 7718 2.51 5 N 1948 2.21 5 O 2014 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 1154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1166": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 11736 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 758, 5868 Classifications: {'peptide': 758} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 38, 'TRANS': 719} Chain breaks: 3 Unresolved non-hydrogen bonds: 137 Unresolved non-hydrogen angles: 159 Unresolved non-hydrogen dihedrals: 115 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 11, 'ARG:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 89 Chain: "B" Number of atoms: 5868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 758, 5868 Classifications: {'peptide': 758} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 38, 'TRANS': 719} Chain breaks: 3 Unresolved non-hydrogen bonds: 137 Unresolved non-hydrogen angles: 159 Unresolved non-hydrogen dihedrals: 115 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 11, 'ARG:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 89 Time building chain proxies: 8.18, per 1000 atoms: 0.70 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.11 Conformation dependent library (CDL) restraints added in 2.3 seconds 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2864 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 9 sheets defined 63.5% alpha, 9.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.42 Creating SS restraints... Processing helix chain 'A' and resid 370 through 381 Processing helix chain 'A' and resid 393 through 408 Processing helix chain 'A' and resid 415 through 424 Processing helix chain 'A' and resid 504 through 510 removed outlier: 3.544A pdb=" N GLU A 508 " --> pdb=" O LEU A 504 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LYS A 509 " --> pdb=" O LYS A 505 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE A 510 " --> pdb=" O LEU A 506 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 504 through 510' Processing helix chain 'A' and resid 568 through 582 Processing helix chain 'A' and resid 584 through 591 removed outlier: 3.539A pdb=" N LEU A 591 " --> pdb=" O GLU A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 607 Processing helix chain 'A' and resid 623 through 638 removed outlier: 4.228A pdb=" N ALA A 627 " --> pdb=" O LEU A 623 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N HIS A 628 " --> pdb=" O ARG A 624 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 693 Processing helix chain 'A' and resid 695 through 702 removed outlier: 3.626A pdb=" N PHE A 700 " --> pdb=" O TYR A 696 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 734 removed outlier: 3.799A pdb=" N LEU A 709 " --> pdb=" O ASP A 705 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE A 713 " --> pdb=" O LEU A 709 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N PHE A 717 " --> pdb=" O ILE A 713 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA A 718 " --> pdb=" O PHE A 714 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER A 721 " --> pdb=" O PHE A 717 " (cutoff:3.500A) Proline residue: A 722 - end of helix Processing helix chain 'A' and resid 739 through 758 Processing helix chain 'A' and resid 768 through 785 removed outlier: 3.565A pdb=" N ALA A 777 " --> pdb=" O VAL A 773 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER A 780 " --> pdb=" O GLU A 776 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N PHE A 781 " --> pdb=" O ALA A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 810 removed outlier: 3.658A pdb=" N ILE A 796 " --> pdb=" O GLY A 792 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N PHE A 802 " --> pdb=" O PHE A 798 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 818 removed outlier: 4.028A pdb=" N PHE A 814 " --> pdb=" O GLU A 811 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU A 815 " --> pdb=" O GLY A 812 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N VAL A 816 " --> pdb=" O SER A 813 " (cutoff:3.500A) Processing helix chain 'A' and resid 820 through 850 removed outlier: 3.547A pdb=" N ILE A 826 " --> pdb=" O PHE A 822 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER A 832 " --> pdb=" O ALA A 828 " (cutoff:3.500A) Processing helix chain 'A' and resid 899 through 924 removed outlier: 3.607A pdb=" N PHE A 912 " --> pdb=" O MET A 908 " (cutoff:3.500A) Processing helix chain 'A' and resid 928 through 935 removed outlier: 4.050A pdb=" N VAL A 934 " --> pdb=" O ARG A 930 " (cutoff:3.500A) Processing helix chain 'A' and resid 938 through 954 removed outlier: 3.592A pdb=" N ILE A 942 " --> pdb=" O PHE A 938 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE A 954 " --> pdb=" O VAL A 950 " (cutoff:3.500A) Processing helix chain 'A' and resid 990 through 997 removed outlier: 3.501A pdb=" N MET A 994 " --> pdb=" O PRO A 990 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 997 through 1020 Processing helix chain 'A' and resid 1021 through 1025 Processing helix chain 'A' and resid 1032 through 1047 Processing helix chain 'A' and resid 1057 through 1068 removed outlier: 3.604A pdb=" N LEU A1068 " --> pdb=" O HIS A1064 " (cutoff:3.500A) Processing helix chain 'A' and resid 1090 through 1102 Processing helix chain 'A' and resid 1103 through 1105 No H-bonds generated for 'chain 'A' and resid 1103 through 1105' Processing helix chain 'A' and resid 1106 through 1111 removed outlier: 3.636A pdb=" N LEU A1110 " --> pdb=" O ILE A1106 " (cutoff:3.500A) Processing helix chain 'A' and resid 1114 through 1129 removed outlier: 3.575A pdb=" N LEU A1118 " --> pdb=" O PRO A1114 " (cutoff:3.500A) Processing helix chain 'A' and resid 1133 through 1142 Processing helix chain 'A' and resid 1145 through 1149 removed outlier: 3.512A pdb=" N HIS A1149 " --> pdb=" O PRO A1146 " (cutoff:3.500A) Processing helix chain 'A' and resid 1152 through 1157 Processing helix chain 'A' and resid 1159 through 1183 removed outlier: 3.773A pdb=" N LEU A1177 " --> pdb=" O CYS A1173 " (cutoff:3.500A) Processing helix chain 'A' and resid 1185 through 1187 No H-bonds generated for 'chain 'A' and resid 1185 through 1187' Processing helix chain 'A' and resid 1188 through 1194 Processing helix chain 'A' and resid 1195 through 1208 removed outlier: 3.892A pdb=" N LEU A1204 " --> pdb=" O ARG A1200 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N THR A1205 " --> pdb=" O MET A1201 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ARG A1206 " --> pdb=" O VAL A1202 " (cutoff:3.500A) Processing helix chain 'A' and resid 1209 through 1217 removed outlier: 3.504A pdb=" N CYS A1215 " --> pdb=" O ARG A1211 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 381 Processing helix chain 'B' and resid 393 through 408 Processing helix chain 'B' and resid 415 through 424 Processing helix chain 'B' and resid 504 through 510 removed outlier: 3.544A pdb=" N GLU B 508 " --> pdb=" O LEU B 504 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LYS B 509 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE B 510 " --> pdb=" O LEU B 506 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 504 through 510' Processing helix chain 'B' and resid 568 through 582 Processing helix chain 'B' and resid 584 through 591 removed outlier: 3.538A pdb=" N LEU B 591 " --> pdb=" O GLU B 587 " (cutoff:3.500A) Processing helix chain 'B' and resid 594 through 607 Processing helix chain 'B' and resid 623 through 638 removed outlier: 4.228A pdb=" N ALA B 627 " --> pdb=" O LEU B 623 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N HIS B 628 " --> pdb=" O ARG B 624 " (cutoff:3.500A) Processing helix chain 'B' and resid 682 through 693 Processing helix chain 'B' and resid 695 through 702 removed outlier: 3.626A pdb=" N PHE B 700 " --> pdb=" O TYR B 696 " (cutoff:3.500A) Processing helix chain 'B' and resid 705 through 734 removed outlier: 3.798A pdb=" N LEU B 709 " --> pdb=" O ASP B 705 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE B 713 " --> pdb=" O LEU B 709 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N PHE B 717 " --> pdb=" O ILE B 713 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA B 718 " --> pdb=" O PHE B 714 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER B 721 " --> pdb=" O PHE B 717 " (cutoff:3.500A) Proline residue: B 722 - end of helix Processing helix chain 'B' and resid 739 through 758 Processing helix chain 'B' and resid 768 through 785 removed outlier: 3.565A pdb=" N ALA B 777 " --> pdb=" O VAL B 773 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER B 780 " --> pdb=" O GLU B 776 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N PHE B 781 " --> pdb=" O ALA B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 788 through 810 removed outlier: 3.658A pdb=" N ILE B 796 " --> pdb=" O GLY B 792 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N PHE B 802 " --> pdb=" O PHE B 798 " (cutoff:3.500A) Processing helix chain 'B' and resid 811 through 818 removed outlier: 4.028A pdb=" N PHE B 814 " --> pdb=" O GLU B 811 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU B 815 " --> pdb=" O GLY B 812 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N VAL B 816 " --> pdb=" O SER B 813 " (cutoff:3.500A) Processing helix chain 'B' and resid 820 through 850 removed outlier: 3.548A pdb=" N ILE B 826 " --> pdb=" O PHE B 822 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER B 832 " --> pdb=" O ALA B 828 " (cutoff:3.500A) Processing helix chain 'B' and resid 899 through 924 removed outlier: 3.606A pdb=" N PHE B 912 " --> pdb=" O MET B 908 " (cutoff:3.500A) Processing helix chain 'B' and resid 928 through 935 removed outlier: 4.050A pdb=" N VAL B 934 " --> pdb=" O ARG B 930 " (cutoff:3.500A) Processing helix chain 'B' and resid 938 through 954 removed outlier: 3.592A pdb=" N ILE B 942 " --> pdb=" O PHE B 938 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE B 954 " --> pdb=" O VAL B 950 " (cutoff:3.500A) Processing helix chain 'B' and resid 990 through 997 removed outlier: 3.501A pdb=" N MET B 994 " --> pdb=" O PRO B 990 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 997 through 1020 Processing helix chain 'B' and resid 1021 through 1025 Processing helix chain 'B' and resid 1032 through 1047 Processing helix chain 'B' and resid 1057 through 1068 removed outlier: 3.604A pdb=" N LEU B1068 " --> pdb=" O HIS B1064 " (cutoff:3.500A) Processing helix chain 'B' and resid 1090 through 1102 Processing helix chain 'B' and resid 1103 through 1105 No H-bonds generated for 'chain 'B' and resid 1103 through 1105' Processing helix chain 'B' and resid 1106 through 1111 removed outlier: 3.636A pdb=" N LEU B1110 " --> pdb=" O ILE B1106 " (cutoff:3.500A) Processing helix chain 'B' and resid 1114 through 1129 removed outlier: 3.575A pdb=" N LEU B1118 " --> pdb=" O PRO B1114 " (cutoff:3.500A) Processing helix chain 'B' and resid 1133 through 1142 Processing helix chain 'B' and resid 1145 through 1149 removed outlier: 3.513A pdb=" N HIS B1149 " --> pdb=" O PRO B1146 " (cutoff:3.500A) Processing helix chain 'B' and resid 1152 through 1157 Processing helix chain 'B' and resid 1159 through 1183 removed outlier: 3.773A pdb=" N LEU B1177 " --> pdb=" O CYS B1173 " (cutoff:3.500A) Processing helix chain 'B' and resid 1185 through 1187 No H-bonds generated for 'chain 'B' and resid 1185 through 1187' Processing helix chain 'B' and resid 1188 through 1194 Processing helix chain 'B' and resid 1195 through 1208 removed outlier: 3.892A pdb=" N LEU B1204 " --> pdb=" O ARG B1200 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N THR B1205 " --> pdb=" O MET B1201 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ARG B1206 " --> pdb=" O VAL B1202 " (cutoff:3.500A) Processing helix chain 'B' and resid 1209 through 1217 removed outlier: 3.503A pdb=" N CYS B1215 " --> pdb=" O ARG B1211 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 359 through 360 removed outlier: 3.685A pdb=" N ARG A 359 " --> pdb=" O GLU A 354 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N THR A 343 " --> pdb=" O VAL A 353 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N LEU A 327 " --> pdb=" O THR A 343 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ARG A 345 " --> pdb=" O VAL A 325 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N VAL A 325 " --> pdb=" O ARG A 345 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N GLU A 326 " --> pdb=" O VAL A 519 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N VAL A 521 " --> pdb=" O GLU A 326 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ASN A 328 " --> pdb=" O VAL A 521 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N CYS A 523 " --> pdb=" O ASN A 328 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N LEU A 330 " --> pdb=" O CYS A 523 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N ALA A 516 " --> pdb=" O VAL A 553 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N PHE A 555 " --> pdb=" O ALA A 516 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N ARG A 554 " --> pdb=" O LEU A 537 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ALA A 384 " --> pdb=" O PHE A 534 " (cutoff:3.500A) removed outlier: 8.438A pdb=" N ARG A 536 " --> pdb=" O ALA A 384 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N LEU A 386 " --> pdb=" O ARG A 536 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ARG A 538 " --> pdb=" O LEU A 386 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ASP A 388 " --> pdb=" O ARG A 538 " (cutoff:3.500A) removed outlier: 10.440A pdb=" N ALA A 540 " --> pdb=" O ASP A 388 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 359 through 360 removed outlier: 3.685A pdb=" N ARG A 359 " --> pdb=" O GLU A 354 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N THR A 343 " --> pdb=" O VAL A 353 " (cutoff:3.500A) removed outlier: 8.494A pdb=" N SER A 428 " --> pdb=" O PRO A 338 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N TRP A 340 " --> pdb=" O SER A 428 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 368 through 369 Processing sheet with id=AA4, first strand: chain 'A' and resid 765 through 766 Processing sheet with id=AA5, first strand: chain 'A' and resid 1069 through 1071 removed outlier: 3.502A pdb=" N GLU A1085 " --> pdb=" O VAL A1070 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 359 through 360 removed outlier: 3.685A pdb=" N ARG B 359 " --> pdb=" O GLU B 354 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N THR B 343 " --> pdb=" O VAL B 353 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N LEU B 327 " --> pdb=" O THR B 343 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ARG B 345 " --> pdb=" O VAL B 325 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N VAL B 325 " --> pdb=" O ARG B 345 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N GLU B 326 " --> pdb=" O VAL B 519 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N VAL B 521 " --> pdb=" O GLU B 326 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ASN B 328 " --> pdb=" O VAL B 521 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N CYS B 523 " --> pdb=" O ASN B 328 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N LEU B 330 " --> pdb=" O CYS B 523 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N ALA B 516 " --> pdb=" O VAL B 553 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N PHE B 555 " --> pdb=" O ALA B 516 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N ARG B 554 " --> pdb=" O LEU B 537 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ALA B 384 " --> pdb=" O PHE B 534 " (cutoff:3.500A) removed outlier: 8.438A pdb=" N ARG B 536 " --> pdb=" O ALA B 384 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N LEU B 386 " --> pdb=" O ARG B 536 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ARG B 538 " --> pdb=" O LEU B 386 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N ASP B 388 " --> pdb=" O ARG B 538 " (cutoff:3.500A) removed outlier: 10.440A pdb=" N ALA B 540 " --> pdb=" O ASP B 388 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 359 through 360 removed outlier: 3.685A pdb=" N ARG B 359 " --> pdb=" O GLU B 354 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N THR B 343 " --> pdb=" O VAL B 353 " (cutoff:3.500A) removed outlier: 8.495A pdb=" N SER B 428 " --> pdb=" O PRO B 338 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N TRP B 340 " --> pdb=" O SER B 428 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 765 through 766 Processing sheet with id=AA9, first strand: chain 'B' and resid 1069 through 1071 removed outlier: 3.501A pdb=" N GLU B1085 " --> pdb=" O VAL B1070 " (cutoff:3.500A) 670 hydrogen bonds defined for protein. 1944 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.08 Time building geometry restraints manager: 5.59 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: 99.86 - 106.70: 412 106.70 - 113.53: 6801 113.53 - 120.36: 4518 120.36 - 127.19: 4469 127.19 - 134.02: 146 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 2.440 nonbonded pdb=" O LEU A 730 " pdb=" OG1 THR A 734 " model vdw 2.292 2.440 nonbonded pdb=" OG SER B 832 " pdb=" OG SER B1129 " model vdw 2.307 2.440 nonbonded pdb=" OG SER A 832 " pdb=" OG SER A1129 " model vdw 2.308 2.440 nonbonded pdb=" O MET B1181 " pdb=" OG SER B1186 " model vdw 2.308 2.440 ... (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 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: 13.200 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.340 Set scattering table: 0.000 Process input model: 36.550 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.460 ------------------------------------------------------------------------------- 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= 0.251 Angle : 0.492 7.339 16346 Z= 0.255 Chirality : 0.041 0.133 1964 Planarity : 0.004 0.063 2040 Dihedral : 10.552 89.452 4266 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.45 % Allowed : 4.50 % Favored : 94.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.21), residues: 1500 helix: -0.49 (0.17), residues: 880 sheet: -0.28 (0.55), residues: 92 loop : 0.57 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 346 HIS 0.006 0.001 HIS A 586 PHE 0.013 0.001 PHE B1189 TYR 0.007 0.001 TYR B1154 ARG 0.002 0.000 ARG B 637 *********************** 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 fitting. rotamer outliers: 18 poor density : 209 time to evaluate : 1.274 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: 0.2490 time to fit residues: 77.5050 Evaluate side-chains 169 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 157 time to evaluate : 1.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 544 ASP Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 927 PHE Chi-restraints excluded: chain A residue 1152 VAL Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 544 ASP Chi-restraints excluded: chain B residue 833 LEU Chi-restraints excluded: chain B residue 927 PHE Chi-restraints excluded: chain B residue 1152 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 126 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 76 optimal weight: 0.3980 chunk 60 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 87 optimal weight: 4.9990 chunk 136 optimal weight: 0.7980 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 12008 Z= 0.319 Angle : 0.593 7.118 16346 Z= 0.302 Chirality : 0.043 0.157 1964 Planarity : 0.005 0.057 2040 Dihedral : 5.304 55.164 1632 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.49 % Allowed : 8.04 % Favored : 89.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.22), residues: 1500 helix: 0.67 (0.18), residues: 876 sheet: -0.02 (0.58), residues: 92 loop : 0.47 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 360 HIS 0.007 0.001 HIS B 586 PHE 0.019 0.002 PHE A1122 TYR 0.012 0.002 TYR B 789 ARG 0.004 0.000 ARG B 631 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 164 time to evaluate : 1.139 Fit side-chains REVERT: A 322 GLU cc_start: 0.6991 (tp30) cc_final: 0.6515 (mp0) REVERT: A 580 MET cc_start: 0.8555 (mmm) cc_final: 0.8325 (mmm) REVERT: A 582 ASP cc_start: 0.7549 (t70) cc_final: 0.7073 (t70) REVERT: A 633 MET cc_start: 0.7284 (mmm) cc_final: 0.6621 (tpt) REVERT: B 322 GLU cc_start: 0.6999 (tp30) cc_final: 0.6509 (mp0) REVERT: B 582 ASP cc_start: 0.7542 (t70) cc_final: 0.7077 (t70) outliers start: 31 outliers final: 21 residues processed: 182 average time/residue: 0.2518 time to fit residues: 64.9004 Evaluate side-chains 162 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 141 time to evaluate : 1.284 ------------------------------------------------------------------------------- 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 544 ASP Chi-restraints excluded: chain A residue 609 SER Chi-restraints excluded: chain A residue 900 THR 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 1183 THR 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 544 ASP Chi-restraints excluded: chain B residue 609 SER Chi-restraints excluded: chain B residue 900 THR 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 1183 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 75 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 136 optimal weight: 0.0050 chunk 147 optimal weight: 0.5980 chunk 121 optimal weight: 4.9990 chunk 135 optimal weight: 0.8980 chunk 46 optimal weight: 3.9990 chunk 109 optimal weight: 0.8980 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12008 Z= 0.209 Angle : 0.532 6.503 16346 Z= 0.266 Chirality : 0.041 0.140 1964 Planarity : 0.004 0.054 2040 Dihedral : 4.828 54.663 1628 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.25 % Allowed : 9.73 % Favored : 88.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.22), residues: 1500 helix: 1.00 (0.17), residues: 880 sheet: 0.22 (0.60), residues: 86 loop : 0.45 (0.27), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 346 HIS 0.006 0.001 HIS A 586 PHE 0.016 0.001 PHE A1189 TYR 0.011 0.001 TYR A 590 ARG 0.005 0.000 ARG B 378 *********************** 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 180 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 152 time to evaluate : 1.358 Fit side-chains REVERT: A 322 GLU cc_start: 0.7059 (tp30) cc_final: 0.6515 (mp0) REVERT: A 580 MET cc_start: 0.8426 (mmm) cc_final: 0.7994 (mmm) REVERT: A 1182 SER cc_start: 0.8396 (OUTLIER) cc_final: 0.7703 (t) REVERT: B 322 GLU cc_start: 0.7068 (tp30) cc_final: 0.6492 (mp0) REVERT: B 580 MET cc_start: 0.8489 (mmm) cc_final: 0.8285 (mmm) REVERT: B 1182 SER cc_start: 0.8346 (OUTLIER) cc_final: 0.7674 (t) outliers start: 28 outliers final: 19 residues processed: 170 average time/residue: 0.2436 time to fit residues: 59.8302 Evaluate side-chains 162 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 141 time to evaluate : 1.785 ------------------------------------------------------------------------------- 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 609 SER Chi-restraints excluded: chain A residue 900 THR Chi-restraints excluded: chain A residue 927 PHE Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1152 VAL Chi-restraints excluded: chain A residue 1182 SER Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 544 ASP Chi-restraints excluded: chain B residue 609 SER Chi-restraints excluded: chain B residue 900 THR Chi-restraints excluded: chain B residue 927 PHE Chi-restraints excluded: chain B residue 983 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 15 optimal weight: 0.0470 chunk 65 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 136 optimal weight: 0.7980 chunk 144 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 129 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12008 Z= 0.203 Angle : 0.511 6.531 16346 Z= 0.255 Chirality : 0.041 0.138 1964 Planarity : 0.004 0.051 2040 Dihedral : 4.671 53.790 1628 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.49 % Allowed : 10.69 % Favored : 86.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.22), residues: 1500 helix: 1.17 (0.18), residues: 882 sheet: 0.11 (0.58), residues: 86 loop : 0.52 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 346 HIS 0.005 0.001 HIS B 586 PHE 0.016 0.001 PHE A1189 TYR 0.009 0.001 TYR B 569 ARG 0.003 0.000 ARG A 631 *********************** 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 198 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 167 time to evaluate : 1.310 Fit side-chains REVERT: A 322 GLU cc_start: 0.6992 (tp30) cc_final: 0.6506 (mp0) REVERT: A 580 MET cc_start: 0.8313 (mmm) cc_final: 0.7975 (mmm) REVERT: A 833 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.7643 (mp) REVERT: A 916 PHE cc_start: 0.8437 (t80) cc_final: 0.8084 (t80) REVERT: B 580 MET cc_start: 0.8319 (mmm) cc_final: 0.8051 (mmm) REVERT: B 916 PHE cc_start: 0.8425 (t80) cc_final: 0.8078 (t80) outliers start: 31 outliers final: 17 residues processed: 191 average time/residue: 0.2288 time to fit residues: 63.5643 Evaluate side-chains 173 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 155 time to evaluate : 1.329 ------------------------------------------------------------------------------- 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 945 LEU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1152 VAL Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 523 CYS Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 544 ASP Chi-restraints excluded: chain B residue 582 ASP Chi-restraints excluded: chain B residue 927 PHE Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1152 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 120 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 74 optimal weight: 0.6980 chunk 130 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1089 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1089 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 12008 Z= 0.395 Angle : 0.597 6.900 16346 Z= 0.299 Chirality : 0.045 0.159 1964 Planarity : 0.004 0.056 2040 Dihedral : 4.889 55.851 1628 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.94 % Allowed : 10.53 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.22), residues: 1500 helix: 0.86 (0.17), residues: 894 sheet: -0.05 (0.57), residues: 86 loop : 0.50 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 346 HIS 0.007 0.001 HIS A 586 PHE 0.019 0.002 PHE B1189 TYR 0.011 0.002 TYR A 789 ARG 0.003 0.000 ARG A 631 *********************** 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 fitting. rotamer outliers: 49 poor density : 144 time to evaluate : 1.270 Fit side-chains REVERT: A 580 MET cc_start: 0.8344 (mmm) cc_final: 0.7932 (mmm) REVERT: A 833 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.7770 (mp) REVERT: A 1089 GLN cc_start: 0.8442 (OUTLIER) cc_final: 0.7042 (pm20) REVERT: A 1182 SER cc_start: 0.8467 (OUTLIER) cc_final: 0.7764 (t) REVERT: B 580 MET cc_start: 0.8319 (mmm) cc_final: 0.7931 (mmm) REVERT: B 833 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.7785 (mp) REVERT: B 1089 GLN cc_start: 0.8431 (OUTLIER) cc_final: 0.7032 (pm20) REVERT: B 1182 SER cc_start: 0.8450 (OUTLIER) cc_final: 0.7757 (t) outliers start: 49 outliers final: 28 residues processed: 178 average time/residue: 0.2214 time to fit residues: 58.4299 Evaluate side-chains 174 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 140 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 523 CYS Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 544 ASP Chi-restraints excluded: chain A residue 582 ASP Chi-restraints excluded: chain A residue 609 SER Chi-restraints excluded: chain A residue 807 MET Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 900 THR 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 1089 GLN Chi-restraints excluded: chain A residue 1152 VAL Chi-restraints excluded: chain A residue 1182 SER Chi-restraints excluded: chain B residue 328 ASN Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 415 ASP 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 582 ASP Chi-restraints excluded: chain B residue 807 MET Chi-restraints excluded: chain B residue 833 LEU Chi-restraints excluded: chain B residue 900 THR 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 1089 GLN Chi-restraints excluded: chain B residue 1152 VAL Chi-restraints excluded: chain B residue 1182 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 48 optimal weight: 0.6980 chunk 130 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 35 optimal weight: 0.5980 chunk 145 optimal weight: 0.7980 chunk 120 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 76 optimal weight: 10.0000 chunk 139 optimal weight: 0.0270 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12008 Z= 0.195 Angle : 0.508 6.414 16346 Z= 0.254 Chirality : 0.041 0.156 1964 Planarity : 0.003 0.050 2040 Dihedral : 4.674 55.826 1628 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.49 % Allowed : 12.62 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.22), residues: 1500 helix: 1.19 (0.18), residues: 892 sheet: 0.08 (0.57), residues: 86 loop : 0.59 (0.28), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 346 HIS 0.005 0.001 HIS A 586 PHE 0.016 0.001 PHE A1189 TYR 0.009 0.001 TYR B 569 ARG 0.002 0.000 ARG B 793 *********************** 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 195 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 164 time to evaluate : 1.176 Fit side-chains REVERT: A 539 GLU cc_start: 0.7296 (mp0) cc_final: 0.6865 (pm20) REVERT: A 580 MET cc_start: 0.8342 (mmm) cc_final: 0.8053 (mmm) REVERT: A 916 PHE cc_start: 0.8404 (t80) cc_final: 0.8048 (t80) REVERT: A 1182 SER cc_start: 0.8363 (OUTLIER) cc_final: 0.7791 (t) REVERT: B 539 GLU cc_start: 0.7290 (mp0) cc_final: 0.6853 (pm20) REVERT: B 580 MET cc_start: 0.8286 (mmm) cc_final: 0.8025 (mmm) REVERT: B 833 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.7700 (mp) REVERT: B 916 PHE cc_start: 0.8397 (t80) cc_final: 0.8043 (t80) REVERT: B 1182 SER cc_start: 0.8342 (OUTLIER) cc_final: 0.7778 (t) outliers start: 31 outliers final: 16 residues processed: 186 average time/residue: 0.2235 time to fit residues: 60.7878 Evaluate side-chains 171 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 152 time to evaluate : 1.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 544 ASP Chi-restraints excluded: chain A residue 582 ASP Chi-restraints excluded: chain A residue 807 MET 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 524 VAL Chi-restraints excluded: chain B residue 544 ASP Chi-restraints excluded: chain B residue 582 ASP Chi-restraints excluded: chain B residue 807 MET Chi-restraints excluded: chain B residue 833 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 16 optimal weight: 0.6980 chunk 82 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 chunk 122 optimal weight: 0.0070 chunk 81 optimal weight: 4.9990 chunk 144 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 chunk 88 optimal weight: 0.0170 chunk 66 optimal weight: 0.8980 chunk 89 optimal weight: 6.9990 chunk 57 optimal weight: 1.9990 overall best weight: 0.7238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.2332 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= 0.208 Angle : 0.516 6.465 16346 Z= 0.258 Chirality : 0.041 0.162 1964 Planarity : 0.003 0.048 2040 Dihedral : 4.543 55.385 1624 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.09 % Allowed : 14.15 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.22), residues: 1500 helix: 1.26 (0.18), residues: 890 sheet: 0.12 (0.57), residues: 86 loop : 0.57 (0.28), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 346 HIS 0.005 0.001 HIS A 586 PHE 0.017 0.001 PHE A1189 TYR 0.009 0.001 TYR B 569 ARG 0.003 0.000 ARG A 631 *********************** 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 192 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 166 time to evaluate : 1.251 Fit side-chains REVERT: A 580 MET cc_start: 0.8372 (mmm) cc_final: 0.8058 (mmm) REVERT: A 636 LYS cc_start: 0.7505 (mmtm) cc_final: 0.7279 (tmtt) REVERT: A 833 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.7675 (mp) REVERT: A 916 PHE cc_start: 0.8407 (t80) cc_final: 0.8006 (t80) REVERT: A 920 LYS cc_start: 0.7556 (mttt) cc_final: 0.7294 (mtmt) REVERT: A 1182 SER cc_start: 0.8376 (OUTLIER) cc_final: 0.7790 (t) REVERT: B 580 MET cc_start: 0.8291 (mmm) cc_final: 0.7906 (mmm) REVERT: B 833 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.7726 (mp) REVERT: B 916 PHE cc_start: 0.8401 (t80) cc_final: 0.8033 (t80) REVERT: B 1182 SER cc_start: 0.8364 (OUTLIER) cc_final: 0.7783 (t) outliers start: 26 outliers final: 17 residues processed: 183 average time/residue: 0.2432 time to fit residues: 64.1002 Evaluate side-chains 177 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 156 time to evaluate : 1.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 544 ASP Chi-restraints excluded: chain A residue 582 ASP Chi-restraints excluded: chain A residue 807 MET Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 927 PHE Chi-restraints excluded: chain A residue 978 TRP Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1152 VAL Chi-restraints excluded: chain A residue 1182 SER Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 544 ASP Chi-restraints excluded: chain B residue 582 ASP Chi-restraints excluded: chain B residue 807 MET Chi-restraints excluded: chain B residue 833 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 86 optimal weight: 9.9990 chunk 43 optimal weight: 0.0060 chunk 28 optimal weight: 0.8980 chunk 91 optimal weight: 0.9990 chunk 98 optimal weight: 6.9990 chunk 71 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 113 optimal weight: 3.9990 chunk 131 optimal weight: 0.9990 chunk 138 optimal weight: 2.9990 chunk 126 optimal weight: 3.9990 overall best weight: 0.9802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 12008 Z= 0.256 Angle : 0.543 9.043 16346 Z= 0.270 Chirality : 0.042 0.181 1964 Planarity : 0.004 0.048 2040 Dihedral : 4.467 54.406 1622 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.73 % Allowed : 13.59 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.22), residues: 1500 helix: 1.18 (0.17), residues: 894 sheet: 0.09 (0.58), residues: 86 loop : 0.58 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 346 HIS 0.006 0.001 HIS A 586 PHE 0.017 0.001 PHE B1189 TYR 0.009 0.001 TYR A 569 ARG 0.003 0.000 ARG B 793 *********************** 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 192 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 158 time to evaluate : 1.206 Fit side-chains REVERT: A 539 GLU cc_start: 0.7381 (mp0) cc_final: 0.6898 (pm20) REVERT: A 580 MET cc_start: 0.8324 (mmm) cc_final: 0.7953 (mmm) REVERT: A 833 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.7724 (mp) REVERT: A 916 PHE cc_start: 0.8429 (t80) cc_final: 0.8033 (t80) REVERT: A 1182 SER cc_start: 0.8377 (OUTLIER) cc_final: 0.7787 (t) REVERT: B 580 MET cc_start: 0.8271 (mmm) cc_final: 0.7888 (mmm) REVERT: B 833 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.7740 (mp) REVERT: B 916 PHE cc_start: 0.8428 (t80) cc_final: 0.8051 (t80) REVERT: B 1182 SER cc_start: 0.8368 (OUTLIER) cc_final: 0.7785 (t) outliers start: 34 outliers final: 23 residues processed: 182 average time/residue: 0.2432 time to fit residues: 63.9278 Evaluate side-chains 178 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 151 time to evaluate : 1.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 544 ASP Chi-restraints excluded: chain A residue 582 ASP Chi-restraints excluded: chain A residue 807 MET Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 900 THR Chi-restraints excluded: chain A residue 927 PHE Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1152 VAL Chi-restraints excluded: chain A residue 1182 SER Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 415 ASP Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 523 CYS Chi-restraints excluded: chain B residue 544 ASP Chi-restraints excluded: chain B residue 582 ASP Chi-restraints excluded: chain B residue 807 MET Chi-restraints excluded: chain B residue 833 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 1.9990 chunk 138 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 105 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 chunk 127 optimal weight: 4.9990 chunk 88 optimal weight: 0.8980 chunk 142 optimal weight: 0.7980 chunk 86 optimal weight: 0.0000 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 12008 Z= 0.245 Angle : 0.532 8.205 16346 Z= 0.266 Chirality : 0.042 0.166 1964 Planarity : 0.004 0.048 2040 Dihedral : 4.467 54.210 1622 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.33 % Allowed : 14.63 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.22), residues: 1500 helix: 1.19 (0.18), residues: 890 sheet: 0.10 (0.58), residues: 86 loop : 0.64 (0.28), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 346 HIS 0.006 0.001 HIS A 586 PHE 0.017 0.001 PHE A1189 TYR 0.009 0.001 TYR A 569 ARG 0.003 0.000 ARG B 793 *********************** 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 183 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 154 time to evaluate : 1.288 Fit side-chains REVERT: A 539 GLU cc_start: 0.7350 (mp0) cc_final: 0.6903 (pm20) REVERT: A 580 MET cc_start: 0.8342 (mmm) cc_final: 0.7994 (mmm) REVERT: A 636 LYS cc_start: 0.7535 (mmtm) cc_final: 0.7325 (tmtt) REVERT: A 833 LEU cc_start: 0.8363 (OUTLIER) cc_final: 0.7688 (mp) REVERT: A 916 PHE cc_start: 0.8357 (t80) cc_final: 0.7801 (t80) REVERT: A 1182 SER cc_start: 0.8360 (OUTLIER) cc_final: 0.7792 (t) REVERT: B 580 MET cc_start: 0.8249 (mmm) cc_final: 0.7867 (mmm) REVERT: B 833 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.7738 (mp) REVERT: B 916 PHE cc_start: 0.8405 (t80) cc_final: 0.8043 (t80) REVERT: B 1182 SER cc_start: 0.8357 (OUTLIER) cc_final: 0.7786 (t) outliers start: 29 outliers final: 23 residues processed: 174 average time/residue: 0.2396 time to fit residues: 60.7974 Evaluate side-chains 178 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 151 time to evaluate : 1.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 542 GLU Chi-restraints excluded: chain A residue 544 ASP Chi-restraints excluded: chain A residue 582 ASP Chi-restraints excluded: chain A residue 807 MET Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 927 PHE Chi-restraints excluded: chain A residue 978 TRP Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1152 VAL Chi-restraints excluded: chain A residue 1182 SER Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 415 ASP Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 544 ASP Chi-restraints excluded: chain B residue 582 ASP Chi-restraints excluded: chain B residue 807 MET Chi-restraints excluded: chain B residue 833 LEU Chi-restraints excluded: chain B residue 900 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 67 optimal weight: 2.9990 chunk 99 optimal weight: 8.9990 chunk 149 optimal weight: 0.6980 chunk 137 optimal weight: 4.9990 chunk 118 optimal weight: 0.0070 chunk 12 optimal weight: 5.9990 chunk 91 optimal weight: 0.9990 chunk 72 optimal weight: 0.9980 chunk 94 optimal weight: 2.9990 chunk 126 optimal weight: 0.0980 chunk 36 optimal weight: 0.9980 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12008 Z= 0.181 Angle : 0.509 8.622 16346 Z= 0.254 Chirality : 0.041 0.174 1964 Planarity : 0.003 0.045 2040 Dihedral : 4.395 54.406 1622 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.49 % Allowed : 14.47 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.22), residues: 1500 helix: 1.29 (0.18), residues: 892 sheet: -0.06 (0.57), residues: 88 loop : 0.74 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 346 HIS 0.005 0.001 HIS A 586 PHE 0.016 0.001 PHE A1189 TYR 0.009 0.001 TYR B 569 ARG 0.002 0.000 ARG A 554 ********************** 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 199 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 168 time to evaluate : 1.351 Fit side-chains REVERT: A 539 GLU cc_start: 0.7365 (mp0) cc_final: 0.6978 (pm20) REVERT: A 580 MET cc_start: 0.8341 (mmm) cc_final: 0.8045 (mmm) REVERT: A 833 LEU cc_start: 0.8347 (OUTLIER) cc_final: 0.7676 (mp) REVERT: A 916 PHE cc_start: 0.8251 (t80) cc_final: 0.7727 (t80) REVERT: A 1182 SER cc_start: 0.8351 (OUTLIER) cc_final: 0.8069 (t) REVERT: B 328 ASN cc_start: 0.7017 (p0) cc_final: 0.6688 (p0) REVERT: B 342 GLU cc_start: 0.8589 (tt0) cc_final: 0.8187 (tt0) REVERT: B 580 MET cc_start: 0.8238 (mmm) cc_final: 0.7899 (mmm) REVERT: B 636 LYS cc_start: 0.7529 (mmtm) cc_final: 0.7321 (tmtt) REVERT: B 833 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.7721 (mp) REVERT: B 916 PHE cc_start: 0.8345 (t80) cc_final: 0.8012 (t80) REVERT: B 1071 MET cc_start: 0.8478 (mmm) cc_final: 0.8267 (mmp) REVERT: B 1182 SER cc_start: 0.8348 (OUTLIER) cc_final: 0.8062 (t) outliers start: 31 outliers final: 24 residues processed: 188 average time/residue: 0.2314 time to fit residues: 63.3018 Evaluate side-chains 188 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 160 time to evaluate : 1.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 542 GLU Chi-restraints excluded: chain A residue 544 ASP Chi-restraints excluded: chain A residue 582 ASP Chi-restraints excluded: chain A residue 807 MET Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 927 PHE Chi-restraints excluded: chain A residue 978 TRP Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1152 VAL Chi-restraints excluded: chain A residue 1182 SER Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 415 ASP Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 523 CYS Chi-restraints excluded: chain B residue 542 GLU Chi-restraints excluded: chain B residue 544 ASP Chi-restraints excluded: chain B residue 582 ASP Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 807 MET Chi-restraints excluded: chain B residue 833 LEU Chi-restraints excluded: chain B residue 927 PHE Chi-restraints excluded: chain B residue 978 TRP Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1152 VAL Chi-restraints excluded: chain B residue 1182 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 109 optimal weight: 0.4980 chunk 17 optimal weight: 3.9990 chunk 33 optimal weight: 0.0470 chunk 119 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 chunk 122 optimal weight: 0.0670 chunk 15 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 104 optimal weight: 0.6980 chunk 6 optimal weight: 5.9990 chunk 86 optimal weight: 4.9990 overall best weight: 0.4416 ------------------------------------------------------------------------------- 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 = 0.3701 r_free = 0.3701 target = 0.153529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.116831 restraints weight = 13345.582| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 1.75 r_work: 0.3128 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.2623 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= 0.164 Angle : 0.504 8.534 16346 Z= 0.252 Chirality : 0.040 0.176 1964 Planarity : 0.003 0.041 2040 Dihedral : 4.333 54.270 1622 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.01 % Allowed : 15.03 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.22), residues: 1500 helix: 1.41 (0.18), residues: 888 sheet: -0.01 (0.58), residues: 88 loop : 0.81 (0.28), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 346 HIS 0.005 0.001 HIS A 586 PHE 0.015 0.001 PHE A1189 TYR 0.009 0.001 TYR A 569 ARG 0.002 0.000 ARG B 793 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2682.88 seconds wall clock time: 49 minutes 17.53 seconds (2957.53 seconds total)