Starting phenix.real_space_refine on Wed Jul 24 10:22:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kgm_37226/07_2024/8kgm_37226.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kgm_37226/07_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_37226/07_2024/8kgm_37226.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kgm_37226/07_2024/8kgm_37226.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kgm_37226/07_2024/8kgm_37226.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kgm_37226/07_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: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 12.17, per 1000 atoms: 0.59 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: 7.67 Conformation dependent library (CDL) restraints added in 3.8 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: 7.63 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: 10.83 Time building geometry restraints manager: 8.47 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 2.520 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 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: 4.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.150 Construct map_model_manager: 0.030 Extract box with map and model: 0.780 Check model and map are aligned: 0.130 Set scattering table: 0.190 Process input model: 65.270 Find NCS groups from input model: 1.230 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: 0.000 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.570 ------------------------------------------------------------------------------- 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 : 2.145 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: 0.3802 time to fit residues: 256.4934 Evaluate side-chains 245 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 244 time to evaluate : 2.649 ------------------------------------------------------------------------------- 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: 5.9990 chunk 183 optimal weight: 6.9990 chunk 101 optimal weight: 5.9990 chunk 62 optimal weight: 0.4980 chunk 123 optimal weight: 10.0000 chunk 97 optimal weight: 3.9990 chunk 189 optimal weight: 5.9990 chunk 73 optimal weight: 0.9990 chunk 115 optimal weight: 6.9990 chunk 141 optimal weight: 5.9990 chunk 219 optimal weight: 10.0000 overall best weight: 3.4988 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 864 GLN ** A 883 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 909 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 981 ASN A1099 HIS B 125 HIS B 175 GLN ** B 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 483 ASN ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 692 GLN B 706 GLN B 748 HIS ** B 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 905 ASN B 909 HIS B1069 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5023 moved from start: 0.3302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 21107 Z= 0.264 Angle : 0.677 13.860 28863 Z= 0.366 Chirality : 0.045 0.193 3215 Planarity : 0.005 0.043 3397 Dihedral : 17.561 174.206 3463 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.10 % Allowed : 2.81 % Favored : 97.10 % 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: -0.99 (0.17), residues: 2359 helix: 0.06 (0.16), residues: 967 sheet: -0.75 (0.27), residues: 363 loop : -1.23 (0.19), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B1170 HIS 0.007 0.001 HIS B 892 PHE 0.028 0.002 PHE B 317 TYR 0.026 0.002 TYR A 698 ARG 0.008 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 264 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 262 time to evaluate : 2.447 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: A 198 MET cc_start: 0.6817 (mmm) cc_final: 0.6459 (mmm) REVERT: A 572 LEU cc_start: 0.7988 (tp) cc_final: 0.7640 (tp) REVERT: A 576 LEU cc_start: 0.7333 (tp) cc_final: 0.7092 (tp) REVERT: A 721 ILE cc_start: 0.8919 (mt) cc_final: 0.8670 (mt) REVERT: A 739 PHE cc_start: 0.8441 (p90) cc_final: 0.7780 (p90) REVERT: A 838 VAL cc_start: 0.8446 (t) cc_final: 0.8197 (t) REVERT: A 854 GLU cc_start: 0.7688 (mm-30) cc_final: 0.7393 (mm-30) REVERT: B 18 MET cc_start: -0.1267 (ptt) cc_final: -0.2756 (mmt) REVERT: B 467 MET cc_start: 0.7792 (mtm) cc_final: 0.6694 (mtp) REVERT: B 541 ASP cc_start: 0.7875 (p0) cc_final: 0.7358 (p0) REVERT: B 586 MET cc_start: 0.8629 (mmm) cc_final: 0.8302 (mmm) REVERT: B 721 ILE cc_start: 0.9223 (pt) cc_final: 0.9009 (pt) REVERT: B 755 ASP cc_start: 0.7190 (p0) cc_final: 0.6342 (p0) REVERT: B 763 ILE cc_start: 0.8267 (tp) cc_final: 0.7825 (tp) REVERT: B 776 TYR cc_start: 0.8514 (m-80) cc_final: 0.8113 (m-80) outliers start: 2 outliers final: 1 residues processed: 264 average time/residue: 0.3361 time to fit residues: 134.9965 Evaluate side-chains 182 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 181 time to evaluate : 2.146 ------------------------------------------------------------------------------- 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: 0.9980 chunk 68 optimal weight: 6.9990 chunk 182 optimal weight: 0.9980 chunk 149 optimal weight: 6.9990 chunk 60 optimal weight: 4.9990 chunk 220 optimal weight: 4.9990 chunk 237 optimal weight: 7.9990 chunk 196 optimal weight: 5.9990 chunk 218 optimal weight: 6.9990 chunk 75 optimal weight: 0.7980 chunk 176 optimal weight: 8.9990 overall best weight: 2.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 402 GLN ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 HIS ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 692 GLN B 759 ASN ** B 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 905 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5092 moved from start: 0.4062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21107 Z= 0.210 Angle : 0.600 11.979 28863 Z= 0.324 Chirality : 0.043 0.251 3215 Planarity : 0.004 0.041 3397 Dihedral : 17.400 175.166 3463 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % 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 (0.17), residues: 2359 helix: 0.63 (0.16), residues: 966 sheet: -0.62 (0.27), residues: 388 loop : -0.80 (0.20), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1170 HIS 0.007 0.001 HIS B 892 PHE 0.045 0.002 PHE B 785 TYR 0.019 0.001 TYR A1079 ARG 0.010 0.001 ARG B 716 *********************** 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 232 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 232 time to evaluate : 2.149 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 446 LEU cc_start: 0.9004 (mt) cc_final: 0.8801 (mt) REVERT: A 739 PHE cc_start: 0.8343 (p90) cc_final: 0.7670 (p90) REVERT: B 18 MET cc_start: -0.1093 (ptt) cc_final: -0.2579 (mmt) REVERT: B 467 MET cc_start: 0.7760 (mtm) cc_final: 0.7194 (mtp) REVERT: B 505 LEU cc_start: 0.8623 (pp) cc_final: 0.8323 (pp) REVERT: B 541 ASP cc_start: 0.7836 (p0) cc_final: 0.7313 (p0) REVERT: B 586 MET cc_start: 0.8685 (mmm) cc_final: 0.8375 (mmm) REVERT: B 755 ASP cc_start: 0.7289 (p0) cc_final: 0.6332 (p0) REVERT: B 760 THR cc_start: 0.7844 (p) cc_final: 0.7641 (p) REVERT: B 764 LYS cc_start: 0.8061 (ptmt) cc_final: 0.7719 (ttmt) REVERT: B 776 TYR cc_start: 0.8345 (m-80) cc_final: 0.8091 (m-80) REVERT: B 1181 ILE cc_start: 0.8385 (mm) cc_final: 0.8124 (mm) outliers start: 0 outliers final: 0 residues processed: 232 average time/residue: 0.3430 time to fit residues: 121.6602 Evaluate side-chains 163 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 2.220 ------------------------------------------------------------------------------- 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: 9.9990 chunk 165 optimal weight: 6.9990 chunk 114 optimal weight: 5.9990 chunk 24 optimal weight: 0.0870 chunk 105 optimal weight: 1.9990 chunk 147 optimal weight: 8.9990 chunk 220 optimal weight: 0.8980 chunk 233 optimal weight: 0.9980 chunk 115 optimal weight: 5.9990 chunk 209 optimal weight: 5.9990 chunk 63 optimal weight: 5.9990 overall best weight: 1.9962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 402 GLN A 677 GLN ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1051 HIS ** B 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 GLN ** B 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 603 GLN B 692 GLN B 930 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5118 moved from start: 0.4489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 21107 Z= 0.197 Angle : 0.588 12.641 28863 Z= 0.314 Chirality : 0.043 0.536 3215 Planarity : 0.003 0.041 3397 Dihedral : 17.309 173.801 3463 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 0.05 % Allowed : 2.52 % Favored : 97.44 % 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: -0.02 (0.18), residues: 2359 helix: 0.90 (0.17), residues: 971 sheet: -0.37 (0.28), residues: 375 loop : -0.68 (0.20), residues: 1013 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1170 HIS 0.006 0.001 HIS B 892 PHE 0.022 0.001 PHE B 388 TYR 0.016 0.001 TYR A 169 ARG 0.006 0.000 ARG B 578 *********************** 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 227 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 226 time to evaluate : 2.014 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: A 434 LEU cc_start: 0.8710 (tp) cc_final: 0.8469 (tp) REVERT: A 435 LEU cc_start: 0.8067 (pp) cc_final: 0.7674 (pp) REVERT: A 446 LEU cc_start: 0.9056 (mt) cc_final: 0.8745 (mt) REVERT: A 467 MET cc_start: 0.7320 (mtt) cc_final: 0.7077 (mmt) REVERT: A 739 PHE cc_start: 0.8315 (p90) cc_final: 0.7617 (p90) REVERT: A 775 LEU cc_start: 0.6630 (tp) cc_final: 0.6353 (tp) REVERT: B 18 MET cc_start: -0.1055 (ptt) cc_final: -0.2458 (mmp) REVERT: B 32 MET cc_start: 0.3055 (tpt) cc_final: 0.2614 (tpt) REVERT: B 296 LYS cc_start: 0.6318 (mmpt) cc_final: 0.5985 (mmtt) REVERT: B 467 MET cc_start: 0.7723 (mtm) cc_final: 0.6914 (mtp) REVERT: B 505 LEU cc_start: 0.8646 (pp) cc_final: 0.8391 (pp) REVERT: B 541 ASP cc_start: 0.7955 (p0) cc_final: 0.7391 (p0) REVERT: B 576 LEU cc_start: 0.7513 (tp) cc_final: 0.7275 (tp) REVERT: B 586 MET cc_start: 0.8676 (mmm) cc_final: 0.8345 (mmm) REVERT: B 666 THR cc_start: 0.7517 (p) cc_final: 0.7209 (t) REVERT: B 755 ASP cc_start: 0.7207 (p0) cc_final: 0.6271 (p0) outliers start: 1 outliers final: 0 residues processed: 227 average time/residue: 0.3373 time to fit residues: 117.2379 Evaluate side-chains 162 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 162 time to evaluate : 2.218 ------------------------------------------------------------------------------- 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: 0.0370 chunk 132 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 174 optimal weight: 10.0000 chunk 96 optimal weight: 20.0000 chunk 199 optimal weight: 4.9990 chunk 161 optimal weight: 6.9990 chunk 0 optimal weight: 40.0000 chunk 119 optimal weight: 5.9990 chunk 209 optimal weight: 6.9990 chunk 59 optimal weight: 7.9990 overall best weight: 3.0066 ------------------------------------------------------------------------------- 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 ** B 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 133 ASN B 175 GLN ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 692 GLN B 905 ASN B1186 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5259 moved from start: 0.5141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 21107 Z= 0.223 Angle : 0.610 10.229 28863 Z= 0.327 Chirality : 0.045 0.884 3215 Planarity : 0.004 0.039 3397 Dihedral : 17.341 173.220 3463 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 16.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.05 % Allowed : 2.71 % Favored : 97.24 % 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: 0.18 (0.18), residues: 2359 helix: 1.00 (0.17), residues: 976 sheet: -0.24 (0.28), residues: 375 loop : -0.52 (0.20), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B1189 HIS 0.007 0.001 HIS B 892 PHE 0.023 0.002 PHE B 785 TYR 0.021 0.002 TYR B 698 ARG 0.029 0.001 ARG A 684 *********************** 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 213 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 212 time to evaluate : 2.248 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 191 MET cc_start: 0.2472 (tmm) cc_final: 0.2253 (tmm) REVERT: A 198 MET cc_start: 0.6558 (mmm) cc_final: 0.5680 (mmm) REVERT: A 434 LEU cc_start: 0.8739 (tp) cc_final: 0.8509 (tp) REVERT: A 435 LEU cc_start: 0.8144 (pp) cc_final: 0.7892 (pp) REVERT: A 446 LEU cc_start: 0.9132 (mt) cc_final: 0.8789 (mt) REVERT: A 467 MET cc_start: 0.7317 (mtt) cc_final: 0.7001 (mmp) REVERT: A 586 MET cc_start: 0.7363 (tpt) cc_final: 0.6979 (mmm) REVERT: A 739 PHE cc_start: 0.8203 (p90) cc_final: 0.7474 (p90) REVERT: B 18 MET cc_start: -0.0825 (ptt) cc_final: -0.2344 (mmp) REVERT: B 296 LYS cc_start: 0.6361 (mmpt) cc_final: 0.6061 (mmtt) REVERT: B 505 LEU cc_start: 0.8542 (pp) cc_final: 0.8212 (pp) REVERT: B 576 LEU cc_start: 0.7656 (tp) cc_final: 0.7310 (tp) REVERT: B 586 MET cc_start: 0.8746 (mmm) cc_final: 0.8429 (mmm) REVERT: B 755 ASP cc_start: 0.7489 (p0) cc_final: 0.6251 (p0) REVERT: B 1148 MET cc_start: 0.8855 (ptt) cc_final: 0.8593 (ptt) outliers start: 1 outliers final: 0 residues processed: 213 average time/residue: 0.3366 time to fit residues: 110.0406 Evaluate side-chains 154 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 2.317 ------------------------------------------------------------------------------- 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: 9.9990 chunk 210 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 137 optimal weight: 30.0000 chunk 57 optimal weight: 0.5980 chunk 234 optimal weight: 9.9990 chunk 194 optimal weight: 0.5980 chunk 108 optimal weight: 10.0000 chunk 19 optimal weight: 50.0000 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 40.0000 overall best weight: 2.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 HIS A 402 GLN A 501 ASN ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 909 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1051 HIS ** 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 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 381 HIS ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 692 GLN B 864 GLN ** B1099 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5311 moved from start: 0.5636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 21107 Z= 0.212 Angle : 0.599 9.461 28863 Z= 0.320 Chirality : 0.046 0.958 3215 Planarity : 0.004 0.043 3397 Dihedral : 17.385 173.691 3463 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 16.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.10 % Allowed : 1.98 % Favored : 97.92 % 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: 0.17 (0.18), residues: 2359 helix: 1.01 (0.17), residues: 982 sheet: -0.37 (0.27), residues: 398 loop : -0.48 (0.21), residues: 979 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1170 HIS 0.006 0.001 HIS A 620 PHE 0.029 0.002 PHE B 596 TYR 0.030 0.002 TYR B 698 ARG 0.008 0.001 ARG B 831 *********************** 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 212 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 210 time to evaluate : 2.230 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: 0.6527 (mmm) cc_final: 0.5888 (mmm) REVERT: A 434 LEU cc_start: 0.8666 (tp) cc_final: 0.8427 (tp) REVERT: A 701 ASP cc_start: 0.8233 (t0) cc_final: 0.7990 (t0) REVERT: A 775 LEU cc_start: 0.6655 (tp) cc_final: 0.6227 (tp) REVERT: A 1148 MET cc_start: 0.8564 (ptt) cc_final: 0.8287 (ptt) REVERT: B 392 MET cc_start: -0.0884 (mtt) cc_final: -0.1099 (ttm) REVERT: B 505 LEU cc_start: 0.8587 (pp) cc_final: 0.8204 (pp) REVERT: B 586 MET cc_start: 0.8693 (mmm) cc_final: 0.8419 (mmm) REVERT: B 698 TYR cc_start: 0.7258 (t80) cc_final: 0.6814 (t80) REVERT: B 703 ILE cc_start: 0.9080 (pt) cc_final: 0.8879 (pt) REVERT: B 755 ASP cc_start: 0.7547 (p0) cc_final: 0.6534 (p0) REVERT: B 1148 MET cc_start: 0.8881 (ptt) cc_final: 0.8663 (ptt) outliers start: 2 outliers final: 2 residues processed: 212 average time/residue: 0.3310 time to fit residues: 108.6434 Evaluate side-chains 151 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 149 time to evaluate : 2.377 ------------------------------------------------------------------------------- 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: 9.9990 chunk 26 optimal weight: 20.0000 chunk 133 optimal weight: 20.0000 chunk 170 optimal weight: 10.0000 chunk 132 optimal weight: 20.0000 chunk 197 optimal weight: 3.9990 chunk 130 optimal weight: 8.9990 chunk 233 optimal weight: 7.9990 chunk 145 optimal weight: 20.0000 chunk 142 optimal weight: 8.9990 chunk 107 optimal weight: 3.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 308 ASN A 402 GLN A 506 GLN ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 880 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 909 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1051 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1186 ASN ** B 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 GLN ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 409 ASN ** B 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 692 GLN ** B1099 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5594 moved from start: 0.6735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.101 21107 Z= 0.411 Angle : 0.791 13.693 28863 Z= 0.425 Chirality : 0.049 0.806 3215 Planarity : 0.006 0.174 3397 Dihedral : 17.880 175.429 3463 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 30.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % 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: -0.43 (0.17), residues: 2359 helix: 0.27 (0.16), residues: 993 sheet: -0.60 (0.28), residues: 382 loop : -0.58 (0.21), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP B 820 HIS 0.011 0.002 HIS A 609 PHE 0.048 0.003 PHE B1107 TYR 0.038 0.003 TYR B 698 ARG 0.020 0.001 ARG B1151 *********************** 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 184 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 184 time to evaluate : 2.039 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: 0.6627 (mmm) cc_final: 0.6123 (mmm) REVERT: A 745 VAL cc_start: 0.9093 (t) cc_final: 0.8791 (p) REVERT: A 775 LEU cc_start: 0.7222 (tp) cc_final: 0.6840 (tp) REVERT: A 1148 MET cc_start: 0.8615 (ptt) cc_final: 0.8256 (ptt) REVERT: B 392 MET cc_start: -0.0812 (mtt) cc_final: -0.2312 (ttm) REVERT: B 434 LEU cc_start: 0.8569 (tp) cc_final: 0.8342 (tp) REVERT: B 505 LEU cc_start: 0.8666 (pp) cc_final: 0.8311 (pp) REVERT: B 543 ASP cc_start: 0.6910 (m-30) cc_final: 0.6430 (m-30) REVERT: B 586 MET cc_start: 0.8867 (mmm) cc_final: 0.8583 (mmm) REVERT: B 755 ASP cc_start: 0.7968 (p0) cc_final: 0.7327 (p0) REVERT: B 760 THR cc_start: 0.8078 (p) cc_final: 0.7861 (p) REVERT: B 764 LYS cc_start: 0.8389 (mtpt) cc_final: 0.8127 (mtpt) REVERT: B 1148 MET cc_start: 0.8825 (ptt) cc_final: 0.8622 (ptt) outliers start: 0 outliers final: 0 residues processed: 184 average time/residue: 0.3335 time to fit residues: 97.2050 Evaluate side-chains 139 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 139 time to evaluate : 2.253 ------------------------------------------------------------------------------- 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: 0.0970 chunk 93 optimal weight: 0.5980 chunk 139 optimal weight: 5.9990 chunk 70 optimal weight: 5.9990 chunk 45 optimal weight: 0.8980 chunk 148 optimal weight: 40.0000 chunk 158 optimal weight: 3.9990 chunk 115 optimal weight: 0.7980 chunk 21 optimal weight: 30.0000 chunk 183 optimal weight: 6.9990 chunk 212 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 909 HIS A1186 ASN ** B 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 557 HIS B 692 GLN B 905 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5339 moved from start: 0.6496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21107 Z= 0.170 Angle : 0.617 10.367 28863 Z= 0.325 Chirality : 0.045 0.511 3215 Planarity : 0.004 0.130 3397 Dihedral : 17.696 174.446 3463 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 15.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % 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: 0.08 (0.18), residues: 2359 helix: 0.85 (0.17), residues: 985 sheet: -0.52 (0.28), residues: 388 loop : -0.39 (0.21), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1189 HIS 0.010 0.001 HIS B 172 PHE 0.027 0.002 PHE B1107 TYR 0.055 0.002 TYR B 824 ARG 0.019 0.001 ARG A 683 *********************** 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 204 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 204 time to evaluate : 2.492 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: 0.6332 (mmm) cc_final: 0.5881 (mmm) REVERT: A 257 MET cc_start: 0.4544 (ppp) cc_final: 0.4336 (ppp) REVERT: A 586 MET cc_start: 0.7401 (tpt) cc_final: 0.6864 (mmm) REVERT: A 1042 LEU cc_start: 0.8402 (mt) cc_final: 0.8065 (mt) REVERT: B 325 MET cc_start: 0.4713 (ptt) cc_final: 0.4340 (ptt) REVERT: B 392 MET cc_start: -0.0985 (mtt) cc_final: -0.2240 (ttm) REVERT: B 468 ILE cc_start: 0.8423 (pt) cc_final: 0.8208 (mt) REVERT: B 505 LEU cc_start: 0.8617 (pp) cc_final: 0.8211 (pp) REVERT: B 586 MET cc_start: 0.8711 (mmm) cc_final: 0.8117 (mmm) REVERT: B 755 ASP cc_start: 0.7396 (p0) cc_final: 0.6613 (p0) REVERT: B 760 THR cc_start: 0.8118 (p) cc_final: 0.7814 (p) REVERT: B 764 LYS cc_start: 0.8203 (mtpt) cc_final: 0.7869 (mtpt) REVERT: B 1148 MET cc_start: 0.8600 (ptt) cc_final: 0.8337 (ptt) outliers start: 0 outliers final: 0 residues processed: 204 average time/residue: 0.3238 time to fit residues: 104.4222 Evaluate side-chains 158 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 158 time to evaluate : 2.449 ------------------------------------------------------------------------------- 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: 0.9990 chunk 203 optimal weight: 4.9990 chunk 217 optimal weight: 10.0000 chunk 130 optimal weight: 9.9990 chunk 94 optimal weight: 10.0000 chunk 170 optimal weight: 0.9980 chunk 66 optimal weight: 4.9990 chunk 196 optimal weight: 10.0000 chunk 205 optimal weight: 5.9990 chunk 216 optimal weight: 1.9990 chunk 142 optimal weight: 6.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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** ** B 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 423 ASN B 692 GLN ** B1099 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5415 moved from start: 0.6726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 21107 Z= 0.216 Angle : 0.624 12.370 28863 Z= 0.332 Chirality : 0.045 0.730 3215 Planarity : 0.004 0.105 3397 Dihedral : 17.666 175.018 3463 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 19.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % 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: 0.02 (0.18), residues: 2359 helix: 0.80 (0.16), residues: 994 sheet: -0.57 (0.28), residues: 392 loop : -0.42 (0.21), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP A1170 HIS 0.009 0.001 HIS B 172 PHE 0.029 0.002 PHE B 596 TYR 0.031 0.002 TYR B 824 ARG 0.016 0.001 ARG A 683 *********************** 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 194 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 194 time to evaluate : 2.316 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: 0.6391 (mmm) cc_final: 0.5948 (mmm) REVERT: A 257 MET cc_start: 0.4651 (ppp) cc_final: 0.4428 (ppp) REVERT: A 586 MET cc_start: 0.7442 (tpt) cc_final: 0.6889 (mmm) REVERT: B 42 MET cc_start: 0.7470 (pmm) cc_final: 0.7186 (pmm) REVERT: B 505 LEU cc_start: 0.8665 (pp) cc_final: 0.8252 (pp) REVERT: B 586 MET cc_start: 0.8740 (mmm) cc_final: 0.8504 (mmm) REVERT: B 755 ASP cc_start: 0.7695 (p0) cc_final: 0.7001 (p0) REVERT: B 764 LYS cc_start: 0.8247 (mtpt) cc_final: 0.7980 (mtpt) outliers start: 0 outliers final: 0 residues processed: 194 average time/residue: 0.3304 time to fit residues: 102.4450 Evaluate side-chains 145 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 145 time to evaluate : 2.045 ------------------------------------------------------------------------------- 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: 0.0270 chunk 140 optimal weight: 20.0000 chunk 109 optimal weight: 2.9990 chunk 159 optimal weight: 8.9990 chunk 241 optimal weight: 7.9990 chunk 221 optimal weight: 2.9990 chunk 191 optimal weight: 0.7980 chunk 19 optimal weight: 40.0000 chunk 148 optimal weight: 0.4980 chunk 117 optimal weight: 2.9990 chunk 152 optimal weight: 4.9990 overall best weight: 1.4642 ------------------------------------------------------------------------------- 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** ** B 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 349 ASN B 692 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5349 moved from start: 0.6803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 21107 Z= 0.175 Angle : 0.604 14.186 28863 Z= 0.319 Chirality : 0.049 1.358 3215 Planarity : 0.004 0.097 3397 Dihedral : 17.586 175.545 3463 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 16.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % 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: 0.99 (0.17), residues: 989 sheet: -0.54 (0.27), residues: 390 loop : -0.36 (0.21), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A1170 HIS 0.008 0.001 HIS B 172 PHE 0.069 0.001 PHE B 596 TYR 0.028 0.001 TYR B 824 ARG 0.012 0.001 ARG A 683 ********************** 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 200 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 200 time to evaluate : 2.429 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: A 198 MET cc_start: 0.6374 (mmm) cc_final: 0.5941 (mmm) REVERT: A 257 MET cc_start: 0.4583 (ppp) cc_final: 0.4325 (ppp) REVERT: A 586 MET cc_start: 0.7309 (tpt) cc_final: 0.6783 (mmm) REVERT: A 764 LYS cc_start: 0.8291 (mtpt) cc_final: 0.8053 (tttm) REVERT: B 32 MET cc_start: 0.3189 (tpt) cc_final: 0.2522 (tpt) REVERT: B 42 MET cc_start: 0.7330 (pmm) cc_final: 0.6756 (pmm) REVERT: B 191 MET cc_start: 0.1065 (tmm) cc_final: 0.0789 (tmm) REVERT: B 257 MET cc_start: -0.4232 (ttt) cc_final: -0.4979 (ptm) REVERT: B 505 LEU cc_start: 0.8637 (pp) cc_final: 0.8293 (pp) REVERT: B 543 ASP cc_start: 0.7260 (m-30) cc_final: 0.6920 (m-30) REVERT: B 586 MET cc_start: 0.8698 (mmm) cc_final: 0.8038 (mmm) REVERT: B 755 ASP cc_start: 0.7624 (p0) cc_final: 0.6931 (p0) REVERT: B 760 THR cc_start: 0.8173 (p) cc_final: 0.7895 (p) REVERT: B 764 LYS cc_start: 0.8235 (mtpt) cc_final: 0.7910 (mtpt) outliers start: 0 outliers final: 0 residues processed: 200 average time/residue: 0.3163 time to fit residues: 99.8151 Evaluate side-chains 155 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 155 time to evaluate : 2.247 ------------------------------------------------------------------------------- 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: 1.9990 chunk 58 optimal weight: 6.9990 chunk 177 optimal weight: 8.9990 chunk 28 optimal weight: 40.0000 chunk 53 optimal weight: 0.9990 chunk 192 optimal weight: 10.0000 chunk 80 optimal weight: 4.9990 chunk 197 optimal weight: 0.0970 chunk 24 optimal weight: 10.0000 chunk 35 optimal weight: 50.0000 chunk 168 optimal weight: 6.9990 overall best weight: 3.0186 ------------------------------------------------------------------------------- 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** ** B 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 692 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.065146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.040673 restraints weight = 184594.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.042061 restraints weight = 119453.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.043071 restraints weight = 86579.556| |-----------------------------------------------------------------------------| r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.7098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21107 Z= 0.217 Angle : 0.615 11.238 28863 Z= 0.329 Chirality : 0.046 0.875 3215 Planarity : 0.004 0.089 3397 Dihedral : 17.578 176.369 3463 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 20.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % 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: 0.10 (0.18), residues: 2359 helix: 0.89 (0.16), residues: 997 sheet: -0.64 (0.27), residues: 394 loop : -0.34 (0.21), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B1170 HIS 0.008 0.001 HIS B 172 PHE 0.030 0.002 PHE B 596 TYR 0.025 0.002 TYR B 824 ARG 0.013 0.001 ARG A 683 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3836.25 seconds wall clock time: 70 minutes 44.81 seconds (4244.81 seconds total)