Starting phenix.real_space_refine on Sun Feb 18 23:38:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7thk_25896/02_2024/7thk_25896.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7thk_25896/02_2024/7thk_25896.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7thk_25896/02_2024/7thk_25896.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7thk_25896/02_2024/7thk_25896.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7thk_25896/02_2024/7thk_25896.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7thk_25896/02_2024/7thk_25896.pdb" } resolution = 3.11 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= 0.081 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 104 5.16 5 C 14819 2.51 5 N 3798 2.21 5 O 4470 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 34": "NH1" <-> "NH2" Residue "A GLU 154": "OE1" <-> "OE2" Residue "A GLU 156": "OE1" <-> "OE2" Residue "A GLU 169": "OE1" <-> "OE2" Residue "A ARG 214": "NH1" <-> "NH2" Residue "A GLU 224": "OE1" <-> "OE2" Residue "A GLU 281": "OE1" <-> "OE2" Residue "A PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 583": "OE1" <-> "OE2" Residue "A GLU 702": "OE1" <-> "OE2" Residue "A GLU 780": "OE1" <-> "OE2" Residue "A GLU 868": "OE1" <-> "OE2" Residue "A GLU 1072": "OE1" <-> "OE2" Residue "B TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 44": "NH1" <-> "NH2" Residue "B PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 154": "OE1" <-> "OE2" Residue "B GLU 156": "OE1" <-> "OE2" Residue "B GLU 169": "OE1" <-> "OE2" Residue "B ARG 214": "NH1" <-> "NH2" Residue "B GLU 281": "OE1" <-> "OE2" Residue "B GLU 309": "OE1" <-> "OE2" Residue "B GLU 324": "OE1" <-> "OE2" Residue "B GLU 340": "OE1" <-> "OE2" Residue "B ARG 357": "NH1" <-> "NH2" Residue "B PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 457": "NH1" <-> "NH2" Residue "B ARG 646": "NH1" <-> "NH2" Residue "B GLU 702": "OE1" <-> "OE2" Residue "B ARG 765": "NH1" <-> "NH2" Residue "B GLU 990": "OE1" <-> "OE2" Residue "C TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 154": "OE1" <-> "OE2" Residue "C GLU 156": "OE1" <-> "OE2" Residue "C GLU 169": "OE1" <-> "OE2" Residue "C ARG 214": "NH1" <-> "NH2" Residue "C PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 281": "OE1" <-> "OE2" Residue "C GLU 340": "OE1" <-> "OE2" Residue "C ARG 355": "NH1" <-> "NH2" Residue "C ARG 646": "NH1" <-> "NH2" Residue "C TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 702": "OE1" <-> "OE2" Residue "C PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 868": "OE1" <-> "OE2" Residue "C GLU 990": "OE1" <-> "OE2" Residue "C ARG 995": "NH1" <-> "NH2" Residue "C TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 23191 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 860, 6662 Classifications: {'peptide': 860} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 40, 'TRANS': 819} Chain breaks: 9 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'HIS:plan': 1, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 42 Chain: "B" Number of atoms: 8108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1043, 8108 Classifications: {'peptide': 1043} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 52, 'TRANS': 990} Chain breaks: 10 Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 115 Unresolved non-hydrogen dihedrals: 78 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 3, 'TYR:plan': 1, 'ASN:plan1': 3, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 68 Chain: "C" Number of atoms: 7889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1022, 7889 Classifications: {'peptide': 1022} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 50, 'TRANS': 971} Chain breaks: 11 Unresolved non-hydrogen bonds: 147 Unresolved non-hydrogen angles: 186 Unresolved non-hydrogen dihedrals: 126 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 4, 'TYR:plan': 2, 'ASN:plan1': 4, 'HIS:plan': 3, 'PHE:plan': 3, 'GLU:plan': 3, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 107 Chain: "A" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "B" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "C" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Time building chain proxies: 14.08, per 1000 atoms: 0.61 Number of scatterers: 23191 At special positions: 0 Unit cell: (126.99, 136.95, 173.47, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 104 16.00 O 4470 8.00 N 3798 7.00 C 14819 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.01 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.04 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.04 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=1.96 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.04 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.04 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.04 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.04 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1301 " - " ASN A 717 " " NAG A1302 " - " ASN A 801 " " NAG A1303 " - " ASN A1074 " " NAG A1304 " - " ASN A1098 " " NAG A1305 " - " ASN A1134 " " NAG A1306 " - " ASN A 709 " " NAG A1307 " - " ASN A 616 " " NAG A1308 " - " ASN A 61 " " NAG A1309 " - " ASN A 282 " " NAG A1310 " - " ASN A 122 " " NAG A1311 " - " ASN A 234 " " NAG A1312 " - " ASN A 165 " " NAG B1301 " - " ASN B 616 " " NAG B1302 " - " ASN B 717 " " NAG B1303 " - " ASN B 801 " " NAG B1304 " - " ASN B1074 " " NAG B1305 " - " ASN B1098 " " NAG B1306 " - " ASN B1134 " " NAG B1307 " - " ASN B 61 " " NAG B1308 " - " ASN B 282 " " NAG B1309 " - " ASN B 122 " " NAG B1310 " - " ASN B 234 " " NAG B1311 " - " ASN B 331 " " NAG B1312 " - " ASN B 709 " " NAG B1313 " - " ASN B 343 " " NAG C1301 " - " ASN C 616 " " NAG C1302 " - " ASN C 717 " " NAG C1303 " - " ASN C 801 " " NAG C1304 " - " ASN C1074 " " NAG C1305 " - " ASN C1098 " " NAG C1306 " - " ASN C1134 " " NAG C1307 " - " ASN C 343 " " NAG C1308 " - " ASN C 331 " " NAG C1309 " - " ASN C 709 " " NAG C1310 " - " ASN C 61 " " NAG C1311 " - " ASN C 282 " " NAG C1312 " - " ASN C 122 " " NAG C1313 " - " ASN C 234 " Time building additional restraints: 11.31 Conformation dependent library (CDL) restraints added in 4.0 seconds 5718 Ramachandran restraints generated. 2859 Oldfield, 0 Emsley, 2859 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5500 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 39 sheets defined 27.4% alpha, 25.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.13 Creating SS restraints... Processing helix chain 'A' and resid 156 through 160 removed outlier: 4.295A pdb=" N TYR A 160 " --> pdb=" O PHE A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 619 through 624 Processing helix chain 'A' and resid 625 through 629 Processing helix chain 'A' and resid 630 through 638 removed outlier: 3.553A pdb=" N TYR A 636 " --> pdb=" O THR A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 747 through 755 removed outlier: 4.194A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.556A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 838 through 842 removed outlier: 3.585A pdb=" N GLY A 842 " --> pdb=" O GLY A 838 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 838 through 842' Processing helix chain 'A' and resid 848 through 856 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.550A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.305A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.656A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 4.268A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 3.823A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASP A 994 " --> pdb=" O GLU A 990 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 3.907A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 160 removed outlier: 4.296A pdb=" N TYR B 160 " --> pdb=" O PHE B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.661A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 371 Processing helix chain 'B' and resid 384 through 390 removed outlier: 4.081A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 410 Processing helix chain 'B' and resid 416 through 421 Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.739A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.832A pdb=" N ALA B 771 " --> pdb=" O LEU B 767 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.668A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 849 through 855 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.707A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.165A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.664A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 4.157A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 removed outlier: 3.912A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ASP B 994 " --> pdb=" O GLU B 990 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 3.866A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASP B1146 " --> pdb=" O GLN B1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 160 removed outlier: 4.296A pdb=" N TYR C 160 " --> pdb=" O PHE C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 383 through 388 removed outlier: 4.291A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 742 Processing helix chain 'C' and resid 746 through 757 Processing helix chain 'C' and resid 757 through 783 removed outlier: 4.349A pdb=" N THR C 761 " --> pdb=" O GLY C 757 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.695A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 850 through 855 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.565A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 910 Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 940 Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 983 removed outlier: 3.667A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 3.579A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 3.743A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASP C1146 " --> pdb=" O GLN C1142 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 4.311A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.316A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N LYS A 187 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE A 210 " --> pdb=" O LYS A 187 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.556A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 8.581A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.774A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 4.086A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER A 172 " --> pdb=" O VAL A 126 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 315 removed outlier: 4.313A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 328 removed outlier: 3.709A pdb=" N ARG A 328 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.941A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.432A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 701 through 704 Processing sheet with id=AA9, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.511A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB2, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AB3, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB4, first strand: chain 'A' and resid 1094 through 1098 Processing sheet with id=AB5, first strand: chain 'B' and resid 27 through 31 removed outlier: 4.310A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N LYS B 187 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE B 210 " --> pdb=" O LYS B 187 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 42 through 43 removed outlier: 6.449A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.054A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 84 through 85 removed outlier: 4.084A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER B 172 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.264A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.552A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ASP B 398 " --> pdb=" O VAL B 512 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.894A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC4, first strand: chain 'B' and resid 654 through 656 removed outlier: 3.609A pdb=" N GLU B 654 " --> pdb=" O ILE B 692 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N THR B 696 " --> pdb=" O VAL B 656 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.649A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.566A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 787 through 790 removed outlier: 5.941A pdb=" N ILE B 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AC9, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD1, first strand: chain 'C' and resid 27 through 31 removed outlier: 4.310A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 8.358A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N LYS C 187 " --> pdb=" O ILE C 210 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE C 210 " --> pdb=" O LYS C 187 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.522A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 84 through 85 removed outlier: 4.085A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ASN C 121 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER C 172 " --> pdb=" O VAL C 126 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 311 through 316 removed outlier: 6.756A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.595A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N THR C 430 " --> pdb=" O PHE C 515 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.543A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AD8, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.898A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.380A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.464A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AE2, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.186A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 1094 through 1097 1009 hydrogen bonds defined for protein. 2772 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: 11.16 Time building geometry restraints manager: 11.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 3752 1.28 - 1.42: 5957 1.42 - 1.55: 13837 1.55 - 1.69: 15 1.69 - 1.83: 131 Bond restraints: 23692 Sorted by residual: bond pdb=" C ARG B 765 " pdb=" O ARG B 765 " ideal model delta sigma weight residual 1.237 1.139 0.097 1.17e-02 7.31e+03 6.91e+01 bond pdb=" C ILE B 651 " pdb=" O ILE B 651 " ideal model delta sigma weight residual 1.238 1.165 0.072 1.09e-02 8.42e+03 4.39e+01 bond pdb=" C ILE B 693 " pdb=" O ILE B 693 " ideal model delta sigma weight residual 1.235 1.169 0.066 1.05e-02 9.07e+03 4.01e+01 bond pdb=" C TYR B 396 " pdb=" O TYR B 396 " ideal model delta sigma weight residual 1.236 1.162 0.074 1.20e-02 6.94e+03 3.79e+01 bond pdb=" CA SER B 359 " pdb=" CB SER B 359 " ideal model delta sigma weight residual 1.533 1.434 0.099 1.82e-02 3.02e+03 2.98e+01 ... (remaining 23687 not shown) Histogram of bond angle deviations from ideal: 96.30 - 104.21: 371 104.21 - 112.12: 11266 112.12 - 120.03: 10242 120.03 - 127.94: 10219 127.94 - 135.84: 130 Bond angle restraints: 32228 Sorted by residual: angle pdb=" C TYR B 636 " pdb=" CA TYR B 636 " pdb=" CB TYR B 636 " ideal model delta sigma weight residual 110.26 124.39 -14.13 1.50e+00 4.44e-01 8.88e+01 angle pdb=" C LYS B 278 " pdb=" CA LYS B 278 " pdb=" CB LYS B 278 " ideal model delta sigma weight residual 112.05 100.60 11.45 1.52e+00 4.33e-01 5.67e+01 angle pdb=" C CYS A 738 " pdb=" CA CYS A 738 " pdb=" CB CYS A 738 " ideal model delta sigma weight residual 110.88 99.08 11.80 1.57e+00 4.06e-01 5.65e+01 angle pdb=" CA GLY C 219 " pdb=" C GLY C 219 " pdb=" O GLY C 219 " ideal model delta sigma weight residual 122.05 115.56 6.49 1.00e+00 1.00e+00 4.22e+01 angle pdb=" CA GLY B1044 " pdb=" C GLY B1044 " pdb=" O GLY B1044 " ideal model delta sigma weight residual 122.29 117.04 5.25 8.10e-01 1.52e+00 4.19e+01 ... (remaining 32223 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 13310 17.90 - 35.79: 1045 35.79 - 53.69: 191 53.69 - 71.59: 57 71.59 - 89.48: 15 Dihedral angle restraints: 14618 sinusoidal: 6104 harmonic: 8514 Sorted by residual: dihedral pdb=" CB CYS B 538 " pdb=" SG CYS B 538 " pdb=" SG CYS B 590 " pdb=" CB CYS B 590 " ideal model delta sinusoidal sigma weight residual -86.00 -165.30 79.30 1 1.00e+01 1.00e-02 7.82e+01 dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual -86.00 -159.88 73.88 1 1.00e+01 1.00e-02 6.93e+01 dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -156.09 70.09 1 1.00e+01 1.00e-02 6.33e+01 ... (remaining 14615 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 2828 0.087 - 0.173: 791 0.173 - 0.260: 160 0.260 - 0.347: 29 0.347 - 0.433: 7 Chirality restraints: 3815 Sorted by residual: chirality pdb=" C2 NAG B1301 " pdb=" C1 NAG B1301 " pdb=" C3 NAG B1301 " pdb=" N2 NAG B1301 " both_signs ideal model delta sigma weight residual False -2.49 -2.06 -0.43 2.00e-01 2.50e+01 4.69e+00 chirality pdb=" CA ASP A 198 " pdb=" N ASP A 198 " pdb=" C ASP A 198 " pdb=" CB ASP A 198 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.62e+00 chirality pdb=" CA LYS C 304 " pdb=" N LYS C 304 " pdb=" C LYS C 304 " pdb=" CB LYS C 304 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.28e+00 ... (remaining 3812 not shown) Planarity restraints: 4138 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1306 " 0.342 2.00e-02 2.50e+03 2.92e-01 1.07e+03 pdb=" C7 NAG A1306 " -0.083 2.00e-02 2.50e+03 pdb=" C8 NAG A1306 " 0.163 2.00e-02 2.50e+03 pdb=" N2 NAG A1306 " -0.518 2.00e-02 2.50e+03 pdb=" O7 NAG A1306 " 0.096 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1309 " 0.316 2.00e-02 2.50e+03 2.67e-01 8.91e+02 pdb=" C7 NAG C1309 " -0.080 2.00e-02 2.50e+03 pdb=" C8 NAG C1309 " 0.185 2.00e-02 2.50e+03 pdb=" N2 NAG C1309 " -0.463 2.00e-02 2.50e+03 pdb=" O7 NAG C1309 " 0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1311 " 0.285 2.00e-02 2.50e+03 2.42e-01 7.34e+02 pdb=" C7 NAG A1311 " -0.071 2.00e-02 2.50e+03 pdb=" C8 NAG A1311 " 0.174 2.00e-02 2.50e+03 pdb=" N2 NAG A1311 " -0.420 2.00e-02 2.50e+03 pdb=" O7 NAG A1311 " 0.032 2.00e-02 2.50e+03 ... (remaining 4135 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 6752 2.83 - 3.35: 19753 3.35 - 3.86: 38583 3.86 - 4.38: 45305 4.38 - 4.90: 78414 Nonbonded interactions: 188807 Sorted by model distance: nonbonded pdb=" O GLY C 880 " pdb=" OG SER C 884 " model vdw 2.312 2.440 nonbonded pdb=" O GLY A 880 " pdb=" OG SER A 884 " model vdw 2.318 2.440 nonbonded pdb=" O GLY B 880 " pdb=" OG SER B 884 " model vdw 2.333 2.440 nonbonded pdb=" O LEU A 877 " pdb=" OG1 THR A 881 " model vdw 2.342 2.440 nonbonded pdb=" OH TYR B 37 " pdb=" O LEU B 54 " model vdw 2.346 2.440 ... (remaining 188802 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 'B' and (resid 26 through 407 or (resid 408 and (name N or name CA or nam \ e C or name O or name CB )) or resid 409 through 414 or (resid 415 and (name N o \ r name CA or name C or name O or name CB )) or resid 416 through 440 or (resid 4 \ 41 and (name N or name CA or name C or name O or name CB )) or resid 442 through \ 443 or (resid 444 and (name N or name CA or name C or name O or name CB )) or r \ esid 445 through 449 or (resid 450 and (name N or name CA or name C or name O or \ name CB )) or resid 451 through 455 or (resid 456 and (name N or name CA or nam \ e C or name O or name CB )) or resid 457 through 469 or (resid 474 through 475 a \ nd (name N or name CA or name C or name O or name CB )) or resid 476 through 497 \ or (resid 498 and (name N or name CA or name C or name O or name CB )) or resid \ 499 or (resid 500 through 501 and (name N or name CA or name C or name O or nam \ e CB )) or resid 502 through 504 or (resid 505 and (name N or name CA or name C \ or name O or name CB )) or resid 506 through 518 or (resid 519 through 520 and ( \ name N or name CA or name C or name O or name CB )) or resid 521 through 585 or \ (resid 586 and (name N or name CA or name C or name O or name CB )) or resid 587 \ through 620 or resid 641 through 827 or resid 849 through 1147 or resid 1301 th \ rough 1313)) selection = (chain 'C' and (resid 26 through 495 or (resid 496 and (name N or name CA or nam \ e C or name O or name CB )) or resid 497 through 987 or (resid 988 through 989 a \ nd (name N or name CA or name C or name O or name CB )) or resid 990 through 114 \ 7 or resid 1301 through 1313)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 21.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 22.750 Check model and map are aligned: 0.380 Set scattering table: 0.220 Process input model: 68.900 Find NCS groups from input model: 1.610 Set up NCS constraints: 0.120 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: 0.020 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 118.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 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 : 0.009 0.099 23692 Z= 0.603 Angle : 1.335 14.133 32228 Z= 0.930 Chirality : 0.083 0.433 3815 Planarity : 0.012 0.292 4100 Dihedral : 13.340 89.482 9010 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 1.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 0.44 % Allowed : 4.49 % Favored : 95.07 % Cbeta Deviations : 0.47 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.14), residues: 2859 helix: -1.42 (0.16), residues: 664 sheet: 0.11 (0.21), residues: 525 loop : -1.34 (0.13), residues: 1670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP B 886 HIS 0.013 0.001 HIS A 954 PHE 0.045 0.003 PHE B 43 TYR 0.031 0.002 TYR A 37 ARG 0.010 0.001 ARG B 34 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5718 Ramachandran restraints generated. 2859 Oldfield, 0 Emsley, 2859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5718 Ramachandran restraints generated. 2859 Oldfield, 0 Emsley, 2859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 2562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 468 time to evaluate : 2.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 ASN cc_start: 0.8008 (m-40) cc_final: 0.7644 (p0) REVERT: A 740 MET cc_start: 0.7291 (tpt) cc_final: 0.6927 (tpt) REVERT: A 1031 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.6925 (mp0) REVERT: B 188 ASN cc_start: 0.6454 (m-40) cc_final: 0.6013 (p0) REVERT: B 314 GLN cc_start: 0.7379 (mt0) cc_final: 0.7120 (mt0) REVERT: B 461 LEU cc_start: 0.7851 (mt) cc_final: 0.7591 (mt) REVERT: B 555 SER cc_start: 0.7161 (t) cc_final: 0.6856 (t) REVERT: B 1031 GLU cc_start: 0.8670 (OUTLIER) cc_final: 0.8230 (mt-10) REVERT: C 205 SER cc_start: 0.7697 (t) cc_final: 0.7480 (p) outliers start: 11 outliers final: 1 residues processed: 476 average time/residue: 0.3620 time to fit residues: 263.5947 Evaluate side-chains 265 residues out of total 2562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 262 time to evaluate : 2.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain C residue 1031 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 246 optimal weight: 2.9990 chunk 221 optimal weight: 1.9990 chunk 122 optimal weight: 4.9990 chunk 75 optimal weight: 1.9990 chunk 149 optimal weight: 0.8980 chunk 118 optimal weight: 0.0570 chunk 228 optimal weight: 0.0050 chunk 88 optimal weight: 0.9980 chunk 139 optimal weight: 0.9990 chunk 170 optimal weight: 2.9990 chunk 265 optimal weight: 1.9990 overall best weight: 0.5914 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 99 ASN A 125 ASN A 207 HIS A 321 GLN A 544 ASN A 919 ASN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 165 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 422 ASN B 542 ASN B 644 GLN B 755 GLN B 907 ASN B 914 ASN B 955 ASN C 360 ASN C 710 ASN C 755 GLN C 787 GLN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN C1005 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 23692 Z= 0.203 Angle : 0.582 9.815 32228 Z= 0.304 Chirality : 0.045 0.261 3815 Planarity : 0.004 0.040 4100 Dihedral : 7.115 65.205 3913 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.16 % Allowed : 9.14 % Favored : 88.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.14), residues: 2859 helix: 0.76 (0.18), residues: 670 sheet: 0.21 (0.21), residues: 590 loop : -1.12 (0.14), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 633 HIS 0.003 0.001 HIS B1048 PHE 0.042 0.002 PHE B 377 TYR 0.022 0.001 TYR C 396 ARG 0.007 0.000 ARG A 567 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5718 Ramachandran restraints generated. 2859 Oldfield, 0 Emsley, 2859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5718 Ramachandran restraints generated. 2859 Oldfield, 0 Emsley, 2859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 2562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 285 time to evaluate : 2.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 ASN cc_start: 0.6435 (OUTLIER) cc_final: 0.5760 (m-40) REVERT: A 1031 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.6705 (mp0) REVERT: B 52 GLN cc_start: 0.8132 (tt0) cc_final: 0.7677 (tm-30) REVERT: B 159 VAL cc_start: 0.7842 (p) cc_final: 0.7580 (t) REVERT: B 314 GLN cc_start: 0.7493 (mt0) cc_final: 0.7154 (mt0) REVERT: B 432 CYS cc_start: 0.6981 (OUTLIER) cc_final: 0.6621 (t) REVERT: B 461 LEU cc_start: 0.7632 (mt) cc_final: 0.7397 (mt) REVERT: B 516 GLU cc_start: 0.7396 (OUTLIER) cc_final: 0.7116 (mt-10) REVERT: B 1031 GLU cc_start: 0.8722 (OUTLIER) cc_final: 0.8477 (mt-10) REVERT: C 205 SER cc_start: 0.7707 (t) cc_final: 0.7501 (p) REVERT: C 574 ASP cc_start: 0.7437 (t0) cc_final: 0.7164 (t0) outliers start: 54 outliers final: 24 residues processed: 326 average time/residue: 0.3364 time to fit residues: 175.3187 Evaluate side-chains 263 residues out of total 2562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 234 time to evaluate : 2.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 919 ASN Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 462 LYS Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 969 LYS Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 147 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 220 optimal weight: 5.9990 chunk 180 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 chunk 265 optimal weight: 1.9990 chunk 286 optimal weight: 1.9990 chunk 236 optimal weight: 2.9990 chunk 263 optimal weight: 2.9990 chunk 90 optimal weight: 0.4980 chunk 213 optimal weight: 0.7980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 115 GLN A 314 GLN A 321 GLN A 641 ASN ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN A1135 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 334 ASN B 370 ASN B 755 GLN B 919 ASN B 935 GLN C 207 HIS C 422 ASN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 23692 Z= 0.299 Angle : 0.586 9.501 32228 Z= 0.305 Chirality : 0.046 0.263 3815 Planarity : 0.004 0.037 4100 Dihedral : 6.649 69.036 3910 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.81 % Allowed : 10.34 % Favored : 86.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.15), residues: 2859 helix: 1.38 (0.20), residues: 685 sheet: 0.19 (0.21), residues: 580 loop : -0.95 (0.15), residues: 1594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 633 HIS 0.006 0.001 HIS A1048 PHE 0.030 0.002 PHE B 906 TYR 0.021 0.002 TYR A1067 ARG 0.005 0.001 ARG A 567 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5718 Ramachandran restraints generated. 2859 Oldfield, 0 Emsley, 2859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5718 Ramachandran restraints generated. 2859 Oldfield, 0 Emsley, 2859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 241 time to evaluate : 2.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 GLU cc_start: 0.7322 (pt0) cc_final: 0.7004 (pt0) REVERT: A 125 ASN cc_start: 0.6809 (m-40) cc_final: 0.6461 (m-40) REVERT: A 156 GLU cc_start: 0.6186 (mm-30) cc_final: 0.5903 (pp20) REVERT: A 560 LEU cc_start: 0.8047 (mt) cc_final: 0.7843 (mt) REVERT: A 1031 GLU cc_start: 0.8508 (OUTLIER) cc_final: 0.7870 (mt-10) REVERT: B 52 GLN cc_start: 0.8164 (tt0) cc_final: 0.7651 (tm-30) REVERT: B 432 CYS cc_start: 0.7057 (OUTLIER) cc_final: 0.6436 (t) REVERT: B 461 LEU cc_start: 0.7565 (mt) cc_final: 0.7299 (mt) REVERT: B 516 GLU cc_start: 0.7472 (OUTLIER) cc_final: 0.7223 (mt-10) REVERT: B 572 THR cc_start: 0.8227 (p) cc_final: 0.7721 (t) REVERT: B 1031 GLU cc_start: 0.8847 (OUTLIER) cc_final: 0.8554 (mt-10) REVERT: C 1031 GLU cc_start: 0.8072 (mm-30) cc_final: 0.7572 (mm-30) outliers start: 70 outliers final: 51 residues processed: 288 average time/residue: 0.3277 time to fit residues: 153.5701 Evaluate side-chains 273 residues out of total 2562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 218 time to evaluate : 2.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 462 LYS Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 262 optimal weight: 4.9990 chunk 199 optimal weight: 10.0000 chunk 137 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 126 optimal weight: 10.0000 chunk 178 optimal weight: 0.5980 chunk 266 optimal weight: 1.9990 chunk 282 optimal weight: 1.9990 chunk 139 optimal weight: 0.6980 chunk 252 optimal weight: 1.9990 chunk 76 optimal weight: 0.6980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 641 ASN ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN C 207 HIS C 957 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.3073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 23692 Z= 0.287 Angle : 0.558 9.459 32228 Z= 0.289 Chirality : 0.045 0.403 3815 Planarity : 0.004 0.040 4100 Dihedral : 6.423 70.765 3910 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 3.05 % Allowed : 11.10 % Favored : 85.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.15), residues: 2859 helix: 1.59 (0.20), residues: 684 sheet: 0.22 (0.21), residues: 558 loop : -0.88 (0.15), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 633 HIS 0.004 0.001 HIS A1048 PHE 0.022 0.002 PHE B 906 TYR 0.020 0.001 TYR A1067 ARG 0.005 0.000 ARG C 190 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5718 Ramachandran restraints generated. 2859 Oldfield, 0 Emsley, 2859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5718 Ramachandran restraints generated. 2859 Oldfield, 0 Emsley, 2859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 228 time to evaluate : 2.501 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 156 GLU cc_start: 0.6157 (mm-30) cc_final: 0.5937 (pp20) REVERT: A 164 ASN cc_start: 0.7133 (m-40) cc_final: 0.6751 (m-40) REVERT: A 1031 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.8292 (mt-10) REVERT: A 1050 MET cc_start: 0.8679 (ptp) cc_final: 0.8187 (ptm) REVERT: B 52 GLN cc_start: 0.8198 (tt0) cc_final: 0.7624 (tm-30) REVERT: B 317 ASN cc_start: 0.7654 (m-40) cc_final: 0.7421 (m110) REVERT: B 461 LEU cc_start: 0.7537 (mt) cc_final: 0.7276 (mt) REVERT: B 516 GLU cc_start: 0.7508 (OUTLIER) cc_final: 0.7257 (mt-10) REVERT: B 572 THR cc_start: 0.8195 (p) cc_final: 0.7732 (t) REVERT: B 740 MET cc_start: 0.7412 (mmm) cc_final: 0.7189 (tpt) REVERT: B 914 ASN cc_start: 0.8490 (p0) cc_final: 0.8192 (p0) REVERT: C 1031 GLU cc_start: 0.8094 (mm-30) cc_final: 0.7631 (mm-30) outliers start: 76 outliers final: 59 residues processed: 281 average time/residue: 0.3165 time to fit residues: 147.1071 Evaluate side-chains 273 residues out of total 2562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 212 time to evaluate : 2.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 462 LYS Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 235 optimal weight: 2.9990 chunk 160 optimal weight: 0.1980 chunk 4 optimal weight: 0.9980 chunk 210 optimal weight: 5.9990 chunk 116 optimal weight: 5.9990 chunk 240 optimal weight: 1.9990 chunk 195 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 144 optimal weight: 2.9990 chunk 253 optimal weight: 4.9990 chunk 71 optimal weight: 0.5980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN A 901 GLN ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN B 755 GLN B1125 ASN C 245 HIS C 804 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.3248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 23692 Z= 0.241 Angle : 0.533 9.446 32228 Z= 0.277 Chirality : 0.044 0.246 3815 Planarity : 0.003 0.042 4100 Dihedral : 6.159 69.215 3907 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.05 % Allowed : 11.90 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.15), residues: 2859 helix: 1.79 (0.20), residues: 686 sheet: 0.21 (0.21), residues: 574 loop : -0.85 (0.15), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 633 HIS 0.005 0.001 HIS B 207 PHE 0.022 0.001 PHE B 92 TYR 0.020 0.001 TYR A1067 ARG 0.010 0.000 ARG B 498 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5718 Ramachandran restraints generated. 2859 Oldfield, 0 Emsley, 2859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5718 Ramachandran restraints generated. 2859 Oldfield, 0 Emsley, 2859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 220 time to evaluate : 2.567 Fit side-chains revert: symmetry clash REVERT: A 96 GLU cc_start: 0.7414 (pt0) cc_final: 0.7125 (pt0) REVERT: A 164 ASN cc_start: 0.7364 (m-40) cc_final: 0.7146 (m-40) REVERT: A 990 GLU cc_start: 0.7358 (OUTLIER) cc_final: 0.6735 (mp0) REVERT: A 1031 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.8322 (mt-10) REVERT: A 1050 MET cc_start: 0.8680 (ptp) cc_final: 0.8211 (ptm) REVERT: B 52 GLN cc_start: 0.8221 (tt0) cc_final: 0.7646 (tm-30) REVERT: B 317 ASN cc_start: 0.7697 (m-40) cc_final: 0.7442 (m110) REVERT: B 461 LEU cc_start: 0.7526 (mt) cc_final: 0.7275 (mt) REVERT: B 516 GLU cc_start: 0.7525 (OUTLIER) cc_final: 0.7282 (mt-10) REVERT: B 572 THR cc_start: 0.8172 (p) cc_final: 0.7735 (t) REVERT: C 129 LYS cc_start: 0.7296 (mtpt) cc_final: 0.6941 (mtpp) REVERT: C 1031 GLU cc_start: 0.8031 (mm-30) cc_final: 0.7646 (mm-30) outliers start: 76 outliers final: 59 residues processed: 275 average time/residue: 0.3028 time to fit residues: 139.2336 Evaluate side-chains 268 residues out of total 2562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 206 time to evaluate : 2.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 627 ASP Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 725 GLU Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 94 optimal weight: 9.9990 chunk 254 optimal weight: 2.9990 chunk 55 optimal weight: 0.5980 chunk 165 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 282 optimal weight: 0.5980 chunk 234 optimal weight: 6.9990 chunk 130 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 93 optimal weight: 0.8980 chunk 148 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN A 314 GLN A 321 GLN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN B1125 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.3373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 23692 Z= 0.207 Angle : 0.521 9.449 32228 Z= 0.270 Chirality : 0.044 0.246 3815 Planarity : 0.003 0.040 4100 Dihedral : 6.011 65.411 3907 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.81 % Allowed : 12.79 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.15), residues: 2859 helix: 1.91 (0.20), residues: 687 sheet: 0.25 (0.21), residues: 568 loop : -0.79 (0.15), residues: 1604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP B 633 HIS 0.004 0.001 HIS B 207 PHE 0.023 0.001 PHE B 92 TYR 0.020 0.001 TYR A1067 ARG 0.007 0.000 ARG C 983 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5718 Ramachandran restraints generated. 2859 Oldfield, 0 Emsley, 2859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5718 Ramachandran restraints generated. 2859 Oldfield, 0 Emsley, 2859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 215 time to evaluate : 2.559 Fit side-chains revert: symmetry clash REVERT: A 96 GLU cc_start: 0.7378 (pt0) cc_final: 0.7094 (pt0) REVERT: A 1031 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.8214 (mt-10) REVERT: A 1050 MET cc_start: 0.8660 (ptp) cc_final: 0.8216 (ptm) REVERT: B 52 GLN cc_start: 0.8212 (tt0) cc_final: 0.7645 (tm-30) REVERT: B 461 LEU cc_start: 0.7519 (mt) cc_final: 0.7294 (mt) REVERT: B 516 GLU cc_start: 0.7460 (OUTLIER) cc_final: 0.7217 (mt-10) REVERT: B 572 THR cc_start: 0.8220 (p) cc_final: 0.7784 (t) REVERT: C 129 LYS cc_start: 0.7372 (mtpt) cc_final: 0.7047 (mtpp) REVERT: C 1031 GLU cc_start: 0.7996 (mm-30) cc_final: 0.7779 (mp0) outliers start: 70 outliers final: 54 residues processed: 266 average time/residue: 0.3264 time to fit residues: 142.9286 Evaluate side-chains 261 residues out of total 2562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 205 time to evaluate : 2.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 627 ASP Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 725 GLU Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 272 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 chunk 160 optimal weight: 1.9990 chunk 206 optimal weight: 6.9990 chunk 159 optimal weight: 0.0470 chunk 237 optimal weight: 0.0060 chunk 157 optimal weight: 0.0570 chunk 281 optimal weight: 3.9990 chunk 176 optimal weight: 0.7980 chunk 171 optimal weight: 1.9990 chunk 129 optimal weight: 6.9990 overall best weight: 0.5814 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN A 314 GLN A 321 GLN A 641 ASN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN B1125 ASN C 955 ASN ** C1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.3471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 23692 Z= 0.183 Angle : 0.509 9.450 32228 Z= 0.264 Chirality : 0.043 0.246 3815 Planarity : 0.003 0.043 4100 Dihedral : 5.894 60.134 3907 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.81 % Allowed : 12.87 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.15), residues: 2859 helix: 1.96 (0.20), residues: 695 sheet: 0.29 (0.21), residues: 602 loop : -0.73 (0.15), residues: 1562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP B 633 HIS 0.004 0.001 HIS B 207 PHE 0.024 0.001 PHE B 92 TYR 0.019 0.001 TYR A1067 ARG 0.012 0.000 ARG C 983 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5718 Ramachandran restraints generated. 2859 Oldfield, 0 Emsley, 2859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5718 Ramachandran restraints generated. 2859 Oldfield, 0 Emsley, 2859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 211 time to evaluate : 2.822 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 156 GLU cc_start: 0.5753 (pp20) cc_final: 0.5278 (mm-30) REVERT: A 1031 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.7543 (mp0) REVERT: B 52 GLN cc_start: 0.8209 (tt0) cc_final: 0.7634 (tm-30) REVERT: B 516 GLU cc_start: 0.7428 (OUTLIER) cc_final: 0.7124 (mt-10) REVERT: B 572 THR cc_start: 0.8234 (p) cc_final: 0.7844 (t) REVERT: C 129 LYS cc_start: 0.7318 (mtpt) cc_final: 0.7025 (mtpt) REVERT: C 1031 GLU cc_start: 0.7971 (mm-30) cc_final: 0.7748 (mp0) outliers start: 70 outliers final: 58 residues processed: 261 average time/residue: 0.3140 time to fit residues: 137.6747 Evaluate side-chains 257 residues out of total 2562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 197 time to evaluate : 2.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 627 ASP Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 174 optimal weight: 3.9990 chunk 112 optimal weight: 4.9990 chunk 168 optimal weight: 0.6980 chunk 84 optimal weight: 1.9990 chunk 55 optimal weight: 0.4980 chunk 54 optimal weight: 0.7980 chunk 178 optimal weight: 1.9990 chunk 191 optimal weight: 3.9990 chunk 139 optimal weight: 0.0020 chunk 26 optimal weight: 0.0870 chunk 221 optimal weight: 0.8980 overall best weight: 0.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN A 314 GLN A 321 GLN A 641 ASN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN B1125 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.3542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 23692 Z= 0.159 Angle : 0.499 9.448 32228 Z= 0.257 Chirality : 0.043 0.242 3815 Planarity : 0.003 0.042 4100 Dihedral : 5.766 56.642 3907 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.57 % Allowed : 13.55 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.16), residues: 2859 helix: 2.07 (0.20), residues: 700 sheet: 0.30 (0.21), residues: 614 loop : -0.74 (0.15), residues: 1545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP B 633 HIS 0.003 0.000 HIS B 207 PHE 0.025 0.001 PHE A 168 TYR 0.019 0.001 TYR A1067 ARG 0.008 0.000 ARG C 983 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5718 Ramachandran restraints generated. 2859 Oldfield, 0 Emsley, 2859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5718 Ramachandran restraints generated. 2859 Oldfield, 0 Emsley, 2859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 211 time to evaluate : 2.499 Fit side-chains revert: symmetry clash REVERT: A 156 GLU cc_start: 0.5771 (pp20) cc_final: 0.5315 (mm-30) REVERT: A 1031 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.7801 (mt-10) REVERT: B 52 GLN cc_start: 0.8195 (tt0) cc_final: 0.7628 (tm-30) REVERT: B 461 LEU cc_start: 0.7446 (mt) cc_final: 0.7165 (mt) REVERT: B 572 THR cc_start: 0.8266 (p) cc_final: 0.7877 (t) REVERT: C 129 LYS cc_start: 0.7367 (mtpt) cc_final: 0.7066 (mtpt) REVERT: C 1031 GLU cc_start: 0.7937 (mm-30) cc_final: 0.7635 (mm-30) outliers start: 64 outliers final: 58 residues processed: 257 average time/residue: 0.3026 time to fit residues: 129.3279 Evaluate side-chains 263 residues out of total 2562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 204 time to evaluate : 2.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 627 ASP Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 256 optimal weight: 2.9990 chunk 269 optimal weight: 1.9990 chunk 245 optimal weight: 0.0980 chunk 262 optimal weight: 0.0870 chunk 157 optimal weight: 0.3980 chunk 114 optimal weight: 9.9990 chunk 205 optimal weight: 4.9990 chunk 80 optimal weight: 0.5980 chunk 236 optimal weight: 0.9980 chunk 248 optimal weight: 4.9990 chunk 261 optimal weight: 0.7980 overall best weight: 0.3958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN A 245 HIS A 314 GLN A 321 GLN A 641 ASN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1125 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.3607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 23692 Z= 0.155 Angle : 0.495 9.445 32228 Z= 0.255 Chirality : 0.043 0.238 3815 Planarity : 0.003 0.056 4100 Dihedral : 5.664 56.135 3907 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.48 % Allowed : 13.63 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.16), residues: 2859 helix: 2.18 (0.20), residues: 694 sheet: 0.30 (0.20), residues: 618 loop : -0.72 (0.15), residues: 1547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP B 633 HIS 0.003 0.000 HIS B 207 PHE 0.024 0.001 PHE B 92 TYR 0.020 0.001 TYR C 396 ARG 0.014 0.000 ARG C 983 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5718 Ramachandran restraints generated. 2859 Oldfield, 0 Emsley, 2859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5718 Ramachandran restraints generated. 2859 Oldfield, 0 Emsley, 2859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 207 time to evaluate : 2.424 Fit side-chains revert: symmetry clash REVERT: A 58 PHE cc_start: 0.7790 (m-80) cc_final: 0.7247 (m-10) REVERT: A 156 GLU cc_start: 0.5735 (pp20) cc_final: 0.5290 (mm-30) REVERT: B 52 GLN cc_start: 0.8185 (tt0) cc_final: 0.7632 (tm-30) outliers start: 62 outliers final: 54 residues processed: 253 average time/residue: 0.3052 time to fit residues: 129.3855 Evaluate side-chains 255 residues out of total 2562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 201 time to evaluate : 2.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 627 ASP Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1105 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 172 optimal weight: 2.9990 chunk 277 optimal weight: 3.9990 chunk 169 optimal weight: 0.5980 chunk 131 optimal weight: 0.9990 chunk 192 optimal weight: 0.1980 chunk 290 optimal weight: 0.9990 chunk 267 optimal weight: 0.6980 chunk 231 optimal weight: 1.9990 chunk 24 optimal weight: 0.0570 chunk 178 optimal weight: 1.9990 chunk 142 optimal weight: 0.0060 overall best weight: 0.3114 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 GLN A 641 ASN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.3665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 23692 Z= 0.145 Angle : 0.490 9.448 32228 Z= 0.252 Chirality : 0.043 0.238 3815 Planarity : 0.003 0.043 4100 Dihedral : 5.438 56.204 3904 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.96 % Allowed : 14.19 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.16), residues: 2859 helix: 2.24 (0.20), residues: 704 sheet: 0.37 (0.20), residues: 606 loop : -0.68 (0.15), residues: 1549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 633 HIS 0.003 0.000 HIS B 207 PHE 0.025 0.001 PHE B 92 TYR 0.018 0.001 TYR A1067 ARG 0.009 0.000 ARG C 983 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5718 Ramachandran restraints generated. 2859 Oldfield, 0 Emsley, 2859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5718 Ramachandran restraints generated. 2859 Oldfield, 0 Emsley, 2859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 207 time to evaluate : 2.666 Fit side-chains revert: symmetry clash REVERT: A 28 TYR cc_start: 0.7970 (m-10) cc_final: 0.7746 (m-10) REVERT: A 58 PHE cc_start: 0.7756 (m-80) cc_final: 0.7246 (m-10) REVERT: A 156 GLU cc_start: 0.5730 (pp20) cc_final: 0.5272 (mm-30) REVERT: A 1119 ASN cc_start: 0.6893 (m-40) cc_final: 0.6602 (m-40) REVERT: B 52 GLN cc_start: 0.8180 (tt0) cc_final: 0.7614 (tm-30) REVERT: B 188 ASN cc_start: 0.5682 (m-40) cc_final: 0.5408 (t0) REVERT: C 439 ASN cc_start: 0.3484 (p0) cc_final: 0.3129 (t0) outliers start: 49 outliers final: 48 residues processed: 247 average time/residue: 0.3070 time to fit residues: 126.5948 Evaluate side-chains 242 residues out of total 2562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 194 time to evaluate : 2.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 627 ASP Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1105 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 184 optimal weight: 1.9990 chunk 246 optimal weight: 0.0570 chunk 70 optimal weight: 1.9990 chunk 213 optimal weight: 0.6980 chunk 34 optimal weight: 3.9990 chunk 64 optimal weight: 0.7980 chunk 232 optimal weight: 0.8980 chunk 97 optimal weight: 9.9990 chunk 238 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 overall best weight: 0.6900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 GLN A 641 ASN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN C 804 GLN ** C1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.173454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.114879 restraints weight = 27306.524| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 2.36 r_work: 0.3198 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.3762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 23692 Z= 0.197 Angle : 0.508 9.446 32228 Z= 0.261 Chirality : 0.044 0.240 3815 Planarity : 0.004 0.058 4100 Dihedral : 5.507 56.125 3904 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.12 % Allowed : 14.15 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.16), residues: 2859 helix: 2.20 (0.20), residues: 693 sheet: 0.34 (0.21), residues: 587 loop : -0.68 (0.15), residues: 1579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 633 HIS 0.003 0.000 HIS B 207 PHE 0.023 0.001 PHE B 92 TYR 0.034 0.001 TYR B 170 ARG 0.016 0.000 ARG C 983 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5370.06 seconds wall clock time: 99 minutes 24.01 seconds (5964.01 seconds total)