Starting phenix.real_space_refine on Fri Aug 9 07:57:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kgm_37226/08_2024/8kgm_37226.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kgm_37226/08_2024/8kgm_37226.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kgm_37226/08_2024/8kgm_37226.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kgm_37226/08_2024/8kgm_37226.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kgm_37226/08_2024/8kgm_37226.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kgm_37226/08_2024/8kgm_37226.cif" } resolution = 4.8 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 6198 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 76 5.49 5 S 96 5.16 5 C 12879 2.51 5 N 3519 2.21 5 O 3924 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 11": "OE1" <-> "OE2" Residue "A GLU 37": "OE1" <-> "OE2" Residue "A GLU 39": "OE1" <-> "OE2" Residue "A GLU 60": "OE1" <-> "OE2" Residue "A GLU 69": "OE1" <-> "OE2" Residue "A GLU 94": "OE1" <-> "OE2" Residue "A GLU 120": "OE1" <-> "OE2" Residue "A GLU 181": "OE1" <-> "OE2" Residue "A GLU 190": "OE1" <-> "OE2" Residue "A GLU 203": "OE1" <-> "OE2" Residue "A GLU 208": "OE1" <-> "OE2" Residue "A GLU 212": "OE1" <-> "OE2" Residue "A GLU 214": "OE1" <-> "OE2" Residue "A GLU 299": "OE1" <-> "OE2" Residue "A GLU 362": "OE1" <-> "OE2" Residue "A GLU 370": "OE1" <-> "OE2" Residue "A GLU 375": "OE1" <-> "OE2" Residue "A TYR 769": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 11": "OE1" <-> "OE2" Residue "B GLU 37": "OE1" <-> "OE2" Residue "B GLU 39": "OE1" <-> "OE2" Residue "B GLU 60": "OE1" <-> "OE2" Residue "B GLU 69": "OE1" <-> "OE2" Residue "B GLU 94": "OE1" <-> "OE2" Residue "B GLU 120": "OE1" <-> "OE2" Residue "B GLU 181": "OE1" <-> "OE2" Residue "B GLU 190": "OE1" <-> "OE2" Residue "B GLU 203": "OE1" <-> "OE2" Residue "B GLU 208": "OE1" <-> "OE2" Residue "B GLU 212": "OE1" <-> "OE2" Residue "B GLU 214": "OE1" <-> "OE2" Residue "B GLU 299": "OE1" <-> "OE2" Residue "B GLU 362": "OE1" <-> "OE2" Residue "B GLU 370": "OE1" <-> "OE2" Residue "B GLU 375": "OE1" <-> "OE2" Residue "B ASP 416": "OD1" <-> "OD2" Residue "B TYR 769": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 923": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1039": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 20494 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1181, 9447 Classifications: {'peptide': 1181} Link IDs: {'PCIS': 3, 'PTRANS': 44, 'TRANS': 1133} Chain breaks: 1 Chain: "B" Number of atoms: 9490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1186, 9490 Classifications: {'peptide': 1186} Link IDs: {'PCIS': 3, 'PTRANS': 44, 'TRANS': 1138} Chain breaks: 1 Chain: "C" Number of atoms: 781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 781 Classifications: {'DNA': 38} Link IDs: {'rna3p': 37} Chain: "D" Number of atoms: 776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 776 Classifications: {'DNA': 38} Link IDs: {'rna3p': 37} Time building chain proxies: 12.33, per 1000 atoms: 0.60 Number of scatterers: 20494 At special positions: 0 Unit cell: (132.84, 127.1, 184.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 96 16.00 P 76 15.00 O 3924 8.00 N 3519 7.00 C 12879 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: 8.82 Conformation dependent library (CDL) restraints added in 4.1 seconds 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4462 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 30 sheets defined 46.9% alpha, 14.2% beta 18 base pairs and 61 stacking pairs defined. Time for finding SS restraints: 7.44 Creating SS restraints... Processing helix chain 'A' and resid 8 through 16 Processing helix chain 'A' and resid 51 through 73 removed outlier: 3.706A pdb=" N PHE A 58 " --> pdb=" O LEU A 54 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE A 61 " --> pdb=" O ILE A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 113 Processing helix chain 'A' and resid 117 through 125 Processing helix chain 'A' and resid 146 through 154 Processing helix chain 'A' and resid 211 through 233 Processing helix chain 'A' and resid 250 through 260 Processing helix chain 'A' and resid 279 through 283 Processing helix chain 'A' and resid 312 through 334 removed outlier: 3.744A pdb=" N THR A 316 " --> pdb=" O GLY A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 348 Processing helix chain 'A' and resid 375 through 381 Processing helix chain 'A' and resid 385 through 403 Processing helix chain 'A' and resid 440 through 450 Processing helix chain 'A' and resid 496 through 501 Processing helix chain 'A' and resid 502 through 512 Processing helix chain 'A' and resid 541 through 546 Processing helix chain 'A' and resid 546 through 560 Processing helix chain 'A' and resid 560 through 567 removed outlier: 4.058A pdb=" N ILE A 564 " --> pdb=" O TRP A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 602 removed outlier: 3.721A pdb=" N LYS A 602 " --> pdb=" O ALA A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 620 removed outlier: 3.759A pdb=" N ALA A 619 " --> pdb=" O GLY A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 630 removed outlier: 4.413A pdb=" N SER A 627 " --> pdb=" O HIS A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 636 removed outlier: 3.948A pdb=" N VAL A 636 " --> pdb=" O ASP A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 644 No H-bonds generated for 'chain 'A' and resid 642 through 644' Processing helix chain 'A' and resid 645 through 654 Processing helix chain 'A' and resid 657 through 665 Processing helix chain 'A' and resid 672 through 683 Processing helix chain 'A' and resid 687 through 692 Processing helix chain 'A' and resid 693 through 707 Processing helix chain 'A' and resid 715 through 729 Processing helix chain 'A' and resid 738 through 749 removed outlier: 3.501A pdb=" N MET A 749 " --> pdb=" O VAL A 745 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 765 Processing helix chain 'A' and resid 787 through 791 removed outlier: 3.912A pdb=" N LEU A 790 " --> pdb=" O SER A 787 " (cutoff:3.500A) Processing helix chain 'A' and resid 806 through 814 Processing helix chain 'A' and resid 815 through 819 Processing helix chain 'A' and resid 842 through 846 removed outlier: 3.566A pdb=" N MET A 846 " --> pdb=" O LEU A 843 " (cutoff:3.500A) Processing helix chain 'A' and resid 864 through 877 removed outlier: 3.653A pdb=" N ILE A 868 " --> pdb=" O GLN A 864 " (cutoff:3.500A) Processing helix chain 'A' and resid 883 through 893 Processing helix chain 'A' and resid 942 through 953 removed outlier: 3.788A pdb=" N SER A 953 " --> pdb=" O SER A 949 " (cutoff:3.500A) Processing helix chain 'A' and resid 953 through 958 removed outlier: 3.818A pdb=" N THR A 958 " --> pdb=" O SER A 954 " (cutoff:3.500A) Processing helix chain 'A' and resid 983 through 990 removed outlier: 4.360A pdb=" N VAL A 987 " --> pdb=" O LEU A 983 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N GLU A 988 " --> pdb=" O ASN A 984 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU A 989 " --> pdb=" O ARG A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 997 through 1003 Processing helix chain 'A' and resid 1027 through 1075 removed outlier: 3.731A pdb=" N ILE A1031 " --> pdb=" O THR A1027 " (cutoff:3.500A) Proline residue: A1037 - end of helix removed outlier: 4.061A pdb=" N ALA A1063 " --> pdb=" O ILE A1059 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE A1064 " --> pdb=" O MET A1060 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N ARG A1066 " --> pdb=" O THR A1062 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N ALA A1072 " --> pdb=" O ILE A1068 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N GLU A1073 " --> pdb=" O ASN A1069 " (cutoff:3.500A) Processing helix chain 'A' and resid 1076 through 1079 removed outlier: 3.507A pdb=" N TYR A1079 " --> pdb=" O LEU A1076 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1076 through 1079' Processing helix chain 'A' and resid 1081 through 1091 Processing helix chain 'A' and resid 1098 through 1104 Processing helix chain 'A' and resid 1109 through 1116 Processing helix chain 'A' and resid 1122 through 1127 Processing helix chain 'A' and resid 1129 through 1133 removed outlier: 3.691A pdb=" N LEU A1133 " --> pdb=" O ALA A1130 " (cutoff:3.500A) Processing helix chain 'A' and resid 1134 through 1159 Processing helix chain 'A' and resid 1168 through 1187 Processing helix chain 'B' and resid 8 through 16 Processing helix chain 'B' and resid 51 through 73 removed outlier: 3.707A pdb=" N PHE B 58 " --> pdb=" O LEU B 54 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE B 61 " --> pdb=" O ILE B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 113 Processing helix chain 'B' and resid 117 through 125 Processing helix chain 'B' and resid 146 through 154 Processing helix chain 'B' and resid 211 through 233 Processing helix chain 'B' and resid 250 through 260 Processing helix chain 'B' and resid 279 through 283 Processing helix chain 'B' and resid 312 through 334 removed outlier: 3.745A pdb=" N THR B 316 " --> pdb=" O GLY B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 348 Processing helix chain 'B' and resid 375 through 381 Processing helix chain 'B' and resid 385 through 405 Processing helix chain 'B' and resid 428 through 431 Processing helix chain 'B' and resid 440 through 450 Processing helix chain 'B' and resid 496 through 501 Processing helix chain 'B' and resid 502 through 513 Processing helix chain 'B' and resid 541 through 560 removed outlier: 4.252A pdb=" N ILE B 548 " --> pdb=" O GLY B 544 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N LEU B 549 " --> pdb=" O CYS B 545 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 566 removed outlier: 3.987A pdb=" N ILE B 564 " --> pdb=" O TRP B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 592 through 603 removed outlier: 3.600A pdb=" N LYS B 602 " --> pdb=" O ALA B 598 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLN B 603 " --> pdb=" O TRP B 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 620 removed outlier: 3.615A pdb=" N HIS B 620 " --> pdb=" O LEU B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 621 through 630 Processing helix chain 'B' and resid 632 through 636 removed outlier: 3.944A pdb=" N VAL B 636 " --> pdb=" O ASP B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 644 through 654 removed outlier: 3.899A pdb=" N LEU B 648 " --> pdb=" O SER B 644 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE B 653 " --> pdb=" O PHE B 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 657 through 664 Processing helix chain 'B' and resid 672 through 683 Processing helix chain 'B' and resid 687 through 692 Processing helix chain 'B' and resid 693 through 707 Processing helix chain 'B' and resid 715 through 729 Processing helix chain 'B' and resid 738 through 749 removed outlier: 3.633A pdb=" N MET B 749 " --> pdb=" O VAL B 745 " (cutoff:3.500A) Processing helix chain 'B' and resid 754 through 767 removed outlier: 3.997A pdb=" N LEU B 758 " --> pdb=" O GLY B 754 " (cutoff:3.500A) Processing helix chain 'B' and resid 806 through 814 Processing helix chain 'B' and resid 815 through 819 Processing helix chain 'B' and resid 842 through 846 Processing helix chain 'B' and resid 864 through 877 removed outlier: 3.616A pdb=" N ILE B 868 " --> pdb=" O GLN B 864 " (cutoff:3.500A) Processing helix chain 'B' and resid 882 through 893 removed outlier: 3.659A pdb=" N LEU B 886 " --> pdb=" O LYS B 882 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 951 Processing helix chain 'B' and resid 953 through 958 removed outlier: 3.514A pdb=" N THR B 958 " --> pdb=" O SER B 954 " (cutoff:3.500A) Processing helix chain 'B' and resid 982 through 990 Processing helix chain 'B' and resid 997 through 1003 Processing helix chain 'B' and resid 1027 through 1075 removed outlier: 3.717A pdb=" N ILE B1031 " --> pdb=" O THR B1027 " (cutoff:3.500A) Proline residue: B1037 - end of helix removed outlier: 4.021A pdb=" N ALA B1063 " --> pdb=" O ILE B1059 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE B1064 " --> pdb=" O MET B1060 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N ARG B1066 " --> pdb=" O THR B1062 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N ALA B1072 " --> pdb=" O ILE B1068 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N GLU B1073 " --> pdb=" O ASN B1069 " (cutoff:3.500A) Processing helix chain 'B' and resid 1076 through 1079 Processing helix chain 'B' and resid 1081 through 1091 Processing helix chain 'B' and resid 1098 through 1103 Processing helix chain 'B' and resid 1109 through 1117 removed outlier: 3.966A pdb=" N LYS B1116 " --> pdb=" O GLU B1112 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA B1117 " --> pdb=" O LEU B1113 " (cutoff:3.500A) Processing helix chain 'B' and resid 1122 through 1127 Processing helix chain 'B' and resid 1129 through 1133 removed outlier: 3.500A pdb=" N LEU B1133 " --> pdb=" O ALA B1130 " (cutoff:3.500A) Processing helix chain 'B' and resid 1134 through 1159 Processing helix chain 'B' and resid 1166 through 1187 removed outlier: 3.972A pdb=" N TRP B1170 " --> pdb=" O GLY B1166 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU B1171 " --> pdb=" O ALA B1167 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N THR B1187 " --> pdb=" O LYS B1183 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 6 Processing sheet with id=AA2, first strand: chain 'A' and resid 32 through 36 Processing sheet with id=AA3, first strand: chain 'A' and resid 179 through 180 Processing sheet with id=AA4, first strand: chain 'A' and resid 179 through 180 removed outlier: 5.330A pdb=" N GLN A 167 " --> pdb=" O ASP A 164 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N TRP A 157 " --> pdb=" O MET A 198 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ILE A 82 " --> pdb=" O TYR A 240 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 128 through 129 Processing sheet with id=AA6, first strand: chain 'A' and resid 299 through 304 removed outlier: 3.889A pdb=" N LYS A 274 " --> pdb=" O SER A 383 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 362 through 363 Processing sheet with id=AA8, first strand: chain 'A' and resid 465 through 469 removed outlier: 3.789A pdb=" N ILE A 468 " --> pdb=" O LEU A 435 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N LEU A 434 " --> pdb=" O VAL A 535 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N CYS A 537 " --> pdb=" O LEU A 434 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ALA A 436 " --> pdb=" O CYS A 537 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N VAL A 569 " --> pdb=" O PHE A 639 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 481 through 484 Processing sheet with id=AB1, first strand: chain 'A' and resid 588 through 590 Processing sheet with id=AB2, first strand: chain 'A' and resid 736 through 737 Processing sheet with id=AB3, first strand: chain 'A' and resid 824 through 827 removed outlier: 3.667A pdb=" N GLU A 833 " --> pdb=" O VAL A 825 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N GLU A 827 " --> pdb=" O ARG A 831 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N ARG A 831 " --> pdb=" O GLU A 827 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 849 through 852 removed outlier: 3.545A pdb=" N GLY A 849 " --> pdb=" O THR A 860 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 909 through 912 removed outlier: 3.722A pdb=" N HIS A 909 " --> pdb=" O TYR A 920 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N TYR A 917 " --> pdb=" O LEU A1009 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 933 through 934 removed outlier: 3.727A pdb=" N GLU A 962 " --> pdb=" O LYS A 977 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1014 through 1016 Processing sheet with id=AB8, first strand: chain 'B' and resid 32 through 36 Processing sheet with id=AB9, first strand: chain 'B' and resid 179 through 180 Processing sheet with id=AC1, first strand: chain 'B' and resid 179 through 180 removed outlier: 5.330A pdb=" N GLN B 167 " --> pdb=" O ASP B 164 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N TRP B 157 " --> pdb=" O MET B 198 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ILE B 82 " --> pdb=" O TYR B 240 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 299 through 304 removed outlier: 3.889A pdb=" N LYS B 274 " --> pdb=" O SER B 383 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 362 through 363 Processing sheet with id=AC4, first strand: chain 'B' and resid 418 through 419 removed outlier: 3.710A pdb=" N ILE B 468 " --> pdb=" O LEU B 435 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N LEU B 434 " --> pdb=" O VAL B 535 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N CYS B 537 " --> pdb=" O LEU B 434 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N ALA B 436 " --> pdb=" O CYS B 537 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N VAL B 569 " --> pdb=" O PHE B 639 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 481 through 485 Processing sheet with id=AC6, first strand: chain 'B' and resid 588 through 590 Processing sheet with id=AC7, first strand: chain 'B' and resid 736 through 737 removed outlier: 3.694A pdb=" N ARG B 736 " --> pdb=" O VAL B 803 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 824 through 827 removed outlier: 3.771A pdb=" N GLU B 833 " --> pdb=" O VAL B 825 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N GLU B 827 " --> pdb=" O ARG B 831 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N ARG B 831 " --> pdb=" O GLU B 827 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 849 through 852 removed outlier: 3.652A pdb=" N GLY B 849 " --> pdb=" O THR B 860 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 909 through 913 removed outlier: 3.514A pdb=" N TYR B 916 " --> pdb=" O PHE B 913 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 925 through 926 removed outlier: 4.202A pdb=" N ILE B 932 " --> pdb=" O VAL B 976 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLU B 962 " --> pdb=" O LYS B 977 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1014 through 1016 895 hydrogen bonds defined for protein. 2523 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 40 hydrogen bonds 72 hydrogen bond angles 0 basepair planarities 18 basepair parallelities 61 stacking parallelities Total time for adding SS restraints: 10.25 Time building geometry restraints manager: 9.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.34: 5987 1.34 - 1.47: 5888 1.47 - 1.60: 9060 1.60 - 1.74: 24 1.74 - 1.87: 148 Bond restraints: 21107 Sorted by residual: bond pdb=" CD GLU A 106 " pdb=" OE2 GLU A 106 " ideal model delta sigma weight residual 1.249 1.329 -0.080 1.90e-02 2.77e+03 1.79e+01 bond pdb=" CD GLU B 106 " pdb=" OE2 GLU B 106 " ideal model delta sigma weight residual 1.249 1.329 -0.080 1.90e-02 2.77e+03 1.78e+01 bond pdb=" CA ARG B 344 " pdb=" C ARG B 344 " ideal model delta sigma weight residual 1.523 1.483 0.040 1.37e-02 5.33e+03 8.60e+00 bond pdb=" CA ARG A 344 " pdb=" C ARG A 344 " ideal model delta sigma weight residual 1.523 1.483 0.040 1.37e-02 5.33e+03 8.34e+00 bond pdb=" CA PHE B 4 " pdb=" C PHE B 4 " ideal model delta sigma weight residual 1.524 1.491 0.033 1.23e-02 6.61e+03 7.22e+00 ... (remaining 21102 not shown) Histogram of bond angle deviations from ideal: 98.34 - 105.97: 842 105.97 - 113.61: 11773 113.61 - 121.24: 10756 121.24 - 128.88: 5288 128.88 - 136.51: 204 Bond angle restraints: 28863 Sorted by residual: angle pdb=" C ARG A 929 " pdb=" N ASN A 930 " pdb=" CA ASN A 930 " ideal model delta sigma weight residual 121.54 130.53 -8.99 1.91e+00 2.74e-01 2.22e+01 angle pdb=" N ARG A 344 " pdb=" CA ARG A 344 " pdb=" C ARG A 344 " ideal model delta sigma weight residual 112.23 106.46 5.77 1.26e+00 6.30e-01 2.10e+01 angle pdb=" N ARG B 344 " pdb=" CA ARG B 344 " pdb=" C ARG B 344 " ideal model delta sigma weight residual 112.23 106.49 5.74 1.26e+00 6.30e-01 2.08e+01 angle pdb=" N ASP B 408 " pdb=" CA ASP B 408 " pdb=" C ASP B 408 " ideal model delta sigma weight residual 112.92 107.49 5.43 1.23e+00 6.61e-01 1.95e+01 angle pdb=" CA LEU A 261 " pdb=" CB LEU A 261 " pdb=" CG LEU A 261 " ideal model delta sigma weight residual 116.30 101.05 15.25 3.50e+00 8.16e-02 1.90e+01 ... (remaining 28858 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.65: 12099 35.65 - 71.29: 454 71.29 - 106.93: 14 106.93 - 142.58: 1 142.58 - 178.22: 3 Dihedral angle restraints: 12571 sinusoidal: 5638 harmonic: 6933 Sorted by residual: dihedral pdb=" CA ARG A 247 " pdb=" C ARG A 247 " pdb=" N THR A 248 " pdb=" CA THR A 248 " ideal model delta harmonic sigma weight residual 180.00 -151.97 -28.03 0 5.00e+00 4.00e-02 3.14e+01 dihedral pdb=" CA ARG B 247 " pdb=" C ARG B 247 " pdb=" N THR B 248 " pdb=" CA THR B 248 " ideal model delta harmonic sigma weight residual -180.00 -152.00 -28.00 0 5.00e+00 4.00e-02 3.14e+01 dihedral pdb=" CA THR A1062 " pdb=" C THR A1062 " pdb=" N ALA A1063 " pdb=" CA ALA A1063 " ideal model delta harmonic sigma weight residual 180.00 153.36 26.64 0 5.00e+00 4.00e-02 2.84e+01 ... (remaining 12568 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 2626 0.075 - 0.151: 538 0.151 - 0.226: 42 0.226 - 0.301: 6 0.301 - 0.377: 3 Chirality restraints: 3215 Sorted by residual: chirality pdb=" CB ILE A 963 " pdb=" CA ILE A 963 " pdb=" CG1 ILE A 963 " pdb=" CG2 ILE A 963 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.38 2.00e-01 2.50e+01 3.55e+00 chirality pdb=" CB ILE B 963 " pdb=" CA ILE B 963 " pdb=" CG1 ILE B 963 " pdb=" CG2 ILE B 963 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.47e+00 chirality pdb=" C3' DT C 44 " pdb=" C4' DT C 44 " pdb=" O3' DT C 44 " pdb=" C2' DT C 44 " both_signs ideal model delta sigma weight residual False -2.66 -2.35 -0.31 2.00e-01 2.50e+01 2.44e+00 ... (remaining 3212 not shown) Planarity restraints: 3397 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B1170 " -0.026 2.00e-02 2.50e+03 2.66e-02 1.77e+01 pdb=" CG TRP B1170 " 0.071 2.00e-02 2.50e+03 pdb=" CD1 TRP B1170 " -0.036 2.00e-02 2.50e+03 pdb=" CD2 TRP B1170 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B1170 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP B1170 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP B1170 " -0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP B1170 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B1170 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP B1170 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A1170 " -0.025 2.00e-02 2.50e+03 2.60e-02 1.69e+01 pdb=" CG TRP A1170 " 0.069 2.00e-02 2.50e+03 pdb=" CD1 TRP A1170 " -0.036 2.00e-02 2.50e+03 pdb=" CD2 TRP A1170 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP A1170 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A1170 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A1170 " -0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP A1170 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A1170 " -0.010 2.00e-02 2.50e+03 pdb=" CH2 TRP A1170 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 531 " 0.037 2.00e-02 2.50e+03 2.57e-02 1.32e+01 pdb=" CG TYR A 531 " -0.060 2.00e-02 2.50e+03 pdb=" CD1 TYR A 531 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR A 531 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR A 531 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR A 531 " 0.008 2.00e-02 2.50e+03 pdb=" CZ TYR A 531 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR A 531 " 0.007 2.00e-02 2.50e+03 ... (remaining 3394 not shown) Histogram of nonbonded interaction distances: 1.50 - 2.18: 20 2.18 - 2.86: 6930 2.86 - 3.54: 26878 3.54 - 4.22: 49374 4.22 - 4.90: 83515 Nonbonded interactions: 166717 Sorted by model distance: nonbonded pdb=" N GLY A 855 " pdb=" OP1 DA C 39 " model vdw 1.497 3.120 nonbonded pdb=" NH1 ARG A 344 " pdb=" NH1 ARG B 344 " model vdw 1.624 3.200 nonbonded pdb=" OD1 ASN A 851 " pdb=" O4' DG D 15 " model vdw 1.698 3.040 nonbonded pdb=" OE2 GLU A 854 " pdb=" C5' DC C 38 " model vdw 1.822 3.440 nonbonded pdb=" O TRP A 856 " pdb=" C4' DA C 39 " model vdw 1.883 3.470 ... (remaining 166712 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 3 through 403 or resid 414 through 1192)) selection = (chain 'B' and (resid 3 through 403 or resid 408 or resid 415 through 1192)) } ncs_group { reference = (chain 'C' and (resid 14 through 18 or resid 20 through 22 or resid 24 through 3 \ 9 or resid 41 through 43 or resid 45 through 49 or resid 51)) selection = (chain 'D' and (resid 4 through 8 or resid 10 through 12 or resid 14 through 29 \ or resid 31 through 33 or resid 35 through 39 or resid 41)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.190 Construct map_model_manager: 0.010 Extract box with map and model: 1.000 Check model and map are aligned: 0.170 Set scattering table: 0.220 Process input model: 65.390 Find NCS groups from input model: 0.990 Set up NCS constraints: 0.080 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4648 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 : 0.008 0.080 21107 Z= 0.545 Angle : 0.982 16.211 28863 Z= 0.544 Chirality : 0.059 0.377 3215 Planarity : 0.007 0.077 3397 Dihedral : 16.569 178.224 8109 Min Nonbonded Distance : 1.497 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.69 % Favored : 96.23 % Rotamer: Outliers : 0.68 % Allowed : 7.50 % Favored : 91.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.85 (0.15), residues: 2359 helix: -1.95 (0.13), residues: 972 sheet: -1.25 (0.28), residues: 349 loop : -1.91 (0.17), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.071 0.004 TRP B1170 HIS 0.014 0.003 HIS B 892 PHE 0.026 0.003 PHE B 739 TYR 0.060 0.003 TYR A 531 ARG 0.018 0.002 ARG B1039 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 448 time to evaluate : 2.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 434 LEU cc_start: 0.8471 (tp) cc_final: 0.8256 (tp) REVERT: A 576 LEU cc_start: 0.7165 (tp) cc_final: 0.6911 (tp) REVERT: A 721 ILE cc_start: 0.9196 (mt) cc_final: 0.8755 (mt) REVERT: A 722 LEU cc_start: 0.9204 (tp) cc_final: 0.8975 (tp) REVERT: A 776 TYR cc_start: 0.7521 (m-80) cc_final: 0.7290 (m-80) REVERT: A 838 VAL cc_start: 0.8600 (t) cc_final: 0.8105 (p) REVERT: A 848 TYR cc_start: 0.5381 (m-80) cc_final: 0.5095 (m-10) REVERT: B 446 LEU cc_start: 0.8713 (mt) cc_final: 0.8382 (mt) REVERT: B 541 ASP cc_start: 0.7602 (p0) cc_final: 0.7139 (p0) REVERT: B 573 LEU cc_start: 0.7945 (tm) cc_final: 0.7643 (tm) REVERT: B 621 ASP cc_start: 0.8433 (t0) cc_final: 0.8230 (t70) REVERT: B 722 LEU cc_start: 0.9066 (tp) cc_final: 0.8824 (tp) REVERT: B 939 LEU cc_start: 0.8310 (mt) cc_final: 0.7875 (mt) REVERT: B 1181 ILE cc_start: 0.8715 (mt) cc_final: 0.8457 (mm) outliers start: 14 outliers final: 1 residues processed: 462 average time/residue: 0.3700 time to fit residues: 248.1575 Evaluate side-chains 245 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 244 time to evaluate : 2.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 204 optimal weight: 1.9990 chunk 183 optimal weight: 0.7980 chunk 101 optimal weight: 7.9990 chunk 62 optimal weight: 0.0970 chunk 123 optimal weight: 7.9990 chunk 97 optimal weight: 0.3980 chunk 189 optimal weight: 5.9990 chunk 73 optimal weight: 0.9990 chunk 115 optimal weight: 4.9990 chunk 141 optimal weight: 5.9990 chunk 219 optimal weight: 10.0000 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 HIS A 283 HIS A 402 GLN A 566 HIS A 677 GLN ** A 909 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 981 ASN B 125 HIS B 175 GLN B 283 HIS B 483 ASN ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 562 GLN B 566 HIS B 692 GLN ** B 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 864 GLN B 892 HIS B 905 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4793 moved from start: 0.2904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 21107 Z= 0.199 Angle : 0.647 13.964 28863 Z= 0.350 Chirality : 0.045 0.214 3215 Planarity : 0.005 0.047 3397 Dihedral : 17.495 174.063 3463 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.10 % Allowed : 2.52 % Favored : 97.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % 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: -1.23 (0.16), residues: 2359 helix: -0.27 (0.16), residues: 982 sheet: -0.51 (0.28), residues: 338 loop : -1.37 (0.18), residues: 1039 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B1170 HIS 0.008 0.001 HIS B 650 PHE 0.027 0.002 PHE B 317 TYR 0.022 0.002 TYR A 698 ARG 0.007 0.001 ARG A 571 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 289 time to evaluate : 2.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 MET cc_start: 0.6725 (mmm) cc_final: 0.6383 (mmm) REVERT: A 572 LEU cc_start: 0.7915 (tp) cc_final: 0.7565 (tp) REVERT: A 721 ILE cc_start: 0.8882 (mt) cc_final: 0.8675 (mt) REVERT: A 722 LEU cc_start: 0.9333 (tp) cc_final: 0.9087 (tp) REVERT: B 18 MET cc_start: -0.1336 (ptt) cc_final: -0.2826 (mmt) REVERT: B 450 LEU cc_start: 0.8894 (tp) cc_final: 0.8534 (tp) REVERT: B 467 MET cc_start: 0.7862 (mtm) cc_final: 0.6810 (mtt) REVERT: B 508 ILE cc_start: 0.8329 (OUTLIER) cc_final: 0.8104 (tp) REVERT: B 541 ASP cc_start: 0.7728 (p0) cc_final: 0.7344 (p0) REVERT: B 586 MET cc_start: 0.8510 (mmm) cc_final: 0.8170 (mmm) REVERT: B 755 ASP cc_start: 0.6730 (p0) cc_final: 0.6250 (p0) REVERT: B 776 TYR cc_start: 0.8396 (m-80) cc_final: 0.7875 (m-80) REVERT: B 939 LEU cc_start: 0.8329 (mt) cc_final: 0.8101 (mt) outliers start: 2 outliers final: 1 residues processed: 291 average time/residue: 0.3605 time to fit residues: 159.4657 Evaluate side-chains 205 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 203 time to evaluate : 2.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 122 optimal weight: 40.0000 chunk 68 optimal weight: 10.0000 chunk 182 optimal weight: 8.9990 chunk 149 optimal weight: 5.9990 chunk 60 optimal weight: 9.9990 chunk 220 optimal weight: 3.9990 chunk 237 optimal weight: 7.9990 chunk 196 optimal weight: 0.9980 chunk 218 optimal weight: 10.0000 chunk 75 optimal weight: 10.0000 chunk 176 optimal weight: 7.9990 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 402 GLN A 506 GLN ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 864 GLN ** A 909 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1099 HIS A1149 GLN ** B 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 286 GLN ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 603 GLN B 748 HIS B 759 ASN ** B 909 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1069 ASN ** B1099 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5247 moved from start: 0.4359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.120 21107 Z= 0.368 Angle : 0.738 12.670 28863 Z= 0.398 Chirality : 0.046 0.227 3215 Planarity : 0.005 0.054 3397 Dihedral : 17.498 175.507 3463 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 17.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % 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: -0.49 (0.17), residues: 2359 helix: 0.45 (0.16), residues: 980 sheet: -0.71 (0.27), residues: 384 loop : -0.84 (0.20), residues: 995 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 599 HIS 0.010 0.002 HIS A 892 PHE 0.035 0.002 PHE B 785 TYR 0.021 0.002 TYR B 837 ARG 0.011 0.001 ARG A 684 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 215 time to evaluate : 2.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 576 LEU cc_start: 0.7356 (tp) cc_final: 0.7145 (tp) REVERT: A 739 PHE cc_start: 0.8467 (p90) cc_final: 0.7521 (p90) REVERT: A 775 LEU cc_start: 0.6685 (tp) cc_final: 0.6285 (tp) REVERT: B 257 MET cc_start: -0.3898 (tmm) cc_final: -0.4701 (ttp) REVERT: B 505 LEU cc_start: 0.8481 (pp) cc_final: 0.8111 (pp) REVERT: B 541 ASP cc_start: 0.8006 (p0) cc_final: 0.7396 (p0) REVERT: B 586 MET cc_start: 0.8770 (mmm) cc_final: 0.8443 (mmm) REVERT: B 621 ASP cc_start: 0.8863 (t0) cc_final: 0.8400 (t70) REVERT: B 716 ARG cc_start: 0.6552 (tpm170) cc_final: 0.6248 (tpm170) REVERT: B 755 ASP cc_start: 0.7714 (p0) cc_final: 0.6157 (p0) REVERT: B 758 LEU cc_start: 0.8936 (pp) cc_final: 0.8720 (mt) REVERT: B 776 TYR cc_start: 0.8335 (m-80) cc_final: 0.8081 (m-80) REVERT: B 838 VAL cc_start: 0.8298 (t) cc_final: 0.8025 (p) REVERT: B 1181 ILE cc_start: 0.8430 (mm) cc_final: 0.8173 (mm) outliers start: 0 outliers final: 0 residues processed: 215 average time/residue: 0.3344 time to fit residues: 111.1983 Evaluate side-chains 155 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 155 time to evaluate : 2.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 217 optimal weight: 5.9990 chunk 165 optimal weight: 5.9990 chunk 114 optimal weight: 0.8980 chunk 24 optimal weight: 9.9990 chunk 105 optimal weight: 0.9980 chunk 147 optimal weight: 8.9990 chunk 220 optimal weight: 1.9990 chunk 233 optimal weight: 9.9990 chunk 115 optimal weight: 6.9990 chunk 209 optimal weight: 6.9990 chunk 63 optimal weight: 4.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 381 HIS A 402 GLN ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 909 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 GLN ** B 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 905 ASN ** B 909 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5206 moved from start: 0.4751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 21107 Z= 0.228 Angle : 0.619 11.646 28863 Z= 0.332 Chirality : 0.045 0.724 3215 Planarity : 0.004 0.044 3397 Dihedral : 17.478 173.517 3463 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.05 % Allowed : 2.27 % Favored : 97.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % 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: -0.12 (0.18), residues: 2359 helix: 0.78 (0.16), residues: 989 sheet: -0.58 (0.27), residues: 383 loop : -0.66 (0.20), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1170 HIS 0.006 0.001 HIS A 892 PHE 0.030 0.002 PHE B 596 TYR 0.017 0.002 TYR A 169 ARG 0.007 0.001 ARG A 683 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 216 time to evaluate : 2.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 MET cc_start: 0.6738 (mmm) cc_final: 0.5923 (mmm) REVERT: A 446 LEU cc_start: 0.9115 (mt) cc_final: 0.8846 (mt) REVERT: A 475 MET cc_start: 0.4189 (mmp) cc_final: 0.3954 (tpp) REVERT: B 296 LYS cc_start: 0.6385 (mmpt) cc_final: 0.6072 (mmtt) REVERT: B 505 LEU cc_start: 0.8341 (pp) cc_final: 0.7958 (pp) REVERT: B 586 MET cc_start: 0.8734 (mmm) cc_final: 0.8445 (mmm) REVERT: B 621 ASP cc_start: 0.8715 (t0) cc_final: 0.8384 (t70) REVERT: B 716 ARG cc_start: 0.6445 (tpm170) cc_final: 0.5998 (tpm170) REVERT: B 722 LEU cc_start: 0.8903 (mt) cc_final: 0.8454 (mm) REVERT: B 755 ASP cc_start: 0.7507 (p0) cc_final: 0.6174 (p0) REVERT: B 758 LEU cc_start: 0.8848 (pp) cc_final: 0.8609 (mt) REVERT: B 838 VAL cc_start: 0.8253 (t) cc_final: 0.8012 (p) outliers start: 1 outliers final: 0 residues processed: 217 average time/residue: 0.3330 time to fit residues: 112.6042 Evaluate side-chains 159 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 2.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 194 optimal weight: 0.8980 chunk 132 optimal weight: 40.0000 chunk 3 optimal weight: 4.9990 chunk 174 optimal weight: 10.0000 chunk 96 optimal weight: 10.0000 chunk 199 optimal weight: 0.9980 chunk 161 optimal weight: 9.9990 chunk 0 optimal weight: 40.0000 chunk 119 optimal weight: 5.9990 chunk 209 optimal weight: 4.9990 chunk 59 optimal weight: 6.9990 overall best weight: 3.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 381 HIS A 402 GLN ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 892 HIS ** A 909 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 47 HIS ** B 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 172 HIS B 175 GLN ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 909 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1099 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5332 moved from start: 0.5452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.144 21107 Z= 0.260 Angle : 0.644 10.297 28863 Z= 0.346 Chirality : 0.046 0.816 3215 Planarity : 0.004 0.047 3397 Dihedral : 17.441 172.856 3463 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 15.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.10 % Allowed : 2.32 % Favored : 97.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % 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: -0.06 (0.18), residues: 2359 helix: 0.74 (0.16), residues: 992 sheet: -0.57 (0.27), residues: 387 loop : -0.50 (0.21), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B1189 HIS 0.006 0.001 HIS A 892 PHE 0.023 0.002 PHE B 785 TYR 0.018 0.002 TYR B1067 ARG 0.010 0.001 ARG A 683 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 204 time to evaluate : 2.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 MET cc_start: 0.6458 (mmm) cc_final: 0.6174 (mmm) REVERT: A 446 LEU cc_start: 0.9143 (mt) cc_final: 0.8848 (mt) REVERT: A 775 LEU cc_start: 0.7133 (tp) cc_final: 0.6040 (tp) REVERT: B 505 LEU cc_start: 0.8357 (pp) cc_final: 0.7988 (pp) REVERT: B 586 MET cc_start: 0.8808 (mmm) cc_final: 0.8522 (mmm) REVERT: B 621 ASP cc_start: 0.8634 (t0) cc_final: 0.8272 (t70) REVERT: B 716 ARG cc_start: 0.6345 (tpm170) cc_final: 0.6050 (tpm170) REVERT: B 755 ASP cc_start: 0.7643 (p0) cc_final: 0.6846 (p0) REVERT: B 838 VAL cc_start: 0.8223 (t) cc_final: 0.8015 (p) REVERT: B 1148 MET cc_start: 0.8783 (ptt) cc_final: 0.8440 (ptt) outliers start: 2 outliers final: 1 residues processed: 206 average time/residue: 0.3204 time to fit residues: 102.2223 Evaluate side-chains 146 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 145 time to evaluate : 2.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 78 optimal weight: 6.9990 chunk 210 optimal weight: 3.9990 chunk 46 optimal weight: 9.9990 chunk 137 optimal weight: 30.0000 chunk 57 optimal weight: 5.9990 chunk 234 optimal weight: 9.9990 chunk 194 optimal weight: 0.0870 chunk 108 optimal weight: 9.9990 chunk 19 optimal weight: 40.0000 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 50.0000 overall best weight: 5.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 HIS A 308 ASN A 402 GLN ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 887 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 909 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 GLN ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 286 GLN B 381 HIS ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN B 905 ASN ** B1099 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5507 moved from start: 0.6400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.108 21107 Z= 0.336 Angle : 0.718 11.002 28863 Z= 0.386 Chirality : 0.048 0.879 3215 Planarity : 0.005 0.052 3397 Dihedral : 17.754 174.916 3463 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 20.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % 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: -0.34 (0.18), residues: 2359 helix: 0.42 (0.16), residues: 1000 sheet: -0.66 (0.27), residues: 390 loop : -0.57 (0.21), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A1170 HIS 0.009 0.002 HIS B 172 PHE 0.028 0.002 PHE B 596 TYR 0.032 0.002 TYR B 837 ARG 0.010 0.001 ARG A 736 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 195 time to evaluate : 2.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 435 LEU cc_start: 0.8730 (pp) cc_final: 0.8381 (pp) REVERT: A 475 MET cc_start: 0.6637 (mmp) cc_final: 0.6192 (mmp) REVERT: A 775 LEU cc_start: 0.6912 (tp) cc_final: 0.6475 (tp) REVERT: A 776 TYR cc_start: 0.6920 (m-80) cc_final: 0.6646 (m-80) REVERT: B 392 MET cc_start: -0.0596 (mtt) cc_final: -0.1434 (mmt) REVERT: B 505 LEU cc_start: 0.8525 (pp) cc_final: 0.8085 (pp) REVERT: B 586 MET cc_start: 0.8823 (mmm) cc_final: 0.8559 (mmm) REVERT: B 621 ASP cc_start: 0.8504 (t0) cc_final: 0.8239 (t70) REVERT: B 716 ARG cc_start: 0.6464 (tpm170) cc_final: 0.6129 (tpm170) REVERT: B 755 ASP cc_start: 0.7824 (p0) cc_final: 0.7088 (p0) REVERT: B 760 THR cc_start: 0.8113 (p) cc_final: 0.7833 (p) REVERT: B 764 LYS cc_start: 0.8501 (mtpt) cc_final: 0.8261 (mtpt) REVERT: B 838 VAL cc_start: 0.8278 (t) cc_final: 0.8021 (p) outliers start: 0 outliers final: 0 residues processed: 195 average time/residue: 0.3399 time to fit residues: 101.6524 Evaluate side-chains 139 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 139 time to evaluate : 2.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 225 optimal weight: 5.9990 chunk 26 optimal weight: 20.0000 chunk 133 optimal weight: 7.9990 chunk 170 optimal weight: 0.7980 chunk 132 optimal weight: 7.9990 chunk 197 optimal weight: 7.9990 chunk 130 optimal weight: 9.9990 chunk 233 optimal weight: 4.9990 chunk 145 optimal weight: 3.9990 chunk 142 optimal weight: 9.9990 chunk 107 optimal weight: 2.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 402 GLN ** A 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 880 ASN ** A 909 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN ** B 909 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1099 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5453 moved from start: 0.6622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 21107 Z= 0.248 Angle : 0.647 9.855 28863 Z= 0.345 Chirality : 0.047 0.918 3215 Planarity : 0.004 0.062 3397 Dihedral : 17.654 175.008 3463 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 16.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % 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: -0.26 (0.18), residues: 2359 helix: 0.54 (0.16), residues: 1012 sheet: -0.77 (0.27), residues: 392 loop : -0.53 (0.21), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A1170 HIS 0.008 0.001 HIS B 172 PHE 0.027 0.002 PHE B 596 TYR 0.020 0.002 TYR B 837 ARG 0.006 0.001 ARG A 683 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 192 time to evaluate : 2.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 MET cc_start: 0.6149 (mmm) cc_final: 0.5777 (mmp) REVERT: A 445 LEU cc_start: 0.8704 (tt) cc_final: 0.8499 (tt) REVERT: B 392 MET cc_start: -0.0909 (mtt) cc_final: -0.1662 (mmt) REVERT: B 505 LEU cc_start: 0.8384 (pp) cc_final: 0.7960 (pp) REVERT: B 586 MET cc_start: 0.8855 (mmm) cc_final: 0.8244 (mmm) REVERT: B 621 ASP cc_start: 0.8527 (t0) cc_final: 0.8235 (t70) REVERT: B 755 ASP cc_start: 0.7531 (p0) cc_final: 0.6934 (p0) REVERT: B 764 LYS cc_start: 0.8301 (mtpt) cc_final: 0.8039 (mtpt) REVERT: B 841 LEU cc_start: 0.8955 (tp) cc_final: 0.8752 (tp) outliers start: 0 outliers final: 0 residues processed: 192 average time/residue: 0.3189 time to fit residues: 96.2778 Evaluate side-chains 140 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 2.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 144 optimal weight: 30.0000 chunk 93 optimal weight: 0.9980 chunk 139 optimal weight: 4.9990 chunk 70 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 148 optimal weight: 8.9990 chunk 158 optimal weight: 20.0000 chunk 115 optimal weight: 5.9990 chunk 21 optimal weight: 40.0000 chunk 183 optimal weight: 3.9990 chunk 212 optimal weight: 6.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 402 GLN ** A 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 603 GLN ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 887 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 909 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 557 HIS ** B 905 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1099 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5422 moved from start: 0.6821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21107 Z= 0.212 Angle : 0.615 10.496 28863 Z= 0.329 Chirality : 0.044 0.408 3215 Planarity : 0.004 0.051 3397 Dihedral : 17.635 175.258 3463 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 15.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % 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: -0.16 (0.18), residues: 2359 helix: 0.64 (0.16), residues: 1013 sheet: -0.75 (0.27), residues: 381 loop : -0.48 (0.21), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 820 HIS 0.007 0.001 HIS B 172 PHE 0.027 0.001 PHE B 596 TYR 0.019 0.002 TYR B1043 ARG 0.010 0.001 ARG B1039 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 195 time to evaluate : 2.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 MET cc_start: 0.5899 (mmm) cc_final: 0.5554 (mmm) REVERT: A 721 ILE cc_start: 0.8892 (mt) cc_final: 0.8686 (mt) REVERT: A 775 LEU cc_start: 0.6945 (tp) cc_final: 0.6456 (tp) REVERT: A 1042 LEU cc_start: 0.8345 (mt) cc_final: 0.8107 (mt) REVERT: B 42 MET cc_start: 0.7540 (pmm) cc_final: 0.7314 (pmm) REVERT: B 392 MET cc_start: 0.1798 (mtp) cc_final: -0.1491 (ttp) REVERT: B 505 LEU cc_start: 0.8405 (pp) cc_final: 0.7932 (pp) REVERT: B 576 LEU cc_start: 0.7253 (tp) cc_final: 0.6922 (tp) REVERT: B 586 MET cc_start: 0.8824 (mmm) cc_final: 0.8231 (mmm) REVERT: B 621 ASP cc_start: 0.8442 (t0) cc_final: 0.8234 (t70) REVERT: B 755 ASP cc_start: 0.7550 (p0) cc_final: 0.6946 (p0) REVERT: B 760 THR cc_start: 0.8114 (p) cc_final: 0.7762 (p) REVERT: B 764 LYS cc_start: 0.8297 (mtpt) cc_final: 0.7974 (mtpt) REVERT: B 841 LEU cc_start: 0.8821 (tp) cc_final: 0.8612 (tp) REVERT: B 1148 MET cc_start: 0.8583 (ptt) cc_final: 0.8372 (ptt) outliers start: 0 outliers final: 0 residues processed: 195 average time/residue: 0.3290 time to fit residues: 101.6754 Evaluate side-chains 150 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 150 time to evaluate : 2.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 223 optimal weight: 6.9990 chunk 203 optimal weight: 7.9990 chunk 217 optimal weight: 8.9990 chunk 130 optimal weight: 40.0000 chunk 94 optimal weight: 1.9990 chunk 170 optimal weight: 7.9990 chunk 66 optimal weight: 5.9990 chunk 196 optimal weight: 4.9990 chunk 205 optimal weight: 4.9990 chunk 216 optimal weight: 10.0000 chunk 142 optimal weight: 20.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 402 GLN ** A 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 887 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 909 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 409 ASN B 804 GLN B 905 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5557 moved from start: 0.7282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 21107 Z= 0.305 Angle : 0.679 9.587 28863 Z= 0.365 Chirality : 0.046 0.510 3215 Planarity : 0.005 0.064 3397 Dihedral : 17.730 176.303 3463 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 20.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.36 (0.17), residues: 2359 helix: 0.45 (0.16), residues: 1014 sheet: -0.86 (0.27), residues: 395 loop : -0.55 (0.21), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B1170 HIS 0.007 0.001 HIS B 172 PHE 0.056 0.002 PHE B 596 TYR 0.023 0.002 TYR B1043 ARG 0.021 0.001 ARG B 447 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 176 time to evaluate : 2.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 MET cc_start: 0.6031 (mmm) cc_final: 0.5754 (mmm) REVERT: A 745 VAL cc_start: 0.8977 (t) cc_final: 0.8602 (p) REVERT: B 325 MET cc_start: 0.5062 (ptt) cc_final: 0.4570 (ptm) REVERT: B 505 LEU cc_start: 0.8478 (pp) cc_final: 0.8003 (pp) REVERT: B 586 MET cc_start: 0.8909 (mmm) cc_final: 0.8291 (mmm) REVERT: B 621 ASP cc_start: 0.8527 (t0) cc_final: 0.8266 (t70) REVERT: B 698 TYR cc_start: 0.7600 (t80) cc_final: 0.7344 (t80) REVERT: B 714 MET cc_start: 0.8598 (tmm) cc_final: 0.8320 (tmm) REVERT: B 755 ASP cc_start: 0.7687 (p0) cc_final: 0.7137 (p0) outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 0.3173 time to fit residues: 88.8792 Evaluate side-chains 126 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 2.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 229 optimal weight: 20.0000 chunk 140 optimal weight: 10.0000 chunk 109 optimal weight: 1.9990 chunk 159 optimal weight: 1.9990 chunk 241 optimal weight: 7.9990 chunk 221 optimal weight: 0.9980 chunk 191 optimal weight: 4.9990 chunk 19 optimal weight: 30.0000 chunk 148 optimal weight: 20.0000 chunk 117 optimal weight: 7.9990 chunk 152 optimal weight: 30.0000 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 402 GLN ** A 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 706 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 887 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 909 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN ** B 905 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 909 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5509 moved from start: 0.7427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 21107 Z= 0.240 Angle : 0.654 13.551 28863 Z= 0.351 Chirality : 0.050 1.235 3215 Planarity : 0.004 0.082 3397 Dihedral : 17.804 177.074 3463 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 18.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % 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: -0.33 (0.18), residues: 2359 helix: 0.49 (0.16), residues: 1016 sheet: -0.86 (0.27), residues: 395 loop : -0.56 (0.21), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B1170 HIS 0.007 0.001 HIS B 172 PHE 0.041 0.002 PHE B 596 TYR 0.024 0.002 TYR B1043 ARG 0.016 0.001 ARG B 447 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 185 time to evaluate : 2.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 MET cc_start: 0.6024 (mmm) cc_final: 0.5703 (mmm) REVERT: A 745 VAL cc_start: 0.8937 (t) cc_final: 0.8617 (p) REVERT: B 42 MET cc_start: 0.7381 (pmm) cc_final: 0.7033 (pmm) REVERT: B 191 MET cc_start: 0.1291 (tmm) cc_final: 0.0988 (tmm) REVERT: B 325 MET cc_start: 0.4882 (ptt) cc_final: 0.4353 (ptm) REVERT: B 505 LEU cc_start: 0.8458 (pp) cc_final: 0.8044 (pp) REVERT: B 586 MET cc_start: 0.8950 (mmm) cc_final: 0.8370 (mmm) REVERT: B 621 ASP cc_start: 0.8495 (t0) cc_final: 0.8292 (t70) REVERT: B 739 PHE cc_start: 0.8267 (p90) cc_final: 0.8018 (p90) REVERT: B 755 ASP cc_start: 0.7622 (p0) cc_final: 0.7053 (p0) outliers start: 0 outliers final: 0 residues processed: 185 average time/residue: 0.3117 time to fit residues: 92.0905 Evaluate side-chains 136 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 2.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 204 optimal weight: 2.9990 chunk 58 optimal weight: 6.9990 chunk 177 optimal weight: 6.9990 chunk 28 optimal weight: 9.9990 chunk 53 optimal weight: 0.9990 chunk 192 optimal weight: 10.0000 chunk 80 optimal weight: 3.9990 chunk 197 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 35 optimal weight: 40.0000 chunk 168 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 402 GLN ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 706 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 887 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 909 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 905 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.064507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.040018 restraints weight = 183920.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.041401 restraints weight = 119025.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.042413 restraints weight = 85881.502| |-----------------------------------------------------------------------------| r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.7452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21107 Z= 0.188 Angle : 0.623 10.832 28863 Z= 0.331 Chirality : 0.046 0.801 3215 Planarity : 0.004 0.061 3397 Dihedral : 17.714 177.893 3463 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 15.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % 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: -0.19 (0.18), residues: 2359 helix: 0.68 (0.16), residues: 1012 sheet: -0.95 (0.27), residues: 411 loop : -0.46 (0.21), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B1170 HIS 0.006 0.001 HIS B 172 PHE 0.023 0.001 PHE B 388 TYR 0.020 0.002 TYR B1043 ARG 0.013 0.001 ARG B 447 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3840.86 seconds wall clock time: 71 minutes 19.06 seconds (4279.06 seconds total)