Starting phenix.real_space_refine on Tue Feb 20 16:21:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtc_32778/02_2024/7wtc_32778_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtc_32778/02_2024/7wtc_32778.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtc_32778/02_2024/7wtc_32778.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtc_32778/02_2024/7wtc_32778.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtc_32778/02_2024/7wtc_32778_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtc_32778/02_2024/7wtc_32778_updated.pdb" } resolution = 4.0 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 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 6 5.49 5 S 172 5.16 5 C 17994 2.51 5 N 4945 2.21 5 O 5301 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 449": "OE1" <-> "OE2" Residue "A GLU 1001": "OE1" <-> "OE2" Residue "A PHE 1023": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 214": "OE1" <-> "OE2" Residue "B GLU 332": "OE1" <-> "OE2" Residue "B GLU 365": "OE1" <-> "OE2" Residue "B GLU 701": "OE1" <-> "OE2" Residue "B GLU 936": "OE1" <-> "OE2" Residue "B GLU 1146": "OE1" <-> "OE2" Residue "C GLU 691": "OE1" <-> "OE2" Residue "C TYR 871": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 932": "OE1" <-> "OE2" Residue "C GLU 1079": "OE1" <-> "OE2" Residue "D GLU 946": "OE1" <-> "OE2" Residue "D GLU 1047": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 28418 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 8869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1146, 8869 Classifications: {'peptide': 1146} Link IDs: {'CIS': 1, 'PTRANS': 65, 'TRANS': 1079} Chain: "B" Number of atoms: 8877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1147, 8877 Classifications: {'peptide': 1147} Link IDs: {'PTRANS': 65, 'TRANS': 1081} Chain: "C" Number of atoms: 5255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 684, 5255 Classifications: {'peptide': 684} Link IDs: {'PTRANS': 45, 'TRANS': 638} Chain: "D" Number of atoms: 5255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 684, 5255 Classifications: {'peptide': 684} Link IDs: {'PTRANS': 45, 'TRANS': 638} Chain: "A" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 66 Unusual residues: {'ACO': 1, 'BTI': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 66 Unusual residues: {'ACO': 1, 'BTI': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Time building chain proxies: 14.57, per 1000 atoms: 0.51 Number of scatterers: 28418 At special positions: 0 Unit cell: (161.7, 162.8, 136.4, 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 172 16.00 P 6 15.00 O 5301 8.00 N 4945 7.00 C 17994 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 752 " - pdb=" SG CYS A 786 " distance=2.03 Simple disulfide: pdb=" SG CYS B 752 " - pdb=" SG CYS B 786 " distance=2.02 Simple disulfide: pdb=" SG CYS C 752 " - pdb=" SG CYS C 786 " distance=2.02 Simple disulfide: pdb=" SG CYS D 752 " - pdb=" SG CYS D 786 " distance=2.02 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=5, symmetry=0 Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 11.50 Conformation dependent library (CDL) restraints added in 5.0 seconds 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6738 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 146 helices and 31 sheets defined 38.3% alpha, 11.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.14 Creating SS restraints... Processing helix chain 'A' and resid 47 through 59 Processing helix chain 'A' and resid 76 through 79 No H-bonds generated for 'chain 'A' and resid 76 through 79' Processing helix chain 'A' and resid 92 through 97 removed outlier: 4.186A pdb=" N TYR A 96 " --> pdb=" O PRO A 92 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU A 97 " --> pdb=" O VAL A 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 92 through 97' Processing helix chain 'A' and resid 99 through 108 Processing helix chain 'A' and resid 125 through 133 Processing helix chain 'A' and resid 143 through 148 Processing helix chain 'A' and resid 152 through 160 Processing helix chain 'A' and resid 177 through 187 removed outlier: 3.602A pdb=" N TYR A 187 " --> pdb=" O PHE A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 226 removed outlier: 4.095A pdb=" N GLU A 215 " --> pdb=" O GLU A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 302 Processing helix chain 'A' and resid 331 through 339 removed outlier: 3.676A pdb=" N THR A 334 " --> pdb=" O VAL A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 353 Processing helix chain 'A' and resid 357 through 360 No H-bonds generated for 'chain 'A' and resid 357 through 360' Processing helix chain 'A' and resid 436 through 449 Processing helix chain 'A' and resid 459 through 466 Processing helix chain 'A' and resid 469 through 472 No H-bonds generated for 'chain 'A' and resid 469 through 472' Processing helix chain 'A' and resid 478 through 480 No H-bonds generated for 'chain 'A' and resid 478 through 480' Processing helix chain 'A' and resid 497 through 510 Processing helix chain 'A' and resid 541 through 548 Processing helix chain 'A' and resid 550 through 559 Processing helix chain 'A' and resid 573 through 576 No H-bonds generated for 'chain 'A' and resid 573 through 576' Processing helix chain 'A' and resid 584 through 597 removed outlier: 3.674A pdb=" N ILE A 590 " --> pdb=" O ASP A 586 " (cutoff:3.500A) Proline residue: A 592 - end of helix Processing helix chain 'A' and resid 609 through 617 Processing helix chain 'A' and resid 623 through 633 removed outlier: 3.574A pdb=" N LEU A 633 " --> pdb=" O GLU A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 669 Processing helix chain 'A' and resid 683 through 696 Processing helix chain 'A' and resid 720 through 733 Processing helix chain 'A' and resid 749 through 760 Processing helix chain 'A' and resid 779 through 788 Processing helix chain 'A' and resid 810 through 816 Processing helix chain 'A' and resid 828 through 842 Processing helix chain 'A' and resid 845 through 847 No H-bonds generated for 'chain 'A' and resid 845 through 847' Processing helix chain 'A' and resid 861 through 864 No H-bonds generated for 'chain 'A' and resid 861 through 864' Processing helix chain 'A' and resid 871 through 881 Processing helix chain 'A' and resid 886 through 900 removed outlier: 3.887A pdb=" N LYS A 891 " --> pdb=" O LYS A 888 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N VAL A 895 " --> pdb=" O LYS A 892 " (cutoff:3.500A) Processing helix chain 'A' and resid 908 through 924 Processing helix chain 'A' and resid 928 through 933 Processing helix chain 'A' and resid 942 through 949 Processing helix chain 'A' and resid 961 through 968 Processing helix chain 'A' and resid 978 through 981 No H-bonds generated for 'chain 'A' and resid 978 through 981' Processing helix chain 'A' and resid 987 through 997 Processing helix chain 'A' and resid 1004 through 1012 Processing helix chain 'A' and resid 1014 through 1027 Processing helix chain 'A' and resid 1035 through 1039 Processing helix chain 'B' and resid 47 through 58 Processing helix chain 'B' and resid 76 through 79 No H-bonds generated for 'chain 'B' and resid 76 through 79' Processing helix chain 'B' and resid 92 through 97 removed outlier: 4.232A pdb=" N TYR B 96 " --> pdb=" O PRO B 92 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N LEU B 97 " --> pdb=" O VAL B 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 92 through 97' Processing helix chain 'B' and resid 99 through 108 Processing helix chain 'B' and resid 125 through 133 Processing helix chain 'B' and resid 143 through 149 Processing helix chain 'B' and resid 152 through 161 Processing helix chain 'B' and resid 177 through 186 Processing helix chain 'B' and resid 210 through 227 Processing helix chain 'B' and resid 285 through 302 Processing helix chain 'B' and resid 331 through 340 removed outlier: 3.868A pdb=" N THR B 334 " --> pdb=" O VAL B 331 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N THR B 340 " --> pdb=" O GLU B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 353 Processing helix chain 'B' and resid 357 through 360 No H-bonds generated for 'chain 'B' and resid 357 through 360' Processing helix chain 'B' and resid 436 through 449 Processing helix chain 'B' and resid 459 through 467 Processing helix chain 'B' and resid 469 through 473 Processing helix chain 'B' and resid 485 through 487 No H-bonds generated for 'chain 'B' and resid 485 through 487' Processing helix chain 'B' and resid 496 through 509 Processing helix chain 'B' and resid 542 through 547 Processing helix chain 'B' and resid 550 through 559 Processing helix chain 'B' and resid 572 through 577 Processing helix chain 'B' and resid 584 through 589 removed outlier: 3.799A pdb=" N LYS B 589 " --> pdb=" O HIS B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 591 through 596 Processing helix chain 'B' and resid 609 through 617 Processing helix chain 'B' and resid 623 through 631 removed outlier: 3.611A pdb=" N LEU B 630 " --> pdb=" O ARG B 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 668 Processing helix chain 'B' and resid 683 through 696 Processing helix chain 'B' and resid 720 through 733 Processing helix chain 'B' and resid 749 through 761 Processing helix chain 'B' and resid 779 through 789 Processing helix chain 'B' and resid 799 through 801 No H-bonds generated for 'chain 'B' and resid 799 through 801' Processing helix chain 'B' and resid 810 through 816 Processing helix chain 'B' and resid 828 through 843 removed outlier: 3.573A pdb=" N TRP B 838 " --> pdb=" O TYR B 834 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N GLY B 843 " --> pdb=" O GLU B 839 " (cutoff:3.500A) Processing helix chain 'B' and resid 851 through 854 Processing helix chain 'B' and resid 861 through 864 No H-bonds generated for 'chain 'B' and resid 861 through 864' Processing helix chain 'B' and resid 871 through 881 Processing helix chain 'B' and resid 887 through 901 removed outlier: 4.264A pdb=" N VAL B 895 " --> pdb=" O LYS B 891 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N GLU B 896 " --> pdb=" O LYS B 892 " (cutoff:3.500A) Processing helix chain 'B' and resid 909 through 924 Processing helix chain 'B' and resid 928 through 933 Processing helix chain 'B' and resid 942 through 949 Processing helix chain 'B' and resid 961 through 968 Processing helix chain 'B' and resid 978 through 981 No H-bonds generated for 'chain 'B' and resid 978 through 981' Processing helix chain 'B' and resid 988 through 998 Processing helix chain 'B' and resid 1004 through 1012 Processing helix chain 'B' and resid 1014 through 1027 Processing helix chain 'B' and resid 1035 through 1039 Processing helix chain 'C' and resid 496 through 509 Processing helix chain 'C' and resid 542 through 546 Processing helix chain 'C' and resid 550 through 559 Processing helix chain 'C' and resid 572 through 577 Processing helix chain 'C' and resid 587 through 589 No H-bonds generated for 'chain 'C' and resid 587 through 589' Processing helix chain 'C' and resid 591 through 597 Processing helix chain 'C' and resid 609 through 617 Processing helix chain 'C' and resid 623 through 631 removed outlier: 3.668A pdb=" N LEU C 630 " --> pdb=" O ARG C 626 " (cutoff:3.500A) Processing helix chain 'C' and resid 656 through 669 Processing helix chain 'C' and resid 683 through 696 Processing helix chain 'C' and resid 720 through 733 Processing helix chain 'C' and resid 749 through 762 removed outlier: 4.305A pdb=" N ARG C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) Processing helix chain 'C' and resid 779 through 789 Processing helix chain 'C' and resid 799 through 801 No H-bonds generated for 'chain 'C' and resid 799 through 801' Processing helix chain 'C' and resid 810 through 816 Processing helix chain 'C' and resid 829 through 845 removed outlier: 3.956A pdb=" N GLY C 843 " --> pdb=" O GLU C 839 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LEU C 844 " --> pdb=" O GLY C 840 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N TYR C 845 " --> pdb=" O ALA C 841 " (cutoff:3.500A) Processing helix chain 'C' and resid 850 through 852 No H-bonds generated for 'chain 'C' and resid 850 through 852' Processing helix chain 'C' and resid 861 through 864 No H-bonds generated for 'chain 'C' and resid 861 through 864' Processing helix chain 'C' and resid 871 through 881 Processing helix chain 'C' and resid 887 through 901 removed outlier: 4.162A pdb=" N VAL C 895 " --> pdb=" O LYS C 891 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N GLU C 896 " --> pdb=" O LYS C 892 " (cutoff:3.500A) Processing helix chain 'C' and resid 912 through 923 Processing helix chain 'C' and resid 928 through 933 Processing helix chain 'C' and resid 942 through 949 Processing helix chain 'C' and resid 961 through 968 Processing helix chain 'C' and resid 978 through 981 No H-bonds generated for 'chain 'C' and resid 978 through 981' Processing helix chain 'C' and resid 988 through 997 removed outlier: 3.549A pdb=" N LYS C 992 " --> pdb=" O GLN C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1004 through 1012 Processing helix chain 'C' and resid 1014 through 1027 removed outlier: 3.593A pdb=" N THR C1026 " --> pdb=" O ASP C1022 " (cutoff:3.500A) Processing helix chain 'C' and resid 1035 through 1040 Processing helix chain 'D' and resid 496 through 510 Processing helix chain 'D' and resid 542 through 547 Processing helix chain 'D' and resid 550 through 559 Processing helix chain 'D' and resid 572 through 577 Processing helix chain 'D' and resid 584 through 597 Proline residue: D 592 - end of helix Processing helix chain 'D' and resid 609 through 617 Processing helix chain 'D' and resid 623 through 633 Processing helix chain 'D' and resid 656 through 668 Processing helix chain 'D' and resid 683 through 696 Processing helix chain 'D' and resid 720 through 732 Processing helix chain 'D' and resid 749 through 762 removed outlier: 4.406A pdb=" N ARG D 762 " --> pdb=" O SER D 758 " (cutoff:3.500A) Processing helix chain 'D' and resid 779 through 789 Processing helix chain 'D' and resid 811 through 817 Processing helix chain 'D' and resid 828 through 845 removed outlier: 4.191A pdb=" N GLY D 843 " --> pdb=" O GLU D 839 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N LEU D 844 " --> pdb=" O GLY D 840 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N TYR D 845 " --> pdb=" O ALA D 841 " (cutoff:3.500A) Processing helix chain 'D' and resid 850 through 854 removed outlier: 4.257A pdb=" N MET D 854 " --> pdb=" O THR D 851 " (cutoff:3.500A) Processing helix chain 'D' and resid 860 through 864 Processing helix chain 'D' and resid 868 through 880 removed outlier: 4.645A pdb=" N THR D 872 " --> pdb=" O GLY D 868 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N ASN D 873 " --> pdb=" O GLY D 869 " (cutoff:3.500A) Processing helix chain 'D' and resid 887 through 901 removed outlier: 3.737A pdb=" N LYS D 891 " --> pdb=" O PHE D 887 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LYS D 892 " --> pdb=" O LYS D 888 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA D 893 " --> pdb=" O GLU D 889 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL D 895 " --> pdb=" O LYS D 891 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N GLU D 896 " --> pdb=" O LYS D 892 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASN D 898 " --> pdb=" O TYR D 894 " (cutoff:3.500A) Processing helix chain 'D' and resid 908 through 924 Processing helix chain 'D' and resid 928 through 933 Processing helix chain 'D' and resid 942 through 949 Processing helix chain 'D' and resid 961 through 967 Processing helix chain 'D' and resid 978 through 981 No H-bonds generated for 'chain 'D' and resid 978 through 981' Processing helix chain 'D' and resid 989 through 997 Processing helix chain 'D' and resid 1004 through 1012 Processing helix chain 'D' and resid 1014 through 1027 Processing helix chain 'D' and resid 1035 through 1039 Processing sheet with id= A, first strand: chain 'A' and resid 137 through 139 removed outlier: 6.686A pdb=" N ARG A 62 " --> pdb=" O VAL A 40 " (cutoff:3.500A) removed outlier: 8.551A pdb=" N VAL A 42 " --> pdb=" O ARG A 62 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N VAL A 64 " --> pdb=" O VAL A 42 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N GLU A 82 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N TYR A 67 " --> pdb=" O GLU A 82 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N TYR A 84 " --> pdb=" O TYR A 67 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 191 through 195 removed outlier: 3.538A pdb=" N ILE A 192 " --> pdb=" O GLU A 236 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 262 through 264 removed outlier: 3.913A pdb=" N ILE A 245 " --> pdb=" O PHE A 312 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N LEU A 313 " --> pdb=" O PHE A 322 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N PHE A 322 " --> pdb=" O LEU A 313 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 249 through 251 Processing sheet with id= E, first strand: chain 'A' and resid 275 through 277 removed outlier: 4.213A pdb=" N VAL A 427 " --> pdb=" O VAL A 378 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 396 through 398 Processing sheet with id= G, first strand: chain 'A' and resid 564 through 567 Processing sheet with id= H, first strand: chain 'A' and resid 767 through 772 removed outlier: 3.898A pdb=" N ILE A 737 " --> pdb=" O VAL A 700 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N MET A 604 " --> pdb=" O GLN A 640 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N LEU A 642 " --> pdb=" O MET A 604 " (cutoff:3.500A) removed outlier: 8.815A pdb=" N ASN A 606 " --> pdb=" O LEU A 642 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 1047 through 1051 removed outlier: 6.841A pdb=" N PHE A1077 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N VAL A1065 " --> pdb=" O GLN A1075 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N GLN A1075 " --> pdb=" O VAL A1065 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 1119 through 1123 removed outlier: 6.918A pdb=" N VAL A1139 " --> pdb=" O ILE A1121 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ILE A1123 " --> pdb=" O LEU A1137 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N LEU A1137 " --> pdb=" O ILE A1123 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N VAL A1149 " --> pdb=" O LEU A1137 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N VAL A1139 " --> pdb=" O THR A1147 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N THR A1147 " --> pdb=" O VAL A1139 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 62 through 64 removed outlier: 3.700A pdb=" N VAL B 64 " --> pdb=" O VAL B 40 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL B 42 " --> pdb=" O VAL B 64 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N ALA B 113 " --> pdb=" O MET B 41 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ARG B 137 " --> pdb=" O VAL B 114 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 65 through 67 Processing sheet with id= M, first strand: chain 'B' and resid 204 through 207 Processing sheet with id= N, first strand: chain 'B' and resid 262 through 264 removed outlier: 3.689A pdb=" N GLU B 324 " --> pdb=" O GLU B 311 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N LEU B 313 " --> pdb=" O PHE B 322 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N PHE B 322 " --> pdb=" O LEU B 313 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 249 through 251 Processing sheet with id= P, first strand: chain 'B' and resid 275 through 277 removed outlier: 4.167A pdb=" N VAL B 427 " --> pdb=" O VAL B 378 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'B' and resid 564 through 566 Processing sheet with id= R, first strand: chain 'B' and resid 767 through 771 removed outlier: 7.337A pdb=" N LEU B 642 " --> pdb=" O ASN B 606 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'B' and resid 1046 through 1051 removed outlier: 3.912A pdb=" N GLU B1046 " --> pdb=" O ALA B1062 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N PHE B1077 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N VAL B1065 " --> pdb=" O GLN B1075 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N GLN B1075 " --> pdb=" O VAL B1065 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'B' and resid 1146 through 1148 removed outlier: 3.526A pdb=" N THR B1147 " --> pdb=" O LEU B1140 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ASP B1122 " --> pdb=" O VAL B1139 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N SER B1141 " --> pdb=" O VAL B1120 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N VAL B1120 " --> pdb=" O SER B1141 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'C' and resid 564 through 567 Processing sheet with id= V, first strand: chain 'C' and resid 603 through 605 removed outlier: 6.856A pdb=" N VAL C 673 " --> pdb=" O MET C 641 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N VAL C 699 " --> pdb=" O PHE C 674 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N VAL C 676 " --> pdb=" O VAL C 699 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N GLU C 701 " --> pdb=" O VAL C 676 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ILE C 737 " --> pdb=" O ALA C 702 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N ILE C 704 " --> pdb=" O ILE C 737 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N CYS C 739 " --> pdb=" O ILE C 704 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'C' and resid 1047 through 1049 removed outlier: 6.612A pdb=" N PHE C1077 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N VAL C1065 " --> pdb=" O GLN C1075 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N GLN C1075 " --> pdb=" O VAL C1065 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'C' and resid 1135 through 1141 removed outlier: 3.589A pdb=" N GLN C1135 " --> pdb=" O SER C1151 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N VAL C1149 " --> pdb=" O LEU C1137 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N VAL C1139 " --> pdb=" O THR C1147 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N THR C1147 " --> pdb=" O VAL C1139 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'C' and resid 1157 through 1160 removed outlier: 6.720A pdb=" N GLU C1176 " --> pdb=" O ARG C1158 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'D' and resid 564 through 566 Processing sheet with id= AA, first strand: chain 'D' and resid 768 through 772 removed outlier: 6.561A pdb=" N LEU D 738 " --> pdb=" O HIS D 769 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N HIS D 771 " --> pdb=" O LEU D 738 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ILE D 740 " --> pdb=" O HIS D 771 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N MET D 604 " --> pdb=" O GLN D 640 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N LEU D 642 " --> pdb=" O MET D 604 " (cutoff:3.500A) removed outlier: 8.516A pdb=" N ASN D 606 " --> pdb=" O LEU D 642 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'D' and resid 1047 through 1050 removed outlier: 6.676A pdb=" N PHE D1077 " --> pdb=" O LEU D1063 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'D' and resid 1129 through 1131 removed outlier: 3.717A pdb=" N ALA D1129 " --> pdb=" O VAL D1157 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'D' and resid 1111 through 1113 removed outlier: 4.089A pdb=" N LEU D1175 " --> pdb=" O ILE D1112 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'D' and resid 1119 through 1123 removed outlier: 7.043A pdb=" N VAL D1139 " --> pdb=" O ILE D1121 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N ILE D1123 " --> pdb=" O LEU D1137 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N LEU D1137 " --> pdb=" O ILE D1123 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N VAL D1149 " --> pdb=" O LEU D1137 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N VAL D1139 " --> pdb=" O THR D1147 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N THR D1147 " --> pdb=" O VAL D1139 " (cutoff:3.500A) 995 hydrogen bonds defined for protein. 2859 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.40 Time building geometry restraints manager: 12.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 4816 1.31 - 1.43: 7257 1.43 - 1.56: 16642 1.56 - 1.69: 31 1.69 - 1.82: 298 Bond restraints: 29044 Sorted by residual: bond pdb=" C6 BTI C1900 " pdb=" S1 BTI C1900 " ideal model delta sigma weight residual 1.811 1.441 0.370 2.00e-02 2.50e+03 3.43e+02 bond pdb=" C6 BTI B2002 " pdb=" S1 BTI B2002 " ideal model delta sigma weight residual 1.811 1.443 0.368 2.00e-02 2.50e+03 3.39e+02 bond pdb=" C6 BTI A1201 " pdb=" S1 BTI A1201 " ideal model delta sigma weight residual 1.811 1.443 0.368 2.00e-02 2.50e+03 3.38e+02 bond pdb=" C6 BTI D1900 " pdb=" S1 BTI D1900 " ideal model delta sigma weight residual 1.811 1.444 0.367 2.00e-02 2.50e+03 3.37e+02 bond pdb=" C3 BTI A1201 " pdb=" N3 BTI A1201 " ideal model delta sigma weight residual 1.356 1.577 -0.221 2.00e-02 2.50e+03 1.22e+02 ... (remaining 29039 not shown) Histogram of bond angle deviations from ideal: 86.62 - 96.65: 2 96.65 - 106.69: 1157 106.69 - 116.72: 19254 116.72 - 126.75: 18596 126.75 - 136.79: 366 Bond angle restraints: 39375 Sorted by residual: angle pdb=" N PRO C 536 " pdb=" CD PRO C 536 " pdb=" CG PRO C 536 " ideal model delta sigma weight residual 103.20 86.62 16.58 1.50e+00 4.44e-01 1.22e+02 angle pdb=" CA PRO C 536 " pdb=" N PRO C 536 " pdb=" CD PRO C 536 " ideal model delta sigma weight residual 112.00 102.32 9.68 1.40e+00 5.10e-01 4.78e+01 angle pdb=" CA PRO C 536 " pdb=" CB PRO C 536 " pdb=" CG PRO C 536 " ideal model delta sigma weight residual 104.50 92.39 12.11 1.90e+00 2.77e-01 4.07e+01 angle pdb=" C LEU B 260 " pdb=" N TYR B 261 " pdb=" CA TYR B 261 " ideal model delta sigma weight residual 121.54 132.72 -11.18 1.91e+00 2.74e-01 3.42e+01 angle pdb=" N VAL D1065 " pdb=" CA VAL D1065 " pdb=" C VAL D1065 " ideal model delta sigma weight residual 112.90 107.47 5.43 9.60e-01 1.09e+00 3.21e+01 ... (remaining 39370 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 15968 17.79 - 35.58: 1446 35.58 - 53.37: 204 53.37 - 71.16: 45 71.16 - 88.95: 28 Dihedral angle restraints: 17691 sinusoidal: 7194 harmonic: 10497 Sorted by residual: dihedral pdb=" CB CYS B 752 " pdb=" SG CYS B 752 " pdb=" SG CYS B 786 " pdb=" CB CYS B 786 " ideal model delta sinusoidal sigma weight residual -86.00 -174.83 88.83 1 1.00e+01 1.00e-02 9.40e+01 dihedral pdb=" CB CYS C 752 " pdb=" SG CYS C 752 " pdb=" SG CYS C 786 " pdb=" CB CYS C 786 " ideal model delta sinusoidal sigma weight residual 93.00 177.92 -84.92 1 1.00e+01 1.00e-02 8.75e+01 dihedral pdb=" CB CYS D 752 " pdb=" SG CYS D 752 " pdb=" SG CYS D 786 " pdb=" CB CYS D 786 " ideal model delta sinusoidal sigma weight residual 93.00 173.77 -80.77 1 1.00e+01 1.00e-02 8.06e+01 ... (remaining 17688 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 3472 0.055 - 0.110: 780 0.110 - 0.165: 107 0.165 - 0.220: 14 0.220 - 0.275: 5 Chirality restraints: 4378 Sorted by residual: chirality pdb=" CB THR B 908 " pdb=" CA THR B 908 " pdb=" OG1 THR B 908 " pdb=" CG2 THR B 908 " both_signs ideal model delta sigma weight residual False 2.55 2.28 0.27 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" C5 BTI B2002 " pdb=" C4 BTI B2002 " pdb=" C6 BTI B2002 " pdb=" N3 BTI B2002 " both_signs ideal model delta sigma weight residual False 2.73 2.99 -0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" CA THR B 908 " pdb=" N THR B 908 " pdb=" C THR B 908 " pdb=" CB THR B 908 " both_signs ideal model delta sigma weight residual False 2.53 2.27 0.26 2.00e-01 2.50e+01 1.67e+00 ... (remaining 4375 not shown) Planarity restraints: 5171 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY C 535 " -0.059 5.00e-02 4.00e+02 8.32e-02 1.11e+01 pdb=" N PRO C 536 " 0.144 5.00e-02 4.00e+02 pdb=" CA PRO C 536 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO C 536 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 542 " -0.185 9.50e-02 1.11e+02 8.33e-02 4.93e+00 pdb=" NE ARG A 542 " 0.016 2.00e-02 2.50e+03 pdb=" CZ ARG A 542 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG A 542 " 0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG A 542 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 947 " -0.014 2.00e-02 2.50e+03 1.63e-02 4.66e+00 pdb=" CG PHE A 947 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 PHE A 947 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 PHE A 947 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE A 947 " 0.018 2.00e-02 2.50e+03 pdb=" CE2 PHE A 947 " -0.005 2.00e-02 2.50e+03 pdb=" CZ PHE A 947 " -0.015 2.00e-02 2.50e+03 ... (remaining 5168 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 569 2.63 - 3.20: 27577 3.20 - 3.76: 46981 3.76 - 4.33: 61851 4.33 - 4.90: 97557 Nonbonded interactions: 234535 Sorted by model distance: nonbonded pdb=" NH1 ARG A 542 " pdb=" O ILE A 634 " model vdw 2.060 2.520 nonbonded pdb=" OD2 ASP B 586 " pdb=" OH TYR B 845 " model vdw 2.070 2.440 nonbonded pdb=" OD2 ASP B 343 " pdb=" ND1 HIS B 346 " model vdw 2.102 2.520 nonbonded pdb=" O ALA C1132 " pdb=" OG SER C1151 " model vdw 2.109 2.440 nonbonded pdb=" O SER D 523 " pdb=" NH1 ARG D1036 " model vdw 2.117 2.520 ... (remaining 234530 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 33 through 1178) selection = (chain 'B' and resid 33 through 1178) } ncs_group { reference = chain 'C' selection = chain 'D' } 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: 0.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 6.440 Check model and map are aligned: 0.430 Set scattering table: 0.260 Process input model: 73.190 Find NCS groups from input model: 1.600 Set up NCS constraints: 0.140 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:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 86.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6506 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 0.370 29044 Z= 0.520 Angle : 0.823 16.581 39375 Z= 0.441 Chirality : 0.048 0.275 4378 Planarity : 0.006 0.083 5171 Dihedral : 13.845 88.949 10941 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 22.27 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.97 % Favored : 91.95 % Rotamer: Outliers : 0.10 % Allowed : 0.60 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -0.78 (0.14), residues: 3653 helix: 0.61 (0.14), residues: 1415 sheet: -0.08 (0.23), residues: 511 loop : -1.63 (0.14), residues: 1727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP B 624 HIS 0.012 0.002 HIS C1019 PHE 0.031 0.002 PHE B 848 TYR 0.021 0.002 TYR D 723 ARG 0.015 0.001 ARG A 542 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 3013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 276 time to evaluate : 3.206 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: B 801 MET cc_start: 0.6900 (mmt) cc_final: 0.6430 (mmt) REVERT: C 671 MET cc_start: 0.5308 (tpt) cc_final: 0.4893 (tpt) REVERT: C 686 MET cc_start: 0.4577 (tpp) cc_final: 0.3845 (tpp) REVERT: C 854 MET cc_start: 0.8561 (tpt) cc_final: 0.8236 (tpp) REVERT: C 894 TYR cc_start: 0.8083 (t80) cc_final: 0.7726 (t80) REVERT: D 555 ARG cc_start: 0.7703 (tpm170) cc_final: 0.7313 (tmm160) REVERT: D 754 MET cc_start: 0.6247 (ppp) cc_final: 0.5330 (ppp) REVERT: D 1095 MET cc_start: 0.2386 (ppp) cc_final: 0.2155 (ppp) outliers start: 3 outliers final: 1 residues processed: 278 average time/residue: 0.4172 time to fit residues: 182.6798 Evaluate side-chains 218 residues out of total 3013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 217 time to evaluate : 3.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1144 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 307 optimal weight: 7.9990 chunk 275 optimal weight: 8.9990 chunk 153 optimal weight: 20.0000 chunk 94 optimal weight: 0.0970 chunk 186 optimal weight: 9.9990 chunk 147 optimal weight: 2.9990 chunk 285 optimal weight: 4.9990 chunk 110 optimal weight: 5.9990 chunk 173 optimal weight: 7.9990 chunk 212 optimal weight: 5.9990 chunk 330 optimal weight: 6.9990 overall best weight: 4.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 256 ASN A 436 HIS A 479 GLN ** A 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 350 HIS ** B 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 510 ASN ** B 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 769 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 807 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 898 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 899 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1040 GLN ** C 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 681 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1075 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6586 moved from start: 0.1140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 29044 Z= 0.271 Angle : 0.685 10.501 39375 Z= 0.351 Chirality : 0.045 0.264 4378 Planarity : 0.005 0.062 5171 Dihedral : 6.770 59.189 4145 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 23.05 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.36 % Favored : 92.55 % Rotamer: Outliers : 0.83 % Allowed : 9.82 % Favored : 89.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.14), residues: 3653 helix: 0.51 (0.13), residues: 1429 sheet: -0.18 (0.23), residues: 497 loop : -1.67 (0.14), residues: 1727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP D 838 HIS 0.008 0.002 HIS C 574 PHE 0.026 0.002 PHE A 876 TYR 0.017 0.002 TYR D 723 ARG 0.011 0.001 ARG A 542 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 3013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 227 time to evaluate : 3.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 PHE cc_start: 0.8439 (m-10) cc_final: 0.8181 (m-10) REVERT: A 604 MET cc_start: 0.7534 (ptm) cc_final: 0.6888 (tmm) REVERT: A 900 MET cc_start: 0.7772 (mpp) cc_final: 0.7520 (mpp) REVERT: A 1095 MET cc_start: 0.6006 (mpp) cc_final: 0.5777 (mpp) REVERT: B 690 MET cc_start: 0.7702 (mmt) cc_final: 0.7485 (tpt) REVERT: B 801 MET cc_start: 0.6890 (mmt) cc_final: 0.6329 (mmt) REVERT: B 1040 GLN cc_start: 0.7635 (OUTLIER) cc_final: 0.7247 (pp30) REVERT: B 1166 MET cc_start: 0.2589 (ptt) cc_final: 0.2241 (ptt) REVERT: C 508 MET cc_start: 0.7390 (mtt) cc_final: 0.7155 (mtt) REVERT: C 671 MET cc_start: 0.5166 (tpt) cc_final: 0.4846 (tpt) REVERT: C 804 MET cc_start: 0.9047 (tpp) cc_final: 0.8740 (tpp) REVERT: C 854 MET cc_start: 0.8556 (tpt) cc_final: 0.8203 (tpp) REVERT: C 855 LYS cc_start: 0.8560 (tmmt) cc_final: 0.8164 (mtmm) REVERT: C 1166 MET cc_start: 0.0406 (ptt) cc_final: 0.0160 (ptt) REVERT: D 555 ARG cc_start: 0.7772 (tpm170) cc_final: 0.7146 (tmm160) outliers start: 25 outliers final: 17 residues processed: 241 average time/residue: 0.3975 time to fit residues: 154.8896 Evaluate side-chains 223 residues out of total 3013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 205 time to evaluate : 3.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 1012 MET Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 993 GLU Chi-restraints excluded: chain B residue 1016 VAL Chi-restraints excluded: chain B residue 1040 GLN Chi-restraints excluded: chain B residue 1067 ASP Chi-restraints excluded: chain C residue 574 HIS Chi-restraints excluded: chain C residue 986 ASP Chi-restraints excluded: chain C residue 1078 PHE Chi-restraints excluded: chain D residue 585 HIS Chi-restraints excluded: chain D residue 826 VAL Chi-restraints excluded: chain D residue 1076 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 183 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 275 optimal weight: 6.9990 chunk 225 optimal weight: 8.9990 chunk 91 optimal weight: 7.9990 chunk 331 optimal weight: 10.0000 chunk 357 optimal weight: 0.0060 chunk 294 optimal weight: 7.9990 chunk 328 optimal weight: 10.0000 chunk 112 optimal weight: 8.9990 chunk 265 optimal weight: 5.9990 overall best weight: 3.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN ** A 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 898 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 899 GLN A 923 GLN ** A1081 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 109 ASN B 208 HIS ** B 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 769 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 807 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 898 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 899 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 681 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1075 GLN ** C1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1093 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6622 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 29044 Z= 0.245 Angle : 0.653 10.926 39375 Z= 0.333 Chirality : 0.044 0.201 4378 Planarity : 0.005 0.043 5171 Dihedral : 6.648 59.656 4141 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 22.52 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.66 % Favored : 92.28 % Rotamer: Outliers : 1.96 % Allowed : 12.94 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -0.90 (0.14), residues: 3653 helix: 0.51 (0.13), residues: 1436 sheet: -0.24 (0.24), residues: 481 loop : -1.68 (0.14), residues: 1736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 838 HIS 0.007 0.001 HIS B 208 PHE 0.042 0.002 PHE C 662 TYR 0.015 0.002 TYR D 503 ARG 0.010 0.001 ARG A 542 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 3013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 223 time to evaluate : 3.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 PHE cc_start: 0.8432 (m-10) cc_final: 0.8141 (m-10) REVERT: A 616 MET cc_start: 0.8211 (tpp) cc_final: 0.7895 (tpp) REVERT: A 900 MET cc_start: 0.7783 (mpp) cc_final: 0.6995 (mpp) REVERT: A 1093 GLN cc_start: 0.8442 (pp30) cc_final: 0.7865 (pp30) REVERT: A 1095 MET cc_start: 0.5944 (mpp) cc_final: 0.5626 (mpp) REVERT: B 261 TYR cc_start: 0.5997 (OUTLIER) cc_final: 0.5411 (m-10) REVERT: B 277 ILE cc_start: 0.3732 (OUTLIER) cc_final: 0.3297 (tt) REVERT: B 690 MET cc_start: 0.7779 (mmt) cc_final: 0.7568 (tpt) REVERT: B 968 LEU cc_start: 0.6989 (OUTLIER) cc_final: 0.6537 (tt) REVERT: B 1058 LEU cc_start: 0.8088 (OUTLIER) cc_final: 0.7882 (pp) REVERT: C 508 MET cc_start: 0.7333 (mtt) cc_final: 0.7027 (mtt) REVERT: C 671 MET cc_start: 0.5119 (tpt) cc_final: 0.4744 (tpt) REVERT: C 854 MET cc_start: 0.8616 (tpt) cc_final: 0.8273 (tpp) REVERT: C 855 LYS cc_start: 0.8572 (tmmt) cc_final: 0.8284 (mtmm) REVERT: C 1166 MET cc_start: 0.0477 (ptt) cc_final: 0.0220 (ptt) REVERT: D 555 ARG cc_start: 0.7832 (tpm170) cc_final: 0.7019 (tmm160) REVERT: D 647 ASN cc_start: 0.7826 (OUTLIER) cc_final: 0.6884 (p0) REVERT: D 754 MET cc_start: 0.6136 (ppp) cc_final: 0.4865 (ppp) outliers start: 59 outliers final: 35 residues processed: 265 average time/residue: 0.3756 time to fit residues: 162.0924 Evaluate side-chains 247 residues out of total 3013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 207 time to evaluate : 3.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 876 PHE Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain A residue 1012 MET Chi-restraints excluded: chain A residue 1043 LYS Chi-restraints excluded: chain A residue 1137 LEU Chi-restraints excluded: chain B residue 208 HIS Chi-restraints excluded: chain B residue 261 TYR Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain B residue 435 ASP Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 738 LEU Chi-restraints excluded: chain B residue 968 LEU Chi-restraints excluded: chain B residue 993 GLU Chi-restraints excluded: chain B residue 1016 VAL Chi-restraints excluded: chain B residue 1037 LEU Chi-restraints excluded: chain B residue 1058 LEU Chi-restraints excluded: chain B residue 1067 ASP Chi-restraints excluded: chain B residue 1123 ILE Chi-restraints excluded: chain C residue 752 CYS Chi-restraints excluded: chain C residue 986 ASP Chi-restraints excluded: chain C residue 1078 PHE Chi-restraints excluded: chain C residue 1088 LEU Chi-restraints excluded: chain C residue 1137 LEU Chi-restraints excluded: chain C residue 1172 ASP Chi-restraints excluded: chain D residue 528 VAL Chi-restraints excluded: chain D residue 585 HIS Chi-restraints excluded: chain D residue 647 ASN Chi-restraints excluded: chain D residue 752 CYS Chi-restraints excluded: chain D residue 826 VAL Chi-restraints excluded: chain D residue 874 LEU Chi-restraints excluded: chain D residue 1007 VAL Chi-restraints excluded: chain D residue 1076 VAL Chi-restraints excluded: chain D residue 1120 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 327 optimal weight: 3.9990 chunk 248 optimal weight: 1.9990 chunk 171 optimal weight: 10.0000 chunk 36 optimal weight: 2.9990 chunk 158 optimal weight: 0.0870 chunk 222 optimal weight: 20.0000 chunk 332 optimal weight: 0.0270 chunk 351 optimal weight: 6.9990 chunk 173 optimal weight: 0.9990 chunk 314 optimal weight: 0.9990 chunk 94 optimal weight: 0.0870 overall best weight: 0.4398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 771 HIS A 898 ASN ** B 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 669 ASN B 681 ASN ** B 769 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 807 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 899 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1040 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 681 ASN ** C1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 498 GLN ** D 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6523 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 29044 Z= 0.165 Angle : 0.598 9.566 39375 Z= 0.296 Chirality : 0.042 0.215 4378 Planarity : 0.004 0.040 5171 Dihedral : 6.309 59.999 4141 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 16.51 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.57 % Favored : 93.40 % Rotamer: Outliers : 1.76 % Allowed : 14.97 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -0.58 (0.14), residues: 3653 helix: 0.86 (0.14), residues: 1425 sheet: -0.03 (0.23), residues: 494 loop : -1.58 (0.14), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 607 HIS 0.004 0.001 HIS B 208 PHE 0.018 0.001 PHE D 920 TYR 0.015 0.001 TYR D 503 ARG 0.007 0.000 ARG A 542 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 3013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 222 time to evaluate : 3.286 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: A 604 MET cc_start: 0.7475 (ptm) cc_final: 0.6716 (tmm) REVERT: B 105 VAL cc_start: 0.9329 (m) cc_final: 0.8835 (p) REVERT: B 108 GLU cc_start: 0.8431 (pt0) cc_final: 0.8196 (pp20) REVERT: B 261 TYR cc_start: 0.5736 (OUTLIER) cc_final: 0.5306 (m-10) REVERT: B 277 ILE cc_start: 0.3571 (OUTLIER) cc_final: 0.3203 (tt) REVERT: B 690 MET cc_start: 0.7755 (mmt) cc_final: 0.7545 (tpt) REVERT: B 801 MET cc_start: 0.6862 (mmt) cc_final: 0.6316 (mmt) REVERT: B 1166 MET cc_start: 0.2691 (ptt) cc_final: 0.2330 (ptt) REVERT: C 671 MET cc_start: 0.4888 (tpt) cc_final: 0.4570 (tpt) REVERT: C 854 MET cc_start: 0.8629 (tpt) cc_final: 0.8221 (tpp) REVERT: C 855 LYS cc_start: 0.8482 (tmmt) cc_final: 0.8162 (mtmm) REVERT: C 881 MET cc_start: 0.8623 (mmm) cc_final: 0.8117 (mmm) REVERT: C 910 SER cc_start: 0.7337 (OUTLIER) cc_final: 0.6919 (p) REVERT: C 1166 MET cc_start: 0.0302 (ptt) cc_final: 0.0026 (ptt) REVERT: D 555 ARG cc_start: 0.7669 (tpm170) cc_final: 0.6847 (tmm160) REVERT: D 754 MET cc_start: 0.6249 (ppp) cc_final: 0.5122 (ppp) outliers start: 53 outliers final: 33 residues processed: 261 average time/residue: 0.4076 time to fit residues: 172.4322 Evaluate side-chains 242 residues out of total 3013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 206 time to evaluate : 3.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 317 HIS Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 862 TYR Chi-restraints excluded: chain A residue 876 PHE Chi-restraints excluded: chain A residue 1137 LEU Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 261 TYR Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain B residue 435 ASP Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 738 LEU Chi-restraints excluded: chain B residue 752 CYS Chi-restraints excluded: chain B residue 910 SER Chi-restraints excluded: chain B residue 993 GLU Chi-restraints excluded: chain C residue 752 CYS Chi-restraints excluded: chain C residue 910 SER Chi-restraints excluded: chain C residue 986 ASP Chi-restraints excluded: chain C residue 1016 VAL Chi-restraints excluded: chain C residue 1103 LYS Chi-restraints excluded: chain C residue 1137 LEU Chi-restraints excluded: chain C residue 1172 ASP Chi-restraints excluded: chain D residue 528 VAL Chi-restraints excluded: chain D residue 585 HIS Chi-restraints excluded: chain D residue 752 CYS Chi-restraints excluded: chain D residue 879 HIS Chi-restraints excluded: chain D residue 920 PHE Chi-restraints excluded: chain D residue 1033 LEU Chi-restraints excluded: chain D residue 1076 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 293 optimal weight: 9.9990 chunk 199 optimal weight: 0.7980 chunk 5 optimal weight: 8.9990 chunk 261 optimal weight: 5.9990 chunk 145 optimal weight: 3.9990 chunk 300 optimal weight: 10.0000 chunk 243 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 179 optimal weight: 10.0000 chunk 315 optimal weight: 0.9990 chunk 88 optimal weight: 9.9990 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 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 GLN A 432 HIS ** A 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 653 ASN ** A1081 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 208 HIS ** B 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 421 HIS ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 769 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 807 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 898 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 899 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1040 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 773 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6648 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 29044 Z= 0.256 Angle : 0.659 10.602 39375 Z= 0.332 Chirality : 0.044 0.223 4378 Planarity : 0.005 0.040 5171 Dihedral : 6.458 59.921 4141 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 23.91 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.21 % Favored : 91.76 % Rotamer: Outliers : 2.82 % Allowed : 15.96 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.14), residues: 3653 helix: 0.64 (0.14), residues: 1442 sheet: -0.23 (0.23), residues: 502 loop : -1.68 (0.15), residues: 1709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 838 HIS 0.007 0.001 HIS B 875 PHE 0.021 0.002 PHE A 876 TYR 0.024 0.002 TYR B 503 ARG 0.010 0.001 ARG A 385 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 3013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 215 time to evaluate : 3.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 PHE cc_start: 0.8551 (m-10) cc_final: 0.8286 (m-10) REVERT: A 283 LEU cc_start: 0.5620 (OUTLIER) cc_final: 0.5227 (tp) REVERT: A 900 MET cc_start: 0.8100 (mpp) cc_final: 0.7264 (mpp) REVERT: B 108 GLU cc_start: 0.8768 (pt0) cc_final: 0.8388 (pp20) REVERT: B 261 TYR cc_start: 0.5918 (OUTLIER) cc_final: 0.5464 (m-10) REVERT: B 277 ILE cc_start: 0.3591 (OUTLIER) cc_final: 0.3131 (tt) REVERT: B 475 THR cc_start: 0.3685 (OUTLIER) cc_final: 0.3297 (t) REVERT: B 801 MET cc_start: 0.6887 (mmt) cc_final: 0.6256 (mmt) REVERT: C 671 MET cc_start: 0.5078 (tpt) cc_final: 0.4628 (tpt) REVERT: C 804 MET cc_start: 0.9173 (tpp) cc_final: 0.8786 (mmt) REVERT: C 854 MET cc_start: 0.8725 (tpt) cc_final: 0.8155 (tpt) REVERT: C 855 LYS cc_start: 0.8607 (tmmt) cc_final: 0.8340 (mtmm) REVERT: C 910 SER cc_start: 0.7456 (OUTLIER) cc_final: 0.7145 (p) REVERT: D 647 ASN cc_start: 0.7873 (OUTLIER) cc_final: 0.6839 (p0) REVERT: D 754 MET cc_start: 0.6202 (ppp) cc_final: 0.5099 (ppp) outliers start: 85 outliers final: 51 residues processed: 280 average time/residue: 0.4300 time to fit residues: 197.8925 Evaluate side-chains 263 residues out of total 3013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 206 time to evaluate : 3.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 317 HIS Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 876 PHE Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain A residue 1012 MET Chi-restraints excluded: chain A residue 1043 LYS Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 261 TYR Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 370 ASN Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain B residue 435 ASP Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 752 CYS Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 910 SER Chi-restraints excluded: chain B residue 1016 VAL Chi-restraints excluded: chain B residue 1037 LEU Chi-restraints excluded: chain B residue 1067 ASP Chi-restraints excluded: chain B residue 1123 ILE Chi-restraints excluded: chain B residue 1139 VAL Chi-restraints excluded: chain C residue 555 ARG Chi-restraints excluded: chain C residue 752 CYS Chi-restraints excluded: chain C residue 848 PHE Chi-restraints excluded: chain C residue 910 SER Chi-restraints excluded: chain C residue 947 PHE Chi-restraints excluded: chain C residue 986 ASP Chi-restraints excluded: chain C residue 1016 VAL Chi-restraints excluded: chain C residue 1050 VAL Chi-restraints excluded: chain C residue 1078 PHE Chi-restraints excluded: chain C residue 1103 LYS Chi-restraints excluded: chain C residue 1137 LEU Chi-restraints excluded: chain C residue 1172 ASP Chi-restraints excluded: chain D residue 528 VAL Chi-restraints excluded: chain D residue 585 HIS Chi-restraints excluded: chain D residue 647 ASN Chi-restraints excluded: chain D residue 752 CYS Chi-restraints excluded: chain D residue 826 VAL Chi-restraints excluded: chain D residue 874 LEU Chi-restraints excluded: chain D residue 879 HIS Chi-restraints excluded: chain D residue 890 VAL Chi-restraints excluded: chain D residue 920 PHE Chi-restraints excluded: chain D residue 1033 LEU Chi-restraints excluded: chain D residue 1067 ASP Chi-restraints excluded: chain D residue 1076 VAL Chi-restraints excluded: chain D residue 1120 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 118 optimal weight: 0.9980 chunk 316 optimal weight: 3.9990 chunk 69 optimal weight: 6.9990 chunk 206 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 352 optimal weight: 5.9990 chunk 292 optimal weight: 0.9990 chunk 163 optimal weight: 6.9990 chunk 29 optimal weight: 9.9990 chunk 116 optimal weight: 10.0000 chunk 184 optimal weight: 10.0000 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 330 GLN A 494 GLN ** A1081 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 669 ASN ** B 769 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 807 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 899 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1040 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6637 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 29044 Z= 0.208 Angle : 0.637 10.094 39375 Z= 0.317 Chirality : 0.043 0.216 4378 Planarity : 0.004 0.052 5171 Dihedral : 6.489 59.410 4141 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 21.21 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.50 % Favored : 92.47 % Rotamer: Outliers : 2.95 % Allowed : 17.19 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -0.79 (0.14), residues: 3653 helix: 0.66 (0.14), residues: 1440 sheet: -0.20 (0.24), residues: 483 loop : -1.67 (0.14), residues: 1730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 838 HIS 0.006 0.001 HIS A 76 PHE 0.018 0.002 PHE D 920 TYR 0.014 0.001 TYR D 503 ARG 0.007 0.001 ARG D 555 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 3013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 216 time to evaluate : 3.530 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: A 283 LEU cc_start: 0.5618 (OUTLIER) cc_final: 0.5283 (tp) REVERT: A 900 MET cc_start: 0.8130 (mpp) cc_final: 0.7214 (mpp) REVERT: A 1093 GLN cc_start: 0.8286 (pp30) cc_final: 0.8031 (pp30) REVERT: B 108 GLU cc_start: 0.8672 (pt0) cc_final: 0.8416 (pp20) REVERT: B 261 TYR cc_start: 0.5885 (OUTLIER) cc_final: 0.5414 (m-10) REVERT: B 277 ILE cc_start: 0.3561 (OUTLIER) cc_final: 0.3111 (tt) REVERT: B 585 HIS cc_start: 0.8346 (OUTLIER) cc_final: 0.8062 (t70) REVERT: B 801 MET cc_start: 0.6905 (mmt) cc_final: 0.6324 (mmt) REVERT: B 1166 MET cc_start: 0.2889 (ptt) cc_final: 0.2676 (ptt) REVERT: C 641 MET cc_start: 0.8706 (tmm) cc_final: 0.8481 (tmm) REVERT: C 671 MET cc_start: 0.5324 (tpt) cc_final: 0.4914 (tpt) REVERT: C 686 MET cc_start: 0.5458 (tpp) cc_final: 0.5219 (tpp) REVERT: C 804 MET cc_start: 0.9219 (tpp) cc_final: 0.8842 (mmt) REVERT: C 810 MET cc_start: 0.8486 (mmt) cc_final: 0.8282 (mmm) REVERT: C 854 MET cc_start: 0.8701 (tpt) cc_final: 0.8126 (tpp) REVERT: C 910 SER cc_start: 0.7338 (OUTLIER) cc_final: 0.7019 (p) REVERT: D 555 ARG cc_start: 0.8335 (tpp-160) cc_final: 0.8050 (tpm170) REVERT: D 647 ASN cc_start: 0.7788 (OUTLIER) cc_final: 0.6826 (p0) REVERT: D 754 MET cc_start: 0.6153 (ppp) cc_final: 0.5105 (ppp) outliers start: 89 outliers final: 55 residues processed: 279 average time/residue: 0.3842 time to fit residues: 174.9518 Evaluate side-chains 263 residues out of total 3013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 202 time to evaluate : 3.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 317 HIS Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 494 GLN Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 862 TYR Chi-restraints excluded: chain A residue 876 PHE Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain A residue 1012 MET Chi-restraints excluded: chain A residue 1137 LEU Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 261 TYR Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 370 ASN Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain B residue 432 HIS Chi-restraints excluded: chain B residue 435 ASP Chi-restraints excluded: chain B residue 470 GLN Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 574 HIS Chi-restraints excluded: chain B residue 585 HIS Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 752 CYS Chi-restraints excluded: chain B residue 906 LYS Chi-restraints excluded: chain B residue 910 SER Chi-restraints excluded: chain B residue 1016 VAL Chi-restraints excluded: chain B residue 1067 ASP Chi-restraints excluded: chain B residue 1088 LEU Chi-restraints excluded: chain B residue 1139 VAL Chi-restraints excluded: chain C residue 555 ARG Chi-restraints excluded: chain C residue 752 CYS Chi-restraints excluded: chain C residue 848 PHE Chi-restraints excluded: chain C residue 910 SER Chi-restraints excluded: chain C residue 986 ASP Chi-restraints excluded: chain C residue 1016 VAL Chi-restraints excluded: chain C residue 1050 VAL Chi-restraints excluded: chain C residue 1078 PHE Chi-restraints excluded: chain C residue 1103 LYS Chi-restraints excluded: chain C residue 1137 LEU Chi-restraints excluded: chain D residue 528 VAL Chi-restraints excluded: chain D residue 584 THR Chi-restraints excluded: chain D residue 585 HIS Chi-restraints excluded: chain D residue 647 ASN Chi-restraints excluded: chain D residue 752 CYS Chi-restraints excluded: chain D residue 874 LEU Chi-restraints excluded: chain D residue 879 HIS Chi-restraints excluded: chain D residue 890 VAL Chi-restraints excluded: chain D residue 903 ASP Chi-restraints excluded: chain D residue 920 PHE Chi-restraints excluded: chain D residue 1033 LEU Chi-restraints excluded: chain D residue 1067 ASP Chi-restraints excluded: chain D residue 1076 VAL Chi-restraints excluded: chain D residue 1120 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 339 optimal weight: 8.9990 chunk 39 optimal weight: 9.9990 chunk 200 optimal weight: 20.0000 chunk 257 optimal weight: 9.9990 chunk 199 optimal weight: 3.9990 chunk 296 optimal weight: 9.9990 chunk 196 optimal weight: 5.9990 chunk 350 optimal weight: 8.9990 chunk 219 optimal weight: 5.9990 chunk 213 optimal weight: 0.9980 chunk 161 optimal weight: 2.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1075 GLN ** A1081 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 248 GLN ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 769 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 807 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1040 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6699 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 29044 Z= 0.267 Angle : 0.689 10.716 39375 Z= 0.347 Chirality : 0.045 0.214 4378 Planarity : 0.005 0.042 5171 Dihedral : 6.599 59.597 4141 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 25.23 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.87 % Favored : 91.10 % Rotamer: Outliers : 2.85 % Allowed : 18.25 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -1.08 (0.14), residues: 3653 helix: 0.38 (0.13), residues: 1455 sheet: -0.52 (0.23), residues: 508 loop : -1.77 (0.15), residues: 1690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 838 HIS 0.008 0.001 HIS B 875 PHE 0.017 0.002 PHE D 920 TYR 0.016 0.002 TYR B 503 ARG 0.009 0.001 ARG A 542 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 3013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 218 time to evaluate : 3.322 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: A 283 LEU cc_start: 0.5612 (OUTLIER) cc_final: 0.5329 (tp) REVERT: A 616 MET cc_start: 0.8041 (tpp) cc_final: 0.7704 (tpp) REVERT: A 900 MET cc_start: 0.8066 (mpp) cc_final: 0.7198 (mpp) REVERT: A 1083 GLN cc_start: 0.6296 (OUTLIER) cc_final: 0.5733 (mm-40) REVERT: A 1143 MET cc_start: 0.2150 (ptm) cc_final: 0.1909 (ptt) REVERT: B 108 GLU cc_start: 0.8876 (pt0) cc_final: 0.8503 (pp20) REVERT: B 261 TYR cc_start: 0.5926 (OUTLIER) cc_final: 0.5438 (m-10) REVERT: B 277 ILE cc_start: 0.3410 (OUTLIER) cc_final: 0.2848 (tt) REVERT: B 585 HIS cc_start: 0.8412 (OUTLIER) cc_final: 0.8188 (t70) REVERT: B 891 LYS cc_start: 0.7242 (tptp) cc_final: 0.6633 (tttt) REVERT: B 939 SER cc_start: 0.7662 (p) cc_final: 0.7222 (t) REVERT: C 671 MET cc_start: 0.5386 (tpt) cc_final: 0.4998 (tpt) REVERT: C 686 MET cc_start: 0.5684 (tpp) cc_final: 0.5412 (tpp) REVERT: C 804 MET cc_start: 0.9186 (tpp) cc_final: 0.8852 (mmt) REVERT: C 854 MET cc_start: 0.8720 (tpt) cc_final: 0.8157 (tpt) REVERT: C 910 SER cc_start: 0.7457 (OUTLIER) cc_final: 0.7155 (p) REVERT: C 988 GLN cc_start: 0.8488 (tp40) cc_final: 0.8104 (mp10) REVERT: D 555 ARG cc_start: 0.8402 (tpp-160) cc_final: 0.8169 (tpm170) REVERT: D 647 ASN cc_start: 0.7905 (OUTLIER) cc_final: 0.6966 (p0) REVERT: D 754 MET cc_start: 0.5937 (ppp) cc_final: 0.4931 (ppp) REVERT: D 801 MET cc_start: 0.7831 (mpp) cc_final: 0.7613 (mpp) outliers start: 86 outliers final: 64 residues processed: 283 average time/residue: 0.4007 time to fit residues: 184.4201 Evaluate side-chains 284 residues out of total 3013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 213 time to evaluate : 3.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 317 HIS Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 862 TYR Chi-restraints excluded: chain A residue 876 PHE Chi-restraints excluded: chain A residue 907 VAL Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain A residue 1012 MET Chi-restraints excluded: chain A residue 1043 LYS Chi-restraints excluded: chain A residue 1083 GLN Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 261 TYR Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 370 ASN Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain B residue 432 HIS Chi-restraints excluded: chain B residue 435 ASP Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 470 GLN Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 574 HIS Chi-restraints excluded: chain B residue 585 HIS Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 629 GLU Chi-restraints excluded: chain B residue 752 CYS Chi-restraints excluded: chain B residue 780 VAL Chi-restraints excluded: chain B residue 906 LYS Chi-restraints excluded: chain B residue 910 SER Chi-restraints excluded: chain B residue 1016 VAL Chi-restraints excluded: chain B residue 1037 LEU Chi-restraints excluded: chain B residue 1067 ASP Chi-restraints excluded: chain B residue 1088 LEU Chi-restraints excluded: chain B residue 1139 VAL Chi-restraints excluded: chain C residue 555 ARG Chi-restraints excluded: chain C residue 752 CYS Chi-restraints excluded: chain C residue 783 MET Chi-restraints excluded: chain C residue 848 PHE Chi-restraints excluded: chain C residue 910 SER Chi-restraints excluded: chain C residue 947 PHE Chi-restraints excluded: chain C residue 986 ASP Chi-restraints excluded: chain C residue 1016 VAL Chi-restraints excluded: chain C residue 1050 VAL Chi-restraints excluded: chain C residue 1078 PHE Chi-restraints excluded: chain C residue 1088 LEU Chi-restraints excluded: chain C residue 1103 LYS Chi-restraints excluded: chain C residue 1137 LEU Chi-restraints excluded: chain D residue 528 VAL Chi-restraints excluded: chain D residue 585 HIS Chi-restraints excluded: chain D residue 647 ASN Chi-restraints excluded: chain D residue 752 CYS Chi-restraints excluded: chain D residue 826 VAL Chi-restraints excluded: chain D residue 874 LEU Chi-restraints excluded: chain D residue 879 HIS Chi-restraints excluded: chain D residue 890 VAL Chi-restraints excluded: chain D residue 903 ASP Chi-restraints excluded: chain D residue 920 PHE Chi-restraints excluded: chain D residue 1033 LEU Chi-restraints excluded: chain D residue 1067 ASP Chi-restraints excluded: chain D residue 1076 VAL Chi-restraints excluded: chain D residue 1095 MET Chi-restraints excluded: chain D residue 1120 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 217 optimal weight: 9.9990 chunk 140 optimal weight: 8.9990 chunk 209 optimal weight: 9.9990 chunk 105 optimal weight: 9.9990 chunk 68 optimal weight: 8.9990 chunk 67 optimal weight: 4.9990 chunk 223 optimal weight: 0.9980 chunk 239 optimal weight: 10.0000 chunk 173 optimal weight: 7.9990 chunk 32 optimal weight: 0.0470 chunk 275 optimal weight: 7.9990 overall best weight: 4.4084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 606 ASN ** A1081 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 178 HIS B 479 GLN ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 769 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 807 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 988 GLN ** B1040 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 597 ASN C1073 GLN ** C1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6748 moved from start: 0.3551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 29044 Z= 0.287 Angle : 0.728 13.901 39375 Z= 0.367 Chirality : 0.046 0.252 4378 Planarity : 0.005 0.051 5171 Dihedral : 6.738 59.507 4141 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 27.61 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.84 % Favored : 91.13 % Rotamer: Outliers : 3.39 % Allowed : 18.39 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.14), residues: 3653 helix: 0.13 (0.13), residues: 1458 sheet: -0.74 (0.23), residues: 501 loop : -1.86 (0.15), residues: 1694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 624 HIS 0.011 0.001 HIS B 875 PHE 0.043 0.002 PHE C 662 TYR 0.020 0.002 TYR B 834 ARG 0.031 0.001 ARG A 496 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 3013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 223 time to evaluate : 3.135 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 283 LEU cc_start: 0.5864 (OUTLIER) cc_final: 0.5508 (tp) REVERT: A 616 MET cc_start: 0.7993 (tpp) cc_final: 0.7446 (tpp) REVERT: A 871 TYR cc_start: 0.7275 (OUTLIER) cc_final: 0.6388 (t80) REVERT: A 1083 GLN cc_start: 0.6223 (OUTLIER) cc_final: 0.5627 (mm-40) REVERT: A 1143 MET cc_start: 0.2607 (ptm) cc_final: 0.2403 (ptt) REVERT: B 261 TYR cc_start: 0.5874 (OUTLIER) cc_final: 0.5490 (m-10) REVERT: B 634 ILE cc_start: 0.8258 (OUTLIER) cc_final: 0.8032 (mp) REVERT: B 783 MET cc_start: 0.8883 (tpp) cc_final: 0.8456 (tpp) REVERT: B 792 ASP cc_start: 0.4368 (OUTLIER) cc_final: 0.4049 (m-30) REVERT: B 891 LYS cc_start: 0.7246 (tptp) cc_final: 0.6619 (tttt) REVERT: B 949 GLN cc_start: 0.8972 (tt0) cc_final: 0.8659 (tm-30) REVERT: B 1166 MET cc_start: 0.3811 (ptt) cc_final: 0.3478 (ptt) REVERT: C 641 MET cc_start: 0.8810 (tmm) cc_final: 0.8565 (tmm) REVERT: C 671 MET cc_start: 0.5277 (tpt) cc_final: 0.4996 (tpt) REVERT: C 686 MET cc_start: 0.5676 (tpp) cc_final: 0.5408 (tpp) REVERT: C 804 MET cc_start: 0.9105 (tpp) cc_final: 0.8729 (mmt) REVERT: C 810 MET cc_start: 0.8565 (mmm) cc_final: 0.8308 (mmt) REVERT: C 854 MET cc_start: 0.8635 (tpt) cc_final: 0.7986 (tpt) REVERT: C 910 SER cc_start: 0.7494 (OUTLIER) cc_final: 0.7210 (p) REVERT: C 988 GLN cc_start: 0.8633 (tp40) cc_final: 0.8124 (mp10) REVERT: D 555 ARG cc_start: 0.8469 (tpp-160) cc_final: 0.8156 (tpm170) REVERT: D 647 ASN cc_start: 0.7802 (OUTLIER) cc_final: 0.6828 (p0) REVERT: D 754 MET cc_start: 0.5948 (ppp) cc_final: 0.4982 (ppp) REVERT: D 801 MET cc_start: 0.7707 (mpp) cc_final: 0.6735 (mpp) REVERT: D 900 MET cc_start: 0.7452 (mtt) cc_final: 0.7150 (mtt) outliers start: 102 outliers final: 74 residues processed: 298 average time/residue: 0.4375 time to fit residues: 210.8449 Evaluate side-chains 296 residues out of total 3013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 214 time to evaluate : 3.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 126 ASP Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 606 ASN Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 805 THR Chi-restraints excluded: chain A residue 862 TYR Chi-restraints excluded: chain A residue 871 TYR Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 876 PHE Chi-restraints excluded: chain A residue 907 VAL Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain A residue 994 LEU Chi-restraints excluded: chain A residue 1012 MET Chi-restraints excluded: chain A residue 1043 LYS Chi-restraints excluded: chain A residue 1083 GLN Chi-restraints excluded: chain A residue 1137 LEU Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 261 TYR Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 370 ASN Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain B residue 432 HIS Chi-restraints excluded: chain B residue 435 ASP Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 470 GLN Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 574 HIS Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 629 GLU Chi-restraints excluded: chain B residue 634 ILE Chi-restraints excluded: chain B residue 752 CYS Chi-restraints excluded: chain B residue 765 ASP Chi-restraints excluded: chain B residue 780 VAL Chi-restraints excluded: chain B residue 792 ASP Chi-restraints excluded: chain B residue 906 LYS Chi-restraints excluded: chain B residue 1016 VAL Chi-restraints excluded: chain B residue 1037 LEU Chi-restraints excluded: chain B residue 1067 ASP Chi-restraints excluded: chain B residue 1088 LEU Chi-restraints excluded: chain B residue 1123 ILE Chi-restraints excluded: chain B residue 1139 VAL Chi-restraints excluded: chain C residue 555 ARG Chi-restraints excluded: chain C residue 566 MET Chi-restraints excluded: chain C residue 732 ARG Chi-restraints excluded: chain C residue 752 CYS Chi-restraints excluded: chain C residue 780 VAL Chi-restraints excluded: chain C residue 783 MET Chi-restraints excluded: chain C residue 848 PHE Chi-restraints excluded: chain C residue 910 SER Chi-restraints excluded: chain C residue 947 PHE Chi-restraints excluded: chain C residue 986 ASP Chi-restraints excluded: chain C residue 1006 ASP Chi-restraints excluded: chain C residue 1016 VAL Chi-restraints excluded: chain C residue 1050 VAL Chi-restraints excluded: chain C residue 1078 PHE Chi-restraints excluded: chain C residue 1088 LEU Chi-restraints excluded: chain C residue 1137 LEU Chi-restraints excluded: chain D residue 528 VAL Chi-restraints excluded: chain D residue 585 HIS Chi-restraints excluded: chain D residue 647 ASN Chi-restraints excluded: chain D residue 752 CYS Chi-restraints excluded: chain D residue 826 VAL Chi-restraints excluded: chain D residue 874 LEU Chi-restraints excluded: chain D residue 879 HIS Chi-restraints excluded: chain D residue 890 VAL Chi-restraints excluded: chain D residue 903 ASP Chi-restraints excluded: chain D residue 920 PHE Chi-restraints excluded: chain D residue 1007 VAL Chi-restraints excluded: chain D residue 1033 LEU Chi-restraints excluded: chain D residue 1067 ASP Chi-restraints excluded: chain D residue 1076 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 319 optimal weight: 3.9990 chunk 336 optimal weight: 0.0470 chunk 306 optimal weight: 8.9990 chunk 326 optimal weight: 0.8980 chunk 196 optimal weight: 30.0000 chunk 142 optimal weight: 20.0000 chunk 256 optimal weight: 6.9990 chunk 100 optimal weight: 0.7980 chunk 295 optimal weight: 2.9990 chunk 309 optimal weight: 7.9990 chunk 325 optimal weight: 6.9990 overall best weight: 1.7482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 GLN ** A 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 464 ASN A 681 ASN ** A 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1081 ASN B 585 HIS B 669 ASN ** B 769 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 807 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1040 GLN ** C 773 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 919 GLN ** C1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6677 moved from start: 0.3601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 29044 Z= 0.188 Angle : 0.685 18.254 39375 Z= 0.333 Chirality : 0.044 0.218 4378 Planarity : 0.004 0.051 5171 Dihedral : 6.521 59.315 4141 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 21.42 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.66 % Favored : 92.28 % Rotamer: Outliers : 2.59 % Allowed : 19.75 % Favored : 77.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -1.05 (0.14), residues: 3653 helix: 0.46 (0.14), residues: 1451 sheet: -0.60 (0.23), residues: 490 loop : -1.77 (0.15), residues: 1712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 624 HIS 0.007 0.001 HIS B 585 PHE 0.018 0.001 PHE D 920 TYR 0.019 0.001 TYR B 834 ARG 0.007 0.000 ARG A 542 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 3013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 218 time to evaluate : 3.153 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 283 LEU cc_start: 0.5790 (OUTLIER) cc_final: 0.5459 (tp) REVERT: A 508 MET cc_start: 0.8316 (mmt) cc_final: 0.7807 (mmt) REVERT: A 871 TYR cc_start: 0.7132 (OUTLIER) cc_final: 0.6377 (t80) REVERT: A 881 MET cc_start: 0.7931 (tmm) cc_final: 0.7594 (mmt) REVERT: A 1143 MET cc_start: 0.2617 (ptm) cc_final: 0.2259 (ptt) REVERT: B 261 TYR cc_start: 0.5626 (OUTLIER) cc_final: 0.5229 (m-10) REVERT: B 634 ILE cc_start: 0.8181 (OUTLIER) cc_final: 0.7966 (mp) REVERT: B 891 LYS cc_start: 0.7145 (tptp) cc_final: 0.6537 (tttt) REVERT: B 1040 GLN cc_start: 0.7920 (OUTLIER) cc_final: 0.7458 (pp30) REVERT: B 1166 MET cc_start: 0.3502 (ptt) cc_final: 0.3135 (ptt) REVERT: C 641 MET cc_start: 0.8615 (tmm) cc_final: 0.8404 (tmm) REVERT: C 671 MET cc_start: 0.5300 (tpt) cc_final: 0.4939 (tpt) REVERT: C 686 MET cc_start: 0.5693 (tpp) cc_final: 0.5466 (tpp) REVERT: C 801 MET cc_start: 0.7763 (mtm) cc_final: 0.7483 (mtt) REVERT: C 804 MET cc_start: 0.9077 (tpp) cc_final: 0.8802 (mmp) REVERT: C 854 MET cc_start: 0.8618 (tpt) cc_final: 0.8089 (tpp) REVERT: C 910 SER cc_start: 0.7520 (OUTLIER) cc_final: 0.7244 (p) REVERT: C 988 GLN cc_start: 0.8577 (tp40) cc_final: 0.8121 (mp10) REVERT: D 555 ARG cc_start: 0.8355 (tpp-160) cc_final: 0.8129 (tpm170) REVERT: D 647 ASN cc_start: 0.7593 (OUTLIER) cc_final: 0.6553 (p0) REVERT: D 754 MET cc_start: 0.6081 (ppp) cc_final: 0.5236 (ppp) REVERT: D 801 MET cc_start: 0.7667 (mpp) cc_final: 0.6591 (mpp) REVERT: D 900 MET cc_start: 0.7302 (mtt) cc_final: 0.7009 (mtt) outliers start: 78 outliers final: 54 residues processed: 275 average time/residue: 0.3922 time to fit residues: 174.8458 Evaluate side-chains 271 residues out of total 3013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 210 time to evaluate : 3.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 862 TYR Chi-restraints excluded: chain A residue 871 TYR Chi-restraints excluded: chain A residue 876 PHE Chi-restraints excluded: chain A residue 907 VAL Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain A residue 994 LEU Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 261 TYR Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 370 ASN Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain B residue 432 HIS Chi-restraints excluded: chain B residue 435 ASP Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 470 GLN Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 629 GLU Chi-restraints excluded: chain B residue 634 ILE Chi-restraints excluded: chain B residue 647 ASN Chi-restraints excluded: chain B residue 752 CYS Chi-restraints excluded: chain B residue 765 ASP Chi-restraints excluded: chain B residue 780 VAL Chi-restraints excluded: chain B residue 1016 VAL Chi-restraints excluded: chain B residue 1040 GLN Chi-restraints excluded: chain B residue 1067 ASP Chi-restraints excluded: chain B residue 1088 LEU Chi-restraints excluded: chain B residue 1139 VAL Chi-restraints excluded: chain C residue 555 ARG Chi-restraints excluded: chain C residue 783 MET Chi-restraints excluded: chain C residue 848 PHE Chi-restraints excluded: chain C residue 910 SER Chi-restraints excluded: chain C residue 986 ASP Chi-restraints excluded: chain C residue 1016 VAL Chi-restraints excluded: chain C residue 1050 VAL Chi-restraints excluded: chain C residue 1078 PHE Chi-restraints excluded: chain C residue 1088 LEU Chi-restraints excluded: chain C residue 1103 LYS Chi-restraints excluded: chain C residue 1137 LEU Chi-restraints excluded: chain D residue 528 VAL Chi-restraints excluded: chain D residue 585 HIS Chi-restraints excluded: chain D residue 647 ASN Chi-restraints excluded: chain D residue 752 CYS Chi-restraints excluded: chain D residue 826 VAL Chi-restraints excluded: chain D residue 879 HIS Chi-restraints excluded: chain D residue 920 PHE Chi-restraints excluded: chain D residue 1007 VAL Chi-restraints excluded: chain D residue 1033 LEU Chi-restraints excluded: chain D residue 1076 VAL Chi-restraints excluded: chain D residue 1120 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 214 optimal weight: 4.9990 chunk 345 optimal weight: 3.9990 chunk 211 optimal weight: 0.9990 chunk 164 optimal weight: 4.9990 chunk 240 optimal weight: 8.9990 chunk 362 optimal weight: 20.0000 chunk 333 optimal weight: 9.9990 chunk 288 optimal weight: 1.9990 chunk 29 optimal weight: 20.0000 chunk 223 optimal weight: 5.9990 chunk 177 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 681 ASN ** A 864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 109 ASN ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 669 ASN ** B 769 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 807 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1081 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 773 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6733 moved from start: 0.3832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 29044 Z= 0.245 Angle : 0.723 16.844 39375 Z= 0.355 Chirality : 0.045 0.266 4378 Planarity : 0.005 0.069 5171 Dihedral : 6.588 58.473 4141 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 25.97 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.87 % Favored : 91.10 % Rotamer: Outliers : 2.56 % Allowed : 19.98 % Favored : 77.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.14), residues: 3653 helix: 0.32 (0.13), residues: 1462 sheet: -0.71 (0.23), residues: 491 loop : -1.78 (0.15), residues: 1700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 838 HIS 0.007 0.001 HIS A 76 PHE 0.031 0.002 PHE C 662 TYR 0.020 0.002 TYR B 834 ARG 0.007 0.001 ARG A 542 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 3013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 212 time to evaluate : 3.204 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 283 LEU cc_start: 0.5853 (OUTLIER) cc_final: 0.5485 (tp) REVERT: A 428 LYS cc_start: 0.7134 (ttpt) cc_final: 0.6375 (mmmt) REVERT: A 508 MET cc_start: 0.8395 (mmt) cc_final: 0.7981 (mmt) REVERT: A 616 MET cc_start: 0.7879 (tpp) cc_final: 0.7449 (tpp) REVERT: A 871 TYR cc_start: 0.7093 (OUTLIER) cc_final: 0.6380 (t80) REVERT: A 881 MET cc_start: 0.8046 (tmm) cc_final: 0.7647 (mmt) REVERT: B 261 TYR cc_start: 0.5617 (OUTLIER) cc_final: 0.5202 (m-10) REVERT: B 508 MET cc_start: 0.7913 (mmt) cc_final: 0.7654 (mmp) REVERT: B 677 PHE cc_start: 0.6327 (OUTLIER) cc_final: 0.4837 (t80) REVERT: B 783 MET cc_start: 0.8868 (tpp) cc_final: 0.8479 (tpp) REVERT: B 792 ASP cc_start: 0.4311 (OUTLIER) cc_final: 0.3980 (m-30) REVERT: B 891 LYS cc_start: 0.7238 (tptp) cc_final: 0.6624 (tttt) REVERT: B 900 MET cc_start: 0.7047 (mmm) cc_final: 0.6837 (mmm) REVERT: B 1166 MET cc_start: 0.3750 (ptt) cc_final: 0.3352 (ptt) REVERT: C 641 MET cc_start: 0.8775 (tmm) cc_final: 0.8520 (tmm) REVERT: C 671 MET cc_start: 0.5348 (tpt) cc_final: 0.4931 (tpt) REVERT: C 686 MET cc_start: 0.5620 (tpp) cc_final: 0.5395 (tpp) REVERT: C 804 MET cc_start: 0.9034 (tpp) cc_final: 0.8653 (mmt) REVERT: C 810 MET cc_start: 0.8565 (mmm) cc_final: 0.8360 (mmt) REVERT: C 854 MET cc_start: 0.8568 (tpt) cc_final: 0.7983 (tpp) REVERT: C 881 MET cc_start: 0.8500 (mmm) cc_final: 0.8299 (mmm) REVERT: C 910 SER cc_start: 0.7524 (OUTLIER) cc_final: 0.7245 (p) REVERT: C 988 GLN cc_start: 0.8657 (tp40) cc_final: 0.8151 (mp10) REVERT: D 647 ASN cc_start: 0.7893 (OUTLIER) cc_final: 0.6935 (p0) REVERT: D 801 MET cc_start: 0.7675 (mpp) cc_final: 0.6682 (mpp) REVERT: D 900 MET cc_start: 0.7425 (mtt) cc_final: 0.7104 (mtt) outliers start: 77 outliers final: 63 residues processed: 267 average time/residue: 0.3934 time to fit residues: 169.4704 Evaluate side-chains 279 residues out of total 3013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 209 time to evaluate : 3.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 385 ARG Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 566 MET Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 805 THR Chi-restraints excluded: chain A residue 862 TYR Chi-restraints excluded: chain A residue 871 TYR Chi-restraints excluded: chain A residue 876 PHE Chi-restraints excluded: chain A residue 907 VAL Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain A residue 994 LEU Chi-restraints excluded: chain A residue 1012 MET Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 261 TYR Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 370 ASN Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain B residue 432 HIS Chi-restraints excluded: chain B residue 435 ASP Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 470 GLN Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 574 HIS Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 629 GLU Chi-restraints excluded: chain B residue 647 ASN Chi-restraints excluded: chain B residue 677 PHE Chi-restraints excluded: chain B residue 752 CYS Chi-restraints excluded: chain B residue 765 ASP Chi-restraints excluded: chain B residue 780 VAL Chi-restraints excluded: chain B residue 792 ASP Chi-restraints excluded: chain B residue 1016 VAL Chi-restraints excluded: chain B residue 1067 ASP Chi-restraints excluded: chain B residue 1088 LEU Chi-restraints excluded: chain B residue 1139 VAL Chi-restraints excluded: chain C residue 555 ARG Chi-restraints excluded: chain C residue 566 MET Chi-restraints excluded: chain C residue 783 MET Chi-restraints excluded: chain C residue 848 PHE Chi-restraints excluded: chain C residue 910 SER Chi-restraints excluded: chain C residue 986 ASP Chi-restraints excluded: chain C residue 1016 VAL Chi-restraints excluded: chain C residue 1050 VAL Chi-restraints excluded: chain C residue 1078 PHE Chi-restraints excluded: chain C residue 1088 LEU Chi-restraints excluded: chain C residue 1103 LYS Chi-restraints excluded: chain C residue 1137 LEU Chi-restraints excluded: chain D residue 528 VAL Chi-restraints excluded: chain D residue 585 HIS Chi-restraints excluded: chain D residue 647 ASN Chi-restraints excluded: chain D residue 752 CYS Chi-restraints excluded: chain D residue 796 VAL Chi-restraints excluded: chain D residue 826 VAL Chi-restraints excluded: chain D residue 879 HIS Chi-restraints excluded: chain D residue 920 PHE Chi-restraints excluded: chain D residue 1007 VAL Chi-restraints excluded: chain D residue 1033 LEU Chi-restraints excluded: chain D residue 1067 ASP Chi-restraints excluded: chain D residue 1076 VAL Chi-restraints excluded: chain D residue 1120 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 229 optimal weight: 9.9990 chunk 307 optimal weight: 20.0000 chunk 88 optimal weight: 9.9990 chunk 266 optimal weight: 10.0000 chunk 42 optimal weight: 8.9990 chunk 80 optimal weight: 5.9990 chunk 289 optimal weight: 0.9980 chunk 121 optimal weight: 0.9990 chunk 296 optimal weight: 6.9990 chunk 36 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 769 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 807 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1081 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 773 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.100006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.081587 restraints weight = 238557.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.082244 restraints weight = 199519.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.082533 restraints weight = 176103.172| |-----------------------------------------------------------------------------| r_work (final): 0.4067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6847 moved from start: 0.4008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 29044 Z= 0.234 Angle : 0.720 16.508 39375 Z= 0.355 Chirality : 0.045 0.241 4378 Planarity : 0.005 0.070 5171 Dihedral : 6.592 59.115 4141 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 25.30 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.54 % Favored : 91.43 % Rotamer: Outliers : 2.49 % Allowed : 20.11 % Favored : 77.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -1.19 (0.14), residues: 3653 helix: 0.29 (0.13), residues: 1463 sheet: -0.68 (0.23), residues: 493 loop : -1.79 (0.15), residues: 1697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 624 HIS 0.007 0.001 HIS A 76 PHE 0.018 0.002 PHE D 553 TYR 0.020 0.002 TYR B 834 ARG 0.011 0.001 ARG A 88 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5045.43 seconds wall clock time: 94 minutes 21.53 seconds (5661.53 seconds total)