Starting phenix.real_space_refine on Sun Jun 30 00:49:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xcj_38245/06_2024/8xcj_38245.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xcj_38245/06_2024/8xcj_38245.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xcj_38245/06_2024/8xcj_38245.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xcj_38245/06_2024/8xcj_38245.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xcj_38245/06_2024/8xcj_38245.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xcj_38245/06_2024/8xcj_38245.pdb" } resolution = 2.98 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= 0.002 sd= 0.088 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 72 5.16 5 C 12528 2.51 5 N 3366 2.21 5 O 3843 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 49": "OE1" <-> "OE2" Residue "A TYR 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 355": "OD1" <-> "OD2" Residue "A ARG 360": "NH1" <-> "NH2" Residue "A ASP 383": "OD1" <-> "OD2" Residue "B GLU 93": "OE1" <-> "OE2" Residue "B ASP 300": "OD1" <-> "OD2" Residue "B ASP 373": "OD1" <-> "OD2" Residue "C GLU 37": "OE1" <-> "OE2" Residue "C GLU 93": "OE1" <-> "OE2" Residue "C ASP 116": "OD1" <-> "OD2" Residue "C ASP 206": "OD1" <-> "OD2" Residue "Z GLU 833": "OE1" <-> "OE2" Residue "Z ASP 952": "OD1" <-> "OD2" Residue "Z ASP 961": "OD1" <-> "OD2" Residue "Z ASP 1031": "OD1" <-> "OD2" Residue "Z GLU 1075": "OE1" <-> "OE2" Residue "J TYR 765": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 927": "OD1" <-> "OD2" Residue "J ASP 996": "OD1" <-> "OD2" Residue "F GLU 846": "OE1" <-> "OE2" Residue "F ASP 961": "OD1" <-> "OD2" Residue "F GLU 1075": "OE1" <-> "OE2" Residue "F ASP 1107": "OD1" <-> "OD2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 19809 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3360 Classifications: {'peptide': 422} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 412} Chain: "B" Number of atoms: 3360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3360 Classifications: {'peptide': 422} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 412} Chain: "C" Number of atoms: 3360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3360 Classifications: {'peptide': 422} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 412} Chain: "Z" Number of atoms: 3243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3243 Classifications: {'peptide': 420} Link IDs: {'PTRANS': 19, 'TRANS': 400} Chain: "J" Number of atoms: 3243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3243 Classifications: {'peptide': 420} Link IDs: {'PTRANS': 19, 'TRANS': 400} Chain: "F" Number of atoms: 3243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3243 Classifications: {'peptide': 420} Link IDs: {'PTRANS': 19, 'TRANS': 400} Time building chain proxies: 11.26, per 1000 atoms: 0.57 Number of scatterers: 19809 At special positions: 0 Unit cell: (111.717, 110.643, 204.098, 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 72 16.00 O 3843 8.00 N 3366 7.00 C 12528 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 38 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 38 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 38 " 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 Time building additional restraints: 6.91 Conformation dependent library (CDL) restraints added in 3.4 seconds 5028 Ramachandran restraints generated. 2514 Oldfield, 0 Emsley, 2514 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4590 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 31 sheets defined 5.1% alpha, 44.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.68 Creating SS restraints... Processing helix chain 'A' and resid 159 through 163 Processing helix chain 'A' and resid 397 through 401 removed outlier: 3.662A pdb=" N GLY A 400 " --> pdb=" O ASP A 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 163 Processing helix chain 'B' and resid 239 through 241 No H-bonds generated for 'chain 'B' and resid 239 through 241' Processing helix chain 'B' and resid 397 through 401 Processing helix chain 'C' and resid 159 through 163 Processing helix chain 'C' and resid 397 through 401 removed outlier: 4.126A pdb=" N GLY C 400 " --> pdb=" O ASP C 397 " (cutoff:3.500A) Processing helix chain 'Z' and resid 758 through 763 Processing helix chain 'Z' and resid 810 through 824 removed outlier: 3.549A pdb=" N ASP Z 816 " --> pdb=" O GLU Z 812 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N PHE Z 817 " --> pdb=" O GLY Z 813 " (cutoff:3.500A) Processing helix chain 'Z' and resid 827 through 832 Processing helix chain 'Z' and resid 907 through 911 Processing helix chain 'J' and resid 758 through 763 removed outlier: 3.618A pdb=" N SER J 762 " --> pdb=" O GLN J 758 " (cutoff:3.500A) Processing helix chain 'J' and resid 811 through 824 Processing helix chain 'J' and resid 825 through 831 Processing helix chain 'J' and resid 907 through 911 Processing helix chain 'F' and resid 758 through 763 Processing helix chain 'F' and resid 810 through 824 Processing helix chain 'F' and resid 827 through 832 Processing helix chain 'F' and resid 907 through 911 Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 14 removed outlier: 3.836A pdb=" N LEU A 46 " --> pdb=" O THR A 62 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N THR A 62 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N PHE A 58 " --> pdb=" O VAL A 50 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N LYS A 52 " --> pdb=" O LYS A 56 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N LYS A 56 " --> pdb=" O LYS A 52 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ALA A 65 " --> pdb=" O PHE A 81 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N PHE A 81 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASN A 131 " --> pdb=" O LEU A 139 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N LEU A 139 " --> pdb=" O ASN A 131 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLY A 150 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N ASN A 165 " --> pdb=" O GLY A 150 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ALA A 168 " --> pdb=" O ASN A 197 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N LEU A 187 " --> pdb=" O GLN A 178 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N GLU A 180 " --> pdb=" O GLY A 185 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N GLY A 185 " --> pdb=" O GLU A 180 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N GLY A 267 " --> pdb=" O ASP A 237 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 110 through 112 removed outlier: 6.818A pdb=" N HIS A 110 " --> pdb=" O TYR A 119 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 252 through 254 Processing sheet with id=AA4, first strand: chain 'A' and resid 376 through 378 Processing sheet with id=AA5, first strand: chain 'B' and resid 2 through 14 removed outlier: 3.599A pdb=" N LEU B 46 " --> pdb=" O THR B 62 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR B 62 " --> pdb=" O LEU B 46 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N PHE B 58 " --> pdb=" O VAL B 50 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N LYS B 52 " --> pdb=" O LYS B 56 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N LYS B 56 " --> pdb=" O LYS B 52 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N SER B 57 " --> pdb=" O GLY B 88 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N GLY B 88 " --> pdb=" O SER B 57 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N TYR B 59 " --> pdb=" O VAL B 86 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N VAL B 86 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ASP B 61 " --> pdb=" O ALA B 84 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ALA B 84 " --> pdb=" O ASP B 61 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ASN B 63 " --> pdb=" O ARG B 82 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N LEU B 139 " --> pdb=" O ASN B 131 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLY B 150 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N ASN B 165 " --> pdb=" O GLY B 150 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ALA B 168 " --> pdb=" O ASN B 197 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N LEU B 187 " --> pdb=" O GLN B 178 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N GLU B 180 " --> pdb=" O GLY B 185 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N GLY B 185 " --> pdb=" O GLU B 180 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N GLY B 267 " --> pdb=" O ASP B 237 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 110 through 112 removed outlier: 6.879A pdb=" N HIS B 110 " --> pdb=" O TYR B 119 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 252 through 254 Processing sheet with id=AA8, first strand: chain 'B' and resid 376 through 378 Processing sheet with id=AA9, first strand: chain 'C' and resid 2 through 14 removed outlier: 3.755A pdb=" N LEU C 46 " --> pdb=" O THR C 62 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N THR C 62 " --> pdb=" O LEU C 46 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N PHE C 58 " --> pdb=" O VAL C 50 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N LYS C 52 " --> pdb=" O LYS C 56 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N LYS C 56 " --> pdb=" O LYS C 52 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ALA C 65 " --> pdb=" O PHE C 81 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N PHE C 81 " --> pdb=" O ALA C 65 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N LEU C 139 " --> pdb=" O ASN C 131 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N GLY C 150 " --> pdb=" O ASN C 165 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N ASN C 165 " --> pdb=" O GLY C 150 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ALA C 168 " --> pdb=" O ASN C 197 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N LEU C 187 " --> pdb=" O GLN C 178 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N GLU C 180 " --> pdb=" O GLY C 185 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N GLY C 185 " --> pdb=" O GLU C 180 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N GLY C 267 " --> pdb=" O ASP C 237 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 110 through 112 removed outlier: 6.849A pdb=" N HIS C 110 " --> pdb=" O TYR C 119 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 252 through 254 Processing sheet with id=AB3, first strand: chain 'C' and resid 376 through 378 Processing sheet with id=AB4, first strand: chain 'Z' and resid 719 through 725 Processing sheet with id=AB5, first strand: chain 'Z' and resid 764 through 769 removed outlier: 5.157A pdb=" N TYR Z 765 " --> pdb=" O PHE Z 748 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N PHE Z 748 " --> pdb=" O TYR Z 765 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'Z' and resid 843 through 845 WARNING: can't find start of bonding for strands! previous: chain 'Z' and resid 843 through 845 current: chain 'Z' and resid 859 through 871 removed outlier: 8.269A pdb=" N TRP Z 859 " --> pdb=" O ASP Z 886 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N ASP Z 886 " --> pdb=" O TRP Z 859 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'Z' and resid 891 through 898 current: chain 'Z' and resid 914 through 918 WARNING: can't find start of bonding for strands! previous: chain 'Z' and resid 923 through 925 current: chain 'Z' and resid 948 through 949 WARNING: can't find start of bonding for strands! previous: chain 'Z' and resid 954 through 957 current: chain 'J' and resid 859 through 871 removed outlier: 8.281A pdb=" N TRP J 859 " --> pdb=" O ASP J 886 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N ASP J 886 " --> pdb=" O TRP J 859 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 890 through 898 current: chain 'J' and resid 914 through 918 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 923 through 925 current: chain 'J' and resid 948 through 949 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 954 through 957 current: chain 'F' and resid 859 through 871 removed outlier: 8.440A pdb=" N TRP F 859 " --> pdb=" O ASP F 886 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N ASP F 886 " --> pdb=" O TRP F 859 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 890 through 898 current: chain 'F' and resid 914 through 919 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 922 through 925 current: chain 'F' and resid 948 through 949 Processing sheet with id=AB7, first strand: chain 'Z' and resid 999 through 1003 WARNING: can't find start of bonding for strands! previous: chain 'Z' and resid 999 through 1003 current: chain 'Z' and resid 1078 through 1086 No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'Z' and resid 1007 through 1010 Processing sheet with id=AB9, first strand: chain 'Z' and resid 1066 through 1073 removed outlier: 5.349A pdb=" N VAL Z1067 " --> pdb=" O MET Z1063 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N MET Z1063 " --> pdb=" O VAL Z1067 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'Z' and resid 1044 through 1048 Processing sheet with id=AC2, first strand: chain 'Z' and resid 1129 through 1132 removed outlier: 6.314A pdb=" N MET F1063 " --> pdb=" O VAL F1067 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N VAL F1067 " --> pdb=" O MET F1063 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'J' and resid 719 through 721 Processing sheet with id=AC4, first strand: chain 'J' and resid 764 through 769 removed outlier: 5.250A pdb=" N TYR J 765 " --> pdb=" O PHE J 748 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N PHE J 748 " --> pdb=" O TYR J 765 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'J' and resid 999 through 1003 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 999 through 1003 current: chain 'J' and resid 1078 through 1086 No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'J' and resid 1007 through 1010 Processing sheet with id=AC7, first strand: chain 'J' and resid 1066 through 1073 removed outlier: 6.448A pdb=" N VAL J1061 " --> pdb=" O ILE J1068 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ASP J1070 " --> pdb=" O LEU J1059 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N LEU J1059 " --> pdb=" O ASP J1070 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ALA J1072 " --> pdb=" O CYS J1057 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N CYS J1057 " --> pdb=" O ALA J1072 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'J' and resid 1044 through 1048 Processing sheet with id=AC9, first strand: chain 'F' and resid 719 through 721 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 719 through 721 current: chain 'F' and resid 728 through 734 Processing sheet with id=AD1, first strand: chain 'F' and resid 764 through 769 removed outlier: 5.422A pdb=" N TYR F 765 " --> pdb=" O PHE F 748 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N PHE F 748 " --> pdb=" O TYR F 765 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 999 through 1003 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 999 through 1003 current: chain 'F' and resid 1078 through 1086 No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'F' and resid 1007 through 1010 Processing sheet with id=AD4, first strand: chain 'F' and resid 1044 through 1048 875 hydrogen bonds defined for protein. 2355 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: 6.48 Time building geometry restraints manager: 7.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.29: 3384 1.29 - 1.42: 5593 1.42 - 1.55: 11188 1.55 - 1.68: 4 1.68 - 1.82: 132 Bond restraints: 20301 Sorted by residual: bond pdb=" CA SER A 359 " pdb=" CB SER A 359 " ideal model delta sigma weight residual 1.528 1.414 0.114 1.49e-02 4.50e+03 5.88e+01 bond pdb=" CA SER C 359 " pdb=" CB SER C 359 " ideal model delta sigma weight residual 1.527 1.435 0.092 1.38e-02 5.25e+03 4.41e+01 bond pdb=" C ILE A 363 " pdb=" O ILE A 363 " ideal model delta sigma weight residual 1.238 1.165 0.072 1.09e-02 8.42e+03 4.37e+01 bond pdb=" C PRO B 361 " pdb=" O PRO B 361 " ideal model delta sigma weight residual 1.235 1.152 0.083 1.30e-02 5.92e+03 4.06e+01 bond pdb=" C PRO C 361 " pdb=" O PRO C 361 " ideal model delta sigma weight residual 1.235 1.156 0.079 1.30e-02 5.92e+03 3.66e+01 ... (remaining 20296 not shown) Histogram of bond angle deviations from ideal: 90.70 - 99.41: 14 99.41 - 108.12: 1012 108.12 - 116.83: 13423 116.83 - 125.53: 12689 125.53 - 134.24: 426 Bond angle restraints: 27564 Sorted by residual: angle pdb=" N PRO Z 944 " pdb=" CA PRO Z 944 " pdb=" CB PRO Z 944 " ideal model delta sigma weight residual 103.08 90.70 12.38 9.70e-01 1.06e+00 1.63e+02 angle pdb=" N PRO J 944 " pdb=" CA PRO J 944 " pdb=" CB PRO J 944 " ideal model delta sigma weight residual 103.08 91.50 11.58 9.70e-01 1.06e+00 1.43e+02 angle pdb=" N PRO F 944 " pdb=" CA PRO F 944 " pdb=" CB PRO F 944 " ideal model delta sigma weight residual 103.08 91.59 11.49 9.70e-01 1.06e+00 1.40e+02 angle pdb=" C PRO F 944 " pdb=" CA PRO F 944 " pdb=" CB PRO F 944 " ideal model delta sigma weight residual 110.92 122.08 -11.16 1.22e+00 6.72e-01 8.37e+01 angle pdb=" N ASN Z 943 " pdb=" CA ASN Z 943 " pdb=" C ASN Z 943 " ideal model delta sigma weight residual 109.83 98.76 11.07 1.27e+00 6.20e-01 7.60e+01 ... (remaining 27559 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.61: 9934 17.61 - 35.23: 1307 35.23 - 52.84: 413 52.84 - 70.45: 104 70.45 - 88.06: 38 Dihedral angle restraints: 11796 sinusoidal: 4578 harmonic: 7218 Sorted by residual: dihedral pdb=" C ARG A 360 " pdb=" N ARG A 360 " pdb=" CA ARG A 360 " pdb=" CB ARG A 360 " ideal model delta harmonic sigma weight residual -122.60 -140.21 17.61 0 2.50e+00 1.60e-01 4.96e+01 dihedral pdb=" N ARG A 360 " pdb=" C ARG A 360 " pdb=" CA ARG A 360 " pdb=" CB ARG A 360 " ideal model delta harmonic sigma weight residual 122.80 139.53 -16.73 0 2.50e+00 1.60e-01 4.48e+01 dihedral pdb=" C ARG C 360 " pdb=" N ARG C 360 " pdb=" CA ARG C 360 " pdb=" CB ARG C 360 " ideal model delta harmonic sigma weight residual -122.60 -138.41 15.81 0 2.50e+00 1.60e-01 4.00e+01 ... (remaining 11793 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.153: 2903 0.153 - 0.306: 4 0.306 - 0.458: 0 0.458 - 0.611: 0 0.611 - 0.764: 3 Chirality restraints: 2910 Sorted by residual: chirality pdb=" CA ARG A 360 " pdb=" N ARG A 360 " pdb=" C ARG A 360 " pdb=" CB ARG A 360 " both_signs ideal model delta sigma weight residual False 2.51 1.75 0.76 2.00e-01 2.50e+01 1.46e+01 chirality pdb=" CA ARG C 360 " pdb=" N ARG C 360 " pdb=" C ARG C 360 " pdb=" CB ARG C 360 " both_signs ideal model delta sigma weight residual False 2.51 1.82 0.69 2.00e-01 2.50e+01 1.19e+01 chirality pdb=" CA ARG B 360 " pdb=" N ARG B 360 " pdb=" C ARG B 360 " pdb=" CB ARG B 360 " both_signs ideal model delta sigma weight residual False 2.51 1.86 0.65 2.00e-01 2.50e+01 1.05e+01 ... (remaining 2907 not shown) Planarity restraints: 3603 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE C 357 " -0.018 2.00e-02 2.50e+03 3.59e-02 1.29e+01 pdb=" C ILE C 357 " 0.062 2.00e-02 2.50e+03 pdb=" O ILE C 357 " -0.023 2.00e-02 2.50e+03 pdb=" N TRP C 358 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN F 943 " 0.061 5.00e-02 4.00e+02 8.89e-02 1.26e+01 pdb=" N PRO F 944 " -0.154 5.00e-02 4.00e+02 pdb=" CA PRO F 944 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO F 944 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN Z 943 " -0.060 5.00e-02 4.00e+02 8.80e-02 1.24e+01 pdb=" N PRO Z 944 " 0.152 5.00e-02 4.00e+02 pdb=" CA PRO Z 944 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO Z 944 " -0.047 5.00e-02 4.00e+02 ... (remaining 3600 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 596 2.69 - 3.24: 17416 3.24 - 3.80: 31298 3.80 - 4.35: 43618 4.35 - 4.90: 74680 Nonbonded interactions: 167608 Sorted by model distance: nonbonded pdb=" OG1 THR A 14 " pdb=" O GLU A 19 " model vdw 2.138 2.440 nonbonded pdb=" OD2 ASP B 383 " pdb=" OH TYR F1111 " model vdw 2.145 2.440 nonbonded pdb=" O ARG C 360 " pdb=" C PRO C 361 " model vdw 2.151 3.270 nonbonded pdb=" O ARG A 360 " pdb=" C PRO A 361 " model vdw 2.161 3.270 nonbonded pdb=" OD1 ASP B 162 " pdb=" OH TYR Z1058 " model vdw 2.169 2.440 ... (remaining 167603 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'F' selection = chain 'J' selection = chain 'Z' } 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: 4.210 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: 0.010 Extract box with map and model: 10.460 Check model and map are aligned: 0.150 Set scattering table: 0.220 Process input model: 49.900 Find NCS groups from input model: 0.980 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.114 20301 Z= 0.263 Angle : 0.694 12.380 27564 Z= 0.431 Chirality : 0.051 0.764 2910 Planarity : 0.005 0.089 3603 Dihedral : 18.494 88.062 7197 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.64 % Allowed : 3.26 % Favored : 96.10 % Rotamer: Outliers : 6.95 % Allowed : 27.21 % Favored : 65.85 % Cbeta Deviations : 0.26 % 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: -0.54 (0.16), residues: 2514 helix: -1.58 (0.55), residues: 96 sheet: 0.68 (0.15), residues: 1175 loop : -1.33 (0.16), residues: 1243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP Z 863 HIS 0.003 0.001 HIS B 268 PHE 0.011 0.001 PHE J1041 TYR 0.013 0.001 TYR Z 786 ARG 0.005 0.000 ARG A 360 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5028 Ramachandran restraints generated. 2514 Oldfield, 0 Emsley, 2514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5028 Ramachandran restraints generated. 2514 Oldfield, 0 Emsley, 2514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 147 time to evaluate : 2.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 ASN cc_start: 0.8813 (p0) cc_final: 0.8519 (p0) REVERT: Z 997 ILE cc_start: 0.7793 (OUTLIER) cc_final: 0.7430 (pp) outliers start: 144 outliers final: 129 residues processed: 287 average time/residue: 0.9034 time to fit residues: 308.6858 Evaluate side-chains 267 residues out of total 2073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 137 time to evaluate : 2.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 VAL Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 89 LYS Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 210 LYS Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 315 LYS Chi-restraints excluded: chain A residue 342 GLN Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 360 ARG Chi-restraints excluded: chain A residue 381 ASN Chi-restraints excluded: chain A residue 384 SER Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 157 SER Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 335 ARG Chi-restraints excluded: chain B residue 360 ARG Chi-restraints excluded: chain C residue 89 LYS Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 153 SER Chi-restraints excluded: chain C residue 166 GLU Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 209 SER Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 317 THR Chi-restraints excluded: chain C residue 360 ARG Chi-restraints excluded: chain C residue 384 SER Chi-restraints excluded: chain Z residue 729 ILE Chi-restraints excluded: chain Z residue 734 HIS Chi-restraints excluded: chain Z residue 800 PHE Chi-restraints excluded: chain Z residue 804 VAL Chi-restraints excluded: chain Z residue 845 LEU Chi-restraints excluded: chain Z residue 852 TRP Chi-restraints excluded: chain Z residue 868 GLU Chi-restraints excluded: chain Z residue 877 VAL Chi-restraints excluded: chain Z residue 921 ASN Chi-restraints excluded: chain Z residue 930 LEU Chi-restraints excluded: chain Z residue 944 PRO Chi-restraints excluded: chain Z residue 956 THR Chi-restraints excluded: chain Z residue 982 CYS Chi-restraints excluded: chain Z residue 997 ILE Chi-restraints excluded: chain Z residue 1021 THR Chi-restraints excluded: chain Z residue 1024 VAL Chi-restraints excluded: chain Z residue 1025 THR Chi-restraints excluded: chain Z residue 1049 SER Chi-restraints excluded: chain Z residue 1077 VAL Chi-restraints excluded: chain Z residue 1096 THR Chi-restraints excluded: chain Z residue 1100 THR Chi-restraints excluded: chain Z residue 1102 THR Chi-restraints excluded: chain Z residue 1103 ARG Chi-restraints excluded: chain Z residue 1105 SER Chi-restraints excluded: chain Z residue 1117 VAL Chi-restraints excluded: chain Z residue 1129 ILE Chi-restraints excluded: chain J residue 723 THR Chi-restraints excluded: chain J residue 728 GLN Chi-restraints excluded: chain J residue 801 VAL Chi-restraints excluded: chain J residue 804 VAL Chi-restraints excluded: chain J residue 824 GLU Chi-restraints excluded: chain J residue 854 ASP Chi-restraints excluded: chain J residue 867 ILE Chi-restraints excluded: chain J residue 870 THR Chi-restraints excluded: chain J residue 877 VAL Chi-restraints excluded: chain J residue 887 THR Chi-restraints excluded: chain J residue 892 LEU Chi-restraints excluded: chain J residue 944 PRO Chi-restraints excluded: chain J residue 952 ASP Chi-restraints excluded: chain J residue 956 THR Chi-restraints excluded: chain J residue 998 VAL Chi-restraints excluded: chain J residue 1012 SER Chi-restraints excluded: chain J residue 1019 THR Chi-restraints excluded: chain J residue 1021 THR Chi-restraints excluded: chain J residue 1023 THR Chi-restraints excluded: chain J residue 1025 THR Chi-restraints excluded: chain J residue 1103 ARG Chi-restraints excluded: chain J residue 1117 VAL Chi-restraints excluded: chain J residue 1121 VAL Chi-restraints excluded: chain F residue 751 LYS Chi-restraints excluded: chain F residue 776 SER Chi-restraints excluded: chain F residue 784 ASP Chi-restraints excluded: chain F residue 801 VAL Chi-restraints excluded: chain F residue 849 SER Chi-restraints excluded: chain F residue 880 ILE Chi-restraints excluded: chain F residue 889 GLU Chi-restraints excluded: chain F residue 905 ILE Chi-restraints excluded: chain F residue 928 VAL Chi-restraints excluded: chain F residue 939 THR Chi-restraints excluded: chain F residue 940 SER Chi-restraints excluded: chain F residue 944 PRO Chi-restraints excluded: chain F residue 955 LEU Chi-restraints excluded: chain F residue 981 ASN Chi-restraints excluded: chain F residue 987 THR Chi-restraints excluded: chain F residue 993 ILE Chi-restraints excluded: chain F residue 1011 SER Chi-restraints excluded: chain F residue 1025 THR Chi-restraints excluded: chain F residue 1035 VAL Chi-restraints excluded: chain F residue 1040 THR Chi-restraints excluded: chain F residue 1052 THR Chi-restraints excluded: chain F residue 1100 THR Chi-restraints excluded: chain F residue 1103 ARG Chi-restraints excluded: chain F residue 1117 VAL Chi-restraints excluded: chain F residue 1121 VAL Chi-restraints excluded: chain F residue 1129 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 212 optimal weight: 4.9990 chunk 191 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 128 optimal weight: 10.0000 chunk 102 optimal weight: 0.9990 chunk 197 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 120 optimal weight: 2.9990 chunk 147 optimal weight: 2.9990 chunk 228 optimal weight: 7.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 860 ASN J 909 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.0698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.099 20301 Z= 0.460 Angle : 0.637 9.149 27564 Z= 0.346 Chirality : 0.049 0.226 2910 Planarity : 0.006 0.142 3603 Dihedral : 10.312 143.417 2947 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.44 % Allowed : 4.26 % Favored : 95.31 % Rotamer: Outliers : 7.72 % Allowed : 25.57 % Favored : 66.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.57 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.16), residues: 2514 helix: -2.04 (0.49), residues: 102 sheet: 0.60 (0.15), residues: 1187 loop : -1.43 (0.16), residues: 1225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP Z 863 HIS 0.007 0.001 HIS A 113 PHE 0.016 0.002 PHE J1041 TYR 0.022 0.002 TYR C 163 ARG 0.004 0.001 ARG F1009 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5028 Ramachandran restraints generated. 2514 Oldfield, 0 Emsley, 2514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5028 Ramachandran restraints generated. 2514 Oldfield, 0 Emsley, 2514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 127 time to evaluate : 2.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.8065 (mt) REVERT: A 356 SER cc_start: 0.9273 (OUTLIER) cc_final: 0.8943 (t) REVERT: A 417 MET cc_start: 0.9304 (pp-130) cc_final: 0.8751 (pp-130) REVERT: B 39 GLU cc_start: 0.8822 (OUTLIER) cc_final: 0.7014 (pp20) REVERT: Z 997 ILE cc_start: 0.7752 (OUTLIER) cc_final: 0.7307 (pp) REVERT: J 1032 ARG cc_start: 0.6986 (OUTLIER) cc_final: 0.6271 (mtp180) REVERT: F 784 ASP cc_start: 0.7367 (OUTLIER) cc_final: 0.7072 (p0) REVERT: F 989 ARG cc_start: 0.7473 (OUTLIER) cc_final: 0.6816 (ttp80) outliers start: 160 outliers final: 93 residues processed: 275 average time/residue: 0.9896 time to fit residues: 318.4165 Evaluate side-chains 221 residues out of total 2073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 121 time to evaluate : 2.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 VAL Chi-restraints excluded: chain A residue 55 ASP Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 89 LYS Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 210 LYS Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 360 ARG Chi-restraints excluded: chain A residue 381 ASN Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 39 GLU Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 360 ARG Chi-restraints excluded: chain C residue 89 LYS Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 209 SER Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain C residue 317 THR Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 360 ARG Chi-restraints excluded: chain Z residue 734 HIS Chi-restraints excluded: chain Z residue 800 PHE Chi-restraints excluded: chain Z residue 804 VAL Chi-restraints excluded: chain Z residue 845 LEU Chi-restraints excluded: chain Z residue 852 TRP Chi-restraints excluded: chain Z residue 853 LYS Chi-restraints excluded: chain Z residue 862 MET Chi-restraints excluded: chain Z residue 868 GLU Chi-restraints excluded: chain Z residue 923 ILE Chi-restraints excluded: chain Z residue 982 CYS Chi-restraints excluded: chain Z residue 997 ILE Chi-restraints excluded: chain Z residue 1049 SER Chi-restraints excluded: chain Z residue 1052 THR Chi-restraints excluded: chain Z residue 1077 VAL Chi-restraints excluded: chain Z residue 1100 THR Chi-restraints excluded: chain Z residue 1102 THR Chi-restraints excluded: chain Z residue 1117 VAL Chi-restraints excluded: chain J residue 728 GLN Chi-restraints excluded: chain J residue 801 VAL Chi-restraints excluded: chain J residue 804 VAL Chi-restraints excluded: chain J residue 824 GLU Chi-restraints excluded: chain J residue 827 LEU Chi-restraints excluded: chain J residue 838 THR Chi-restraints excluded: chain J residue 854 ASP Chi-restraints excluded: chain J residue 867 ILE Chi-restraints excluded: chain J residue 877 VAL Chi-restraints excluded: chain J residue 892 LEU Chi-restraints excluded: chain J residue 893 SER Chi-restraints excluded: chain J residue 952 ASP Chi-restraints excluded: chain J residue 955 LEU Chi-restraints excluded: chain J residue 998 VAL Chi-restraints excluded: chain J residue 1012 SER Chi-restraints excluded: chain J residue 1023 THR Chi-restraints excluded: chain J residue 1025 THR Chi-restraints excluded: chain J residue 1032 ARG Chi-restraints excluded: chain J residue 1103 ARG Chi-restraints excluded: chain J residue 1117 VAL Chi-restraints excluded: chain J residue 1121 VAL Chi-restraints excluded: chain F residue 784 ASP Chi-restraints excluded: chain F residue 804 VAL Chi-restraints excluded: chain F residue 868 GLU Chi-restraints excluded: chain F residue 880 ILE Chi-restraints excluded: chain F residue 928 VAL Chi-restraints excluded: chain F residue 939 THR Chi-restraints excluded: chain F residue 940 SER Chi-restraints excluded: chain F residue 955 LEU Chi-restraints excluded: chain F residue 981 ASN Chi-restraints excluded: chain F residue 987 THR Chi-restraints excluded: chain F residue 989 ARG Chi-restraints excluded: chain F residue 1035 VAL Chi-restraints excluded: chain F residue 1040 THR Chi-restraints excluded: chain F residue 1052 THR Chi-restraints excluded: chain F residue 1099 LEU Chi-restraints excluded: chain F residue 1100 THR Chi-restraints excluded: chain F residue 1103 ARG Chi-restraints excluded: chain F residue 1117 VAL Chi-restraints excluded: chain F residue 1121 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 127 optimal weight: 6.9990 chunk 71 optimal weight: 1.9990 chunk 190 optimal weight: 0.5980 chunk 155 optimal weight: 0.6980 chunk 63 optimal weight: 0.9980 chunk 229 optimal weight: 2.9990 chunk 247 optimal weight: 4.9990 chunk 204 optimal weight: 0.0770 chunk 227 optimal weight: 5.9990 chunk 78 optimal weight: 0.8980 chunk 183 optimal weight: 10.0000 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN C 169 ASN C 340 ASN Z 860 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.0629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.097 20301 Z= 0.183 Angle : 0.512 8.705 27564 Z= 0.282 Chirality : 0.045 0.162 2910 Planarity : 0.005 0.137 3603 Dihedral : 8.068 59.406 2861 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.40 % Allowed : 3.70 % Favored : 95.90 % Rotamer: Outliers : 6.13 % Allowed : 26.58 % Favored : 67.29 % 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: -0.49 (0.16), residues: 2514 helix: -1.64 (0.53), residues: 96 sheet: 0.68 (0.15), residues: 1176 loop : -1.24 (0.17), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP Z 863 HIS 0.002 0.000 HIS B 268 PHE 0.011 0.001 PHE Z 848 TYR 0.012 0.001 TYR B 32 ARG 0.006 0.000 ARG B 335 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5028 Ramachandran restraints generated. 2514 Oldfield, 0 Emsley, 2514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5028 Ramachandran restraints generated. 2514 Oldfield, 0 Emsley, 2514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 155 time to evaluate : 2.207 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 11 ILE cc_start: 0.9112 (OUTLIER) cc_final: 0.8755 (tp) REVERT: A 340 ASN cc_start: 0.8695 (p0) cc_final: 0.8266 (p0) REVERT: A 355 ASP cc_start: 0.8433 (p0) cc_final: 0.8167 (p0) REVERT: B 39 GLU cc_start: 0.8693 (OUTLIER) cc_final: 0.7396 (pp20) REVERT: B 116 ASP cc_start: 0.8695 (t0) cc_final: 0.8403 (t0) REVERT: B 179 MET cc_start: 0.9206 (OUTLIER) cc_final: 0.8996 (mtp) REVERT: Z 751 LYS cc_start: 0.8665 (tppt) cc_final: 0.8458 (tppp) REVERT: Z 831 LEU cc_start: 0.7198 (OUTLIER) cc_final: 0.6821 (tt) REVERT: Z 852 TRP cc_start: 0.6913 (OUTLIER) cc_final: 0.5456 (p-90) REVERT: Z 997 ILE cc_start: 0.7665 (OUTLIER) cc_final: 0.7243 (pp) REVERT: Z 1009 ARG cc_start: 0.8993 (OUTLIER) cc_final: 0.8030 (ptm-80) REVERT: J 809 ASP cc_start: 0.8446 (m-30) cc_final: 0.7829 (p0) REVERT: F 844 ARG cc_start: 0.7349 (ptm160) cc_final: 0.6594 (ptt180) outliers start: 127 outliers final: 69 residues processed: 269 average time/residue: 0.9386 time to fit residues: 299.5428 Evaluate side-chains 218 residues out of total 2073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 142 time to evaluate : 2.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 VAL Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 89 LYS Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 210 LYS Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 381 ASN Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 39 GLU Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 360 ARG Chi-restraints excluded: chain C residue 89 LYS Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 209 SER Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain Z residue 800 PHE Chi-restraints excluded: chain Z residue 804 VAL Chi-restraints excluded: chain Z residue 831 LEU Chi-restraints excluded: chain Z residue 845 LEU Chi-restraints excluded: chain Z residue 852 TRP Chi-restraints excluded: chain Z residue 862 MET Chi-restraints excluded: chain Z residue 877 VAL Chi-restraints excluded: chain Z residue 987 THR Chi-restraints excluded: chain Z residue 997 ILE Chi-restraints excluded: chain Z residue 1009 ARG Chi-restraints excluded: chain Z residue 1100 THR Chi-restraints excluded: chain Z residue 1102 THR Chi-restraints excluded: chain Z residue 1117 VAL Chi-restraints excluded: chain Z residue 1129 ILE Chi-restraints excluded: chain J residue 804 VAL Chi-restraints excluded: chain J residue 810 ASP Chi-restraints excluded: chain J residue 824 GLU Chi-restraints excluded: chain J residue 827 LEU Chi-restraints excluded: chain J residue 838 THR Chi-restraints excluded: chain J residue 854 ASP Chi-restraints excluded: chain J residue 867 ILE Chi-restraints excluded: chain J residue 870 THR Chi-restraints excluded: chain J residue 892 LEU Chi-restraints excluded: chain J residue 948 SER Chi-restraints excluded: chain J residue 998 VAL Chi-restraints excluded: chain J residue 1103 ARG Chi-restraints excluded: chain J residue 1117 VAL Chi-restraints excluded: chain F residue 721 GLU Chi-restraints excluded: chain F residue 732 THR Chi-restraints excluded: chain F residue 804 VAL Chi-restraints excluded: chain F residue 880 ILE Chi-restraints excluded: chain F residue 928 VAL Chi-restraints excluded: chain F residue 939 THR Chi-restraints excluded: chain F residue 940 SER Chi-restraints excluded: chain F residue 981 ASN Chi-restraints excluded: chain F residue 987 THR Chi-restraints excluded: chain F residue 1035 VAL Chi-restraints excluded: chain F residue 1040 THR Chi-restraints excluded: chain F residue 1100 THR Chi-restraints excluded: chain F residue 1129 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 226 optimal weight: 5.9990 chunk 172 optimal weight: 20.0000 chunk 118 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 109 optimal weight: 5.9990 chunk 153 optimal weight: 4.9990 chunk 230 optimal weight: 0.6980 chunk 243 optimal weight: 5.9990 chunk 120 optimal weight: 0.7980 chunk 218 optimal weight: 20.0000 chunk 65 optimal weight: 3.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 HIS B 340 ASN Z 860 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.0939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.087 20301 Z= 0.469 Angle : 0.634 8.777 27564 Z= 0.344 Chirality : 0.049 0.247 2910 Planarity : 0.006 0.137 3603 Dihedral : 7.932 59.331 2814 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.40 % Allowed : 4.30 % Favored : 95.31 % Rotamer: Outliers : 7.43 % Allowed : 26.05 % Favored : 66.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.19 % 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: -0.66 (0.16), residues: 2514 helix: -2.03 (0.48), residues: 103 sheet: 0.60 (0.15), residues: 1190 loop : -1.38 (0.16), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP Z 863 HIS 0.006 0.001 HIS A 113 PHE 0.018 0.002 PHE Z 848 TYR 0.020 0.002 TYR C 163 ARG 0.005 0.001 ARG B 335 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5028 Ramachandran restraints generated. 2514 Oldfield, 0 Emsley, 2514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5028 Ramachandran restraints generated. 2514 Oldfield, 0 Emsley, 2514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 132 time to evaluate : 2.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 ILE cc_start: 0.9213 (OUTLIER) cc_final: 0.8741 (tp) REVERT: A 37 GLU cc_start: 0.8806 (OUTLIER) cc_final: 0.7699 (mm-30) REVERT: A 95 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.8106 (mt) REVERT: A 355 ASP cc_start: 0.8517 (p0) cc_final: 0.8241 (p0) REVERT: B 39 GLU cc_start: 0.8807 (OUTLIER) cc_final: 0.7292 (pp20) REVERT: B 179 MET cc_start: 0.9211 (OUTLIER) cc_final: 0.9008 (mtp) REVERT: B 371 LYS cc_start: 0.9396 (OUTLIER) cc_final: 0.8689 (tttp) REVERT: Z 751 LYS cc_start: 0.8709 (tppt) cc_final: 0.8043 (tmmm) REVERT: Z 852 TRP cc_start: 0.6939 (OUTLIER) cc_final: 0.5406 (p-90) REVERT: Z 853 LYS cc_start: 0.7025 (OUTLIER) cc_final: 0.6607 (tptm) REVERT: Z 962 ILE cc_start: 0.8353 (OUTLIER) cc_final: 0.8108 (mt) REVERT: J 728 GLN cc_start: 0.8352 (OUTLIER) cc_final: 0.8150 (tm-30) REVERT: J 809 ASP cc_start: 0.8598 (m-30) cc_final: 0.7810 (p0) REVERT: J 954 LYS cc_start: 0.8940 (OUTLIER) cc_final: 0.8594 (tptp) REVERT: J 1032 ARG cc_start: 0.6871 (OUTLIER) cc_final: 0.6176 (mtp180) REVERT: J 1042 ARG cc_start: 0.8445 (OUTLIER) cc_final: 0.7791 (ttm170) REVERT: F 784 ASP cc_start: 0.7319 (OUTLIER) cc_final: 0.7075 (p0) REVERT: F 1063 MET cc_start: 0.8536 (OUTLIER) cc_final: 0.7537 (tpt) outliers start: 154 outliers final: 93 residues processed: 271 average time/residue: 0.9701 time to fit residues: 307.5919 Evaluate side-chains 233 residues out of total 2073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 125 time to evaluate : 2.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 VAL Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 55 ASP Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 89 LYS Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 210 LYS Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 381 ASN Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 39 GLU Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 157 SER Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 360 ARG Chi-restraints excluded: chain B residue 371 LYS Chi-restraints excluded: chain C residue 89 LYS Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 209 SER Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain C residue 317 THR Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain Z residue 734 HIS Chi-restraints excluded: chain Z residue 753 ILE Chi-restraints excluded: chain Z residue 804 VAL Chi-restraints excluded: chain Z residue 845 LEU Chi-restraints excluded: chain Z residue 852 TRP Chi-restraints excluded: chain Z residue 853 LYS Chi-restraints excluded: chain Z residue 862 MET Chi-restraints excluded: chain Z residue 877 VAL Chi-restraints excluded: chain Z residue 923 ILE Chi-restraints excluded: chain Z residue 956 THR Chi-restraints excluded: chain Z residue 962 ILE Chi-restraints excluded: chain Z residue 997 ILE Chi-restraints excluded: chain Z residue 1021 THR Chi-restraints excluded: chain Z residue 1052 THR Chi-restraints excluded: chain Z residue 1077 VAL Chi-restraints excluded: chain Z residue 1100 THR Chi-restraints excluded: chain Z residue 1102 THR Chi-restraints excluded: chain Z residue 1117 VAL Chi-restraints excluded: chain Z residue 1127 LEU Chi-restraints excluded: chain Z residue 1129 ILE Chi-restraints excluded: chain J residue 728 GLN Chi-restraints excluded: chain J residue 804 VAL Chi-restraints excluded: chain J residue 810 ASP Chi-restraints excluded: chain J residue 824 GLU Chi-restraints excluded: chain J residue 827 LEU Chi-restraints excluded: chain J residue 838 THR Chi-restraints excluded: chain J residue 854 ASP Chi-restraints excluded: chain J residue 867 ILE Chi-restraints excluded: chain J residue 870 THR Chi-restraints excluded: chain J residue 877 VAL Chi-restraints excluded: chain J residue 892 LEU Chi-restraints excluded: chain J residue 893 SER Chi-restraints excluded: chain J residue 948 SER Chi-restraints excluded: chain J residue 952 ASP Chi-restraints excluded: chain J residue 954 LYS Chi-restraints excluded: chain J residue 955 LEU Chi-restraints excluded: chain J residue 956 THR Chi-restraints excluded: chain J residue 998 VAL Chi-restraints excluded: chain J residue 1021 THR Chi-restraints excluded: chain J residue 1032 ARG Chi-restraints excluded: chain J residue 1042 ARG Chi-restraints excluded: chain J residue 1103 ARG Chi-restraints excluded: chain J residue 1117 VAL Chi-restraints excluded: chain F residue 732 THR Chi-restraints excluded: chain F residue 776 SER Chi-restraints excluded: chain F residue 784 ASP Chi-restraints excluded: chain F residue 804 VAL Chi-restraints excluded: chain F residue 868 GLU Chi-restraints excluded: chain F residue 880 ILE Chi-restraints excluded: chain F residue 928 VAL Chi-restraints excluded: chain F residue 955 LEU Chi-restraints excluded: chain F residue 973 LEU Chi-restraints excluded: chain F residue 981 ASN Chi-restraints excluded: chain F residue 987 THR Chi-restraints excluded: chain F residue 1011 SER Chi-restraints excluded: chain F residue 1035 VAL Chi-restraints excluded: chain F residue 1040 THR Chi-restraints excluded: chain F residue 1052 THR Chi-restraints excluded: chain F residue 1063 MET Chi-restraints excluded: chain F residue 1099 LEU Chi-restraints excluded: chain F residue 1100 THR Chi-restraints excluded: chain F residue 1117 VAL Chi-restraints excluded: chain F residue 1129 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 202 optimal weight: 1.9990 chunk 138 optimal weight: 20.0000 chunk 3 optimal weight: 0.9990 chunk 181 optimal weight: 7.9990 chunk 100 optimal weight: 0.7980 chunk 207 optimal weight: 0.6980 chunk 168 optimal weight: 7.9990 chunk 0 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 218 optimal weight: 8.9990 chunk 61 optimal weight: 2.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN ** C 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 734 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.0861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 20301 Z= 0.277 Angle : 0.561 8.385 27564 Z= 0.307 Chirality : 0.046 0.254 2910 Planarity : 0.005 0.133 3603 Dihedral : 7.606 59.708 2810 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.40 % Allowed : 4.30 % Favored : 95.31 % Rotamer: Outliers : 6.71 % Allowed : 26.58 % Favored : 66.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.19 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.16), residues: 2514 helix: -1.72 (0.52), residues: 97 sheet: 0.65 (0.15), residues: 1181 loop : -1.34 (0.16), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP Z 863 HIS 0.003 0.001 HIS Z 734 PHE 0.021 0.001 PHE Z 848 TYR 0.015 0.001 TYR C 163 ARG 0.004 0.000 ARG B 335 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5028 Ramachandran restraints generated. 2514 Oldfield, 0 Emsley, 2514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5028 Ramachandran restraints generated. 2514 Oldfield, 0 Emsley, 2514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 142 time to evaluate : 2.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 ILE cc_start: 0.9164 (OUTLIER) cc_final: 0.8744 (tp) REVERT: A 37 GLU cc_start: 0.8865 (OUTLIER) cc_final: 0.7820 (mm-30) REVERT: A 340 ASN cc_start: 0.8815 (p0) cc_final: 0.8275 (p0) REVERT: A 355 ASP cc_start: 0.8516 (p0) cc_final: 0.8238 (p0) REVERT: A 417 MET cc_start: 0.9207 (pp-130) cc_final: 0.8842 (pp-130) REVERT: B 39 GLU cc_start: 0.8786 (OUTLIER) cc_final: 0.7264 (pp20) REVERT: B 179 MET cc_start: 0.9214 (OUTLIER) cc_final: 0.9010 (mtp) REVERT: Z 852 TRP cc_start: 0.6896 (OUTLIER) cc_final: 0.5360 (p-90) REVERT: Z 853 LYS cc_start: 0.7026 (OUTLIER) cc_final: 0.6604 (tptm) REVERT: Z 962 ILE cc_start: 0.8322 (OUTLIER) cc_final: 0.8044 (mt) REVERT: Z 1009 ARG cc_start: 0.9002 (OUTLIER) cc_final: 0.8059 (ptm-80) REVERT: J 728 GLN cc_start: 0.8344 (OUTLIER) cc_final: 0.8136 (tm-30) REVERT: J 809 ASP cc_start: 0.8543 (m-30) cc_final: 0.7823 (p0) REVERT: J 954 LYS cc_start: 0.8929 (OUTLIER) cc_final: 0.8627 (tptp) REVERT: J 1042 ARG cc_start: 0.8462 (OUTLIER) cc_final: 0.7832 (ttm170) outliers start: 139 outliers final: 89 residues processed: 271 average time/residue: 0.9748 time to fit residues: 311.3589 Evaluate side-chains 237 residues out of total 2073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 137 time to evaluate : 2.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 VAL Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 89 LYS Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 210 LYS Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 381 ASN Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 39 GLU Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 157 SER Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 360 ARG Chi-restraints excluded: chain C residue 89 LYS Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 209 SER Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain Z residue 734 HIS Chi-restraints excluded: chain Z residue 835 VAL Chi-restraints excluded: chain Z residue 845 LEU Chi-restraints excluded: chain Z residue 852 TRP Chi-restraints excluded: chain Z residue 853 LYS Chi-restraints excluded: chain Z residue 862 MET Chi-restraints excluded: chain Z residue 877 VAL Chi-restraints excluded: chain Z residue 921 ASN Chi-restraints excluded: chain Z residue 956 THR Chi-restraints excluded: chain Z residue 962 ILE Chi-restraints excluded: chain Z residue 987 THR Chi-restraints excluded: chain Z residue 997 ILE Chi-restraints excluded: chain Z residue 1009 ARG Chi-restraints excluded: chain Z residue 1021 THR Chi-restraints excluded: chain Z residue 1052 THR Chi-restraints excluded: chain Z residue 1100 THR Chi-restraints excluded: chain Z residue 1102 THR Chi-restraints excluded: chain Z residue 1117 VAL Chi-restraints excluded: chain Z residue 1129 ILE Chi-restraints excluded: chain J residue 723 THR Chi-restraints excluded: chain J residue 728 GLN Chi-restraints excluded: chain J residue 810 ASP Chi-restraints excluded: chain J residue 824 GLU Chi-restraints excluded: chain J residue 827 LEU Chi-restraints excluded: chain J residue 838 THR Chi-restraints excluded: chain J residue 854 ASP Chi-restraints excluded: chain J residue 867 ILE Chi-restraints excluded: chain J residue 870 THR Chi-restraints excluded: chain J residue 877 VAL Chi-restraints excluded: chain J residue 892 LEU Chi-restraints excluded: chain J residue 948 SER Chi-restraints excluded: chain J residue 952 ASP Chi-restraints excluded: chain J residue 954 LYS Chi-restraints excluded: chain J residue 955 LEU Chi-restraints excluded: chain J residue 998 VAL Chi-restraints excluded: chain J residue 1021 THR Chi-restraints excluded: chain J residue 1042 ARG Chi-restraints excluded: chain J residue 1103 ARG Chi-restraints excluded: chain J residue 1117 VAL Chi-restraints excluded: chain J residue 1121 VAL Chi-restraints excluded: chain F residue 732 THR Chi-restraints excluded: chain F residue 776 SER Chi-restraints excluded: chain F residue 804 VAL Chi-restraints excluded: chain F residue 880 ILE Chi-restraints excluded: chain F residue 928 VAL Chi-restraints excluded: chain F residue 955 LEU Chi-restraints excluded: chain F residue 973 LEU Chi-restraints excluded: chain F residue 981 ASN Chi-restraints excluded: chain F residue 987 THR Chi-restraints excluded: chain F residue 1025 THR Chi-restraints excluded: chain F residue 1035 VAL Chi-restraints excluded: chain F residue 1040 THR Chi-restraints excluded: chain F residue 1052 THR Chi-restraints excluded: chain F residue 1099 LEU Chi-restraints excluded: chain F residue 1100 THR Chi-restraints excluded: chain F residue 1117 VAL Chi-restraints excluded: chain F residue 1129 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 81 optimal weight: 0.9990 chunk 219 optimal weight: 9.9990 chunk 48 optimal weight: 1.9990 chunk 143 optimal weight: 9.9990 chunk 60 optimal weight: 0.9990 chunk 243 optimal weight: 4.9990 chunk 202 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 chunk 80 optimal weight: 0.9980 chunk 128 optimal weight: 10.0000 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 921 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.0923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 20301 Z= 0.255 Angle : 0.553 8.067 27564 Z= 0.302 Chirality : 0.046 0.242 2910 Planarity : 0.005 0.131 3603 Dihedral : 7.468 59.696 2808 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.40 % Allowed : 4.22 % Favored : 95.39 % Rotamer: Outliers : 6.37 % Allowed : 27.30 % Favored : 66.33 % 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: -0.53 (0.16), residues: 2514 helix: -1.66 (0.53), residues: 97 sheet: 0.68 (0.15), residues: 1181 loop : -1.30 (0.17), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP Z 863 HIS 0.008 0.001 HIS Z 734 PHE 0.019 0.001 PHE Z 848 TYR 0.015 0.001 TYR Z 765 ARG 0.003 0.000 ARG B 335 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5028 Ramachandran restraints generated. 2514 Oldfield, 0 Emsley, 2514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5028 Ramachandran restraints generated. 2514 Oldfield, 0 Emsley, 2514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 143 time to evaluate : 2.336 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 11 ILE cc_start: 0.9163 (OUTLIER) cc_final: 0.8750 (tp) REVERT: A 340 ASN cc_start: 0.8800 (p0) cc_final: 0.8240 (p0) REVERT: A 355 ASP cc_start: 0.8529 (p0) cc_final: 0.8238 (p0) REVERT: A 417 MET cc_start: 0.9252 (pp-130) cc_final: 0.8879 (pp-130) REVERT: B 37 GLU cc_start: 0.8844 (OUTLIER) cc_final: 0.7897 (mm-30) REVERT: B 39 GLU cc_start: 0.8780 (OUTLIER) cc_final: 0.7252 (pp20) REVERT: B 179 MET cc_start: 0.9206 (OUTLIER) cc_final: 0.8973 (mtp) REVERT: Z 962 ILE cc_start: 0.8312 (OUTLIER) cc_final: 0.8046 (mt) REVERT: Z 1009 ARG cc_start: 0.9034 (OUTLIER) cc_final: 0.8034 (ptm-80) REVERT: J 728 GLN cc_start: 0.8344 (OUTLIER) cc_final: 0.8144 (tm-30) REVERT: J 809 ASP cc_start: 0.8556 (m-30) cc_final: 0.7857 (p0) REVERT: J 954 LYS cc_start: 0.8927 (OUTLIER) cc_final: 0.8410 (tptp) REVERT: J 1042 ARG cc_start: 0.8445 (OUTLIER) cc_final: 0.7807 (ttm170) REVERT: F 844 ARG cc_start: 0.7287 (ptm160) cc_final: 0.6482 (ptt180) REVERT: F 846 GLU cc_start: 0.5768 (OUTLIER) cc_final: 0.5421 (tm-30) REVERT: F 882 LEU cc_start: 0.7873 (OUTLIER) cc_final: 0.7654 (tp) REVERT: F 961 ASP cc_start: 0.8322 (OUTLIER) cc_final: 0.7895 (m-30) REVERT: F 1103 ARG cc_start: 0.8932 (OUTLIER) cc_final: 0.8383 (ptm160) outliers start: 132 outliers final: 87 residues processed: 261 average time/residue: 0.9747 time to fit residues: 299.0014 Evaluate side-chains 236 residues out of total 2073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 136 time to evaluate : 2.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 VAL Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 55 ASP Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 89 LYS Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 210 LYS Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 381 ASN Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 37 GLU Chi-restraints excluded: chain B residue 39 GLU Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 157 SER Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 360 ARG Chi-restraints excluded: chain C residue 89 LYS Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 209 SER Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain Z residue 845 LEU Chi-restraints excluded: chain Z residue 862 MET Chi-restraints excluded: chain Z residue 877 VAL Chi-restraints excluded: chain Z residue 921 ASN Chi-restraints excluded: chain Z residue 962 ILE Chi-restraints excluded: chain Z residue 987 THR Chi-restraints excluded: chain Z residue 997 ILE Chi-restraints excluded: chain Z residue 1009 ARG Chi-restraints excluded: chain Z residue 1021 THR Chi-restraints excluded: chain Z residue 1052 THR Chi-restraints excluded: chain Z residue 1100 THR Chi-restraints excluded: chain Z residue 1102 THR Chi-restraints excluded: chain Z residue 1117 VAL Chi-restraints excluded: chain Z residue 1129 ILE Chi-restraints excluded: chain J residue 722 LEU Chi-restraints excluded: chain J residue 723 THR Chi-restraints excluded: chain J residue 728 GLN Chi-restraints excluded: chain J residue 804 VAL Chi-restraints excluded: chain J residue 810 ASP Chi-restraints excluded: chain J residue 824 GLU Chi-restraints excluded: chain J residue 854 ASP Chi-restraints excluded: chain J residue 867 ILE Chi-restraints excluded: chain J residue 870 THR Chi-restraints excluded: chain J residue 877 VAL Chi-restraints excluded: chain J residue 892 LEU Chi-restraints excluded: chain J residue 948 SER Chi-restraints excluded: chain J residue 952 ASP Chi-restraints excluded: chain J residue 954 LYS Chi-restraints excluded: chain J residue 955 LEU Chi-restraints excluded: chain J residue 956 THR Chi-restraints excluded: chain J residue 998 VAL Chi-restraints excluded: chain J residue 1021 THR Chi-restraints excluded: chain J residue 1042 ARG Chi-restraints excluded: chain J residue 1103 ARG Chi-restraints excluded: chain J residue 1117 VAL Chi-restraints excluded: chain J residue 1121 VAL Chi-restraints excluded: chain F residue 732 THR Chi-restraints excluded: chain F residue 776 SER Chi-restraints excluded: chain F residue 804 VAL Chi-restraints excluded: chain F residue 846 GLU Chi-restraints excluded: chain F residue 880 ILE Chi-restraints excluded: chain F residue 882 LEU Chi-restraints excluded: chain F residue 928 VAL Chi-restraints excluded: chain F residue 955 LEU Chi-restraints excluded: chain F residue 961 ASP Chi-restraints excluded: chain F residue 973 LEU Chi-restraints excluded: chain F residue 981 ASN Chi-restraints excluded: chain F residue 987 THR Chi-restraints excluded: chain F residue 1011 SER Chi-restraints excluded: chain F residue 1025 THR Chi-restraints excluded: chain F residue 1035 VAL Chi-restraints excluded: chain F residue 1052 THR Chi-restraints excluded: chain F residue 1099 LEU Chi-restraints excluded: chain F residue 1100 THR Chi-restraints excluded: chain F residue 1103 ARG Chi-restraints excluded: chain F residue 1117 VAL Chi-restraints excluded: chain F residue 1129 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 235 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 138 optimal weight: 20.0000 chunk 178 optimal weight: 4.9990 chunk 137 optimal weight: 4.9990 chunk 205 optimal weight: 0.9990 chunk 136 optimal weight: 1.9990 chunk 242 optimal weight: 2.9990 chunk 152 optimal weight: 3.9990 chunk 148 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN Z 734 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.1087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.084 20301 Z= 0.422 Angle : 0.642 25.271 27564 Z= 0.342 Chirality : 0.048 0.273 2910 Planarity : 0.006 0.195 3603 Dihedral : 7.721 59.500 2805 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.40 % Allowed : 4.53 % Favored : 95.07 % Rotamer: Outliers : 6.71 % Allowed : 27.26 % Favored : 66.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.38 % 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: -0.66 (0.16), residues: 2514 helix: -1.74 (0.51), residues: 97 sheet: 0.62 (0.15), residues: 1182 loop : -1.43 (0.16), residues: 1235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP Z 863 HIS 0.005 0.001 HIS Z 734 PHE 0.018 0.002 PHE Z 848 TYR 0.021 0.002 TYR C 163 ARG 0.003 0.000 ARG Z 932 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5028 Ramachandran restraints generated. 2514 Oldfield, 0 Emsley, 2514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5028 Ramachandran restraints generated. 2514 Oldfield, 0 Emsley, 2514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 135 time to evaluate : 2.191 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 11 ILE cc_start: 0.9210 (OUTLIER) cc_final: 0.8737 (tp) REVERT: A 37 GLU cc_start: 0.8763 (OUTLIER) cc_final: 0.7725 (mm-30) REVERT: A 95 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.8104 (mt) REVERT: A 355 ASP cc_start: 0.8520 (p0) cc_final: 0.8257 (p0) REVERT: B 37 GLU cc_start: 0.8786 (OUTLIER) cc_final: 0.7917 (mm-30) REVERT: B 39 GLU cc_start: 0.8815 (OUTLIER) cc_final: 0.7006 (pp20) REVERT: B 116 ASP cc_start: 0.8819 (t0) cc_final: 0.8537 (t0) REVERT: Z 787 PHE cc_start: 0.6953 (m-80) cc_final: 0.6292 (m-10) REVERT: Z 844 ARG cc_start: 0.7360 (ptm160) cc_final: 0.7090 (ptm160) REVERT: Z 962 ILE cc_start: 0.8319 (OUTLIER) cc_final: 0.8049 (mt) REVERT: Z 1009 ARG cc_start: 0.9053 (OUTLIER) cc_final: 0.7988 (ptm-80) REVERT: J 809 ASP cc_start: 0.8670 (m-30) cc_final: 0.7843 (p0) REVERT: J 954 LYS cc_start: 0.8936 (OUTLIER) cc_final: 0.8624 (tptp) REVERT: J 1009 ARG cc_start: 0.8956 (OUTLIER) cc_final: 0.7052 (ptm-80) REVERT: J 1042 ARG cc_start: 0.8514 (OUTLIER) cc_final: 0.7895 (ttm170) REVERT: F 844 ARG cc_start: 0.7214 (ptm160) cc_final: 0.6371 (ptt180) REVERT: F 846 GLU cc_start: 0.5731 (OUTLIER) cc_final: 0.5369 (tm-30) REVERT: F 882 LEU cc_start: 0.8020 (OUTLIER) cc_final: 0.7808 (tp) REVERT: F 1103 ARG cc_start: 0.8962 (OUTLIER) cc_final: 0.8380 (ptm160) outliers start: 139 outliers final: 100 residues processed: 263 average time/residue: 0.9853 time to fit residues: 303.0882 Evaluate side-chains 246 residues out of total 2073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 133 time to evaluate : 1.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 VAL Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 55 ASP Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 89 LYS Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 210 LYS Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 381 ASN Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 37 GLU Chi-restraints excluded: chain B residue 39 GLU Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 157 SER Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 360 ARG Chi-restraints excluded: chain C residue 89 LYS Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 209 SER Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 282 ASP Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain C residue 317 THR Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain Z residue 734 HIS Chi-restraints excluded: chain Z residue 753 ILE Chi-restraints excluded: chain Z residue 835 VAL Chi-restraints excluded: chain Z residue 845 LEU Chi-restraints excluded: chain Z residue 862 MET Chi-restraints excluded: chain Z residue 877 VAL Chi-restraints excluded: chain Z residue 921 ASN Chi-restraints excluded: chain Z residue 925 MET Chi-restraints excluded: chain Z residue 956 THR Chi-restraints excluded: chain Z residue 962 ILE Chi-restraints excluded: chain Z residue 987 THR Chi-restraints excluded: chain Z residue 997 ILE Chi-restraints excluded: chain Z residue 1009 ARG Chi-restraints excluded: chain Z residue 1021 THR Chi-restraints excluded: chain Z residue 1052 THR Chi-restraints excluded: chain Z residue 1077 VAL Chi-restraints excluded: chain Z residue 1100 THR Chi-restraints excluded: chain Z residue 1102 THR Chi-restraints excluded: chain Z residue 1117 VAL Chi-restraints excluded: chain Z residue 1129 ILE Chi-restraints excluded: chain J residue 723 THR Chi-restraints excluded: chain J residue 728 GLN Chi-restraints excluded: chain J residue 804 VAL Chi-restraints excluded: chain J residue 810 ASP Chi-restraints excluded: chain J residue 824 GLU Chi-restraints excluded: chain J residue 854 ASP Chi-restraints excluded: chain J residue 867 ILE Chi-restraints excluded: chain J residue 870 THR Chi-restraints excluded: chain J residue 877 VAL Chi-restraints excluded: chain J residue 892 LEU Chi-restraints excluded: chain J residue 893 SER Chi-restraints excluded: chain J residue 948 SER Chi-restraints excluded: chain J residue 952 ASP Chi-restraints excluded: chain J residue 954 LYS Chi-restraints excluded: chain J residue 955 LEU Chi-restraints excluded: chain J residue 956 THR Chi-restraints excluded: chain J residue 997 ILE Chi-restraints excluded: chain J residue 998 VAL Chi-restraints excluded: chain J residue 1009 ARG Chi-restraints excluded: chain J residue 1021 THR Chi-restraints excluded: chain J residue 1042 ARG Chi-restraints excluded: chain J residue 1103 ARG Chi-restraints excluded: chain J residue 1117 VAL Chi-restraints excluded: chain J residue 1121 VAL Chi-restraints excluded: chain F residue 732 THR Chi-restraints excluded: chain F residue 776 SER Chi-restraints excluded: chain F residue 804 VAL Chi-restraints excluded: chain F residue 846 GLU Chi-restraints excluded: chain F residue 880 ILE Chi-restraints excluded: chain F residue 882 LEU Chi-restraints excluded: chain F residue 928 VAL Chi-restraints excluded: chain F residue 950 THR Chi-restraints excluded: chain F residue 955 LEU Chi-restraints excluded: chain F residue 973 LEU Chi-restraints excluded: chain F residue 977 THR Chi-restraints excluded: chain F residue 981 ASN Chi-restraints excluded: chain F residue 987 THR Chi-restraints excluded: chain F residue 1011 SER Chi-restraints excluded: chain F residue 1025 THR Chi-restraints excluded: chain F residue 1035 VAL Chi-restraints excluded: chain F residue 1052 THR Chi-restraints excluded: chain F residue 1099 LEU Chi-restraints excluded: chain F residue 1100 THR Chi-restraints excluded: chain F residue 1103 ARG Chi-restraints excluded: chain F residue 1117 VAL Chi-restraints excluded: chain F residue 1129 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 150 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 145 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 47 optimal weight: 0.5980 chunk 154 optimal weight: 3.9990 chunk 165 optimal weight: 0.7980 chunk 120 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 190 optimal weight: 0.8980 chunk 220 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 826 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.0998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 20301 Z= 0.195 Angle : 0.549 16.467 27564 Z= 0.297 Chirality : 0.045 0.238 2910 Planarity : 0.005 0.165 3603 Dihedral : 7.334 59.934 2805 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.40 % Allowed : 3.90 % Favored : 95.70 % Rotamer: Outliers : 5.07 % Allowed : 28.65 % Favored : 66.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.19 % 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: -0.48 (0.16), residues: 2514 helix: -1.16 (0.56), residues: 91 sheet: 0.67 (0.15), residues: 1191 loop : -1.28 (0.17), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP Z 863 HIS 0.008 0.001 HIS Z 734 PHE 0.013 0.001 PHE Z 848 TYR 0.017 0.001 TYR Z 765 ARG 0.002 0.000 ARG B 335 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5028 Ramachandran restraints generated. 2514 Oldfield, 0 Emsley, 2514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5028 Ramachandran restraints generated. 2514 Oldfield, 0 Emsley, 2514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 145 time to evaluate : 1.730 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 11 ILE cc_start: 0.9132 (OUTLIER) cc_final: 0.8749 (tp) REVERT: A 340 ASN cc_start: 0.8727 (p0) cc_final: 0.8174 (p0) REVERT: A 355 ASP cc_start: 0.8500 (p0) cc_final: 0.8211 (p0) REVERT: A 375 LYS cc_start: 0.9154 (OUTLIER) cc_final: 0.8699 (mmtm) REVERT: B 39 GLU cc_start: 0.8613 (OUTLIER) cc_final: 0.7291 (pp20) REVERT: B 116 ASP cc_start: 0.8710 (t0) cc_final: 0.8425 (t0) REVERT: Z 962 ILE cc_start: 0.8272 (OUTLIER) cc_final: 0.7987 (mt) REVERT: Z 1009 ARG cc_start: 0.8966 (OUTLIER) cc_final: 0.7992 (ptm-80) REVERT: J 809 ASP cc_start: 0.8539 (m-30) cc_final: 0.7794 (p0) REVERT: J 846 GLU cc_start: 0.6684 (OUTLIER) cc_final: 0.6143 (pp20) REVERT: J 954 LYS cc_start: 0.8923 (OUTLIER) cc_final: 0.8641 (tptp) REVERT: F 844 ARG cc_start: 0.7256 (ptm160) cc_final: 0.6435 (ptt180) outliers start: 105 outliers final: 79 residues processed: 243 average time/residue: 1.0160 time to fit residues: 288.0323 Evaluate side-chains 221 residues out of total 2073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 135 time to evaluate : 2.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 VAL Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 210 LYS Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 375 LYS Chi-restraints excluded: chain A residue 381 ASN Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 39 GLU Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 360 ARG Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 209 SER Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain Z residue 800 PHE Chi-restraints excluded: chain Z residue 835 VAL Chi-restraints excluded: chain Z residue 845 LEU Chi-restraints excluded: chain Z residue 862 MET Chi-restraints excluded: chain Z residue 877 VAL Chi-restraints excluded: chain Z residue 921 ASN Chi-restraints excluded: chain Z residue 962 ILE Chi-restraints excluded: chain Z residue 987 THR Chi-restraints excluded: chain Z residue 997 ILE Chi-restraints excluded: chain Z residue 1009 ARG Chi-restraints excluded: chain Z residue 1021 THR Chi-restraints excluded: chain Z residue 1100 THR Chi-restraints excluded: chain Z residue 1102 THR Chi-restraints excluded: chain Z residue 1117 VAL Chi-restraints excluded: chain Z residue 1129 ILE Chi-restraints excluded: chain J residue 723 THR Chi-restraints excluded: chain J residue 804 VAL Chi-restraints excluded: chain J residue 810 ASP Chi-restraints excluded: chain J residue 824 GLU Chi-restraints excluded: chain J residue 846 GLU Chi-restraints excluded: chain J residue 854 ASP Chi-restraints excluded: chain J residue 867 ILE Chi-restraints excluded: chain J residue 870 THR Chi-restraints excluded: chain J residue 877 VAL Chi-restraints excluded: chain J residue 892 LEU Chi-restraints excluded: chain J residue 948 SER Chi-restraints excluded: chain J residue 954 LYS Chi-restraints excluded: chain J residue 955 LEU Chi-restraints excluded: chain J residue 998 VAL Chi-restraints excluded: chain J residue 1021 THR Chi-restraints excluded: chain J residue 1103 ARG Chi-restraints excluded: chain J residue 1117 VAL Chi-restraints excluded: chain J residue 1121 VAL Chi-restraints excluded: chain F residue 732 THR Chi-restraints excluded: chain F residue 776 SER Chi-restraints excluded: chain F residue 804 VAL Chi-restraints excluded: chain F residue 880 ILE Chi-restraints excluded: chain F residue 889 GLU Chi-restraints excluded: chain F residue 928 VAL Chi-restraints excluded: chain F residue 950 THR Chi-restraints excluded: chain F residue 955 LEU Chi-restraints excluded: chain F residue 973 LEU Chi-restraints excluded: chain F residue 977 THR Chi-restraints excluded: chain F residue 981 ASN Chi-restraints excluded: chain F residue 987 THR Chi-restraints excluded: chain F residue 1011 SER Chi-restraints excluded: chain F residue 1035 VAL Chi-restraints excluded: chain F residue 1052 THR Chi-restraints excluded: chain F residue 1099 LEU Chi-restraints excluded: chain F residue 1100 THR Chi-restraints excluded: chain F residue 1117 VAL Chi-restraints excluded: chain F residue 1129 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 232 optimal weight: 4.9990 chunk 212 optimal weight: 30.0000 chunk 226 optimal weight: 9.9990 chunk 136 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 chunk 177 optimal weight: 6.9990 chunk 69 optimal weight: 5.9990 chunk 204 optimal weight: 1.9990 chunk 214 optimal weight: 0.4980 chunk 225 optimal weight: 5.9990 chunk 148 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 826 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.1074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 20301 Z= 0.304 Angle : 0.585 12.998 27564 Z= 0.316 Chirality : 0.046 0.252 2910 Planarity : 0.005 0.152 3603 Dihedral : 7.352 59.260 2797 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.40 % Allowed : 4.02 % Favored : 95.58 % Rotamer: Outliers : 5.31 % Allowed : 28.65 % Favored : 66.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.38 % 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: -0.51 (0.16), residues: 2514 helix: -1.22 (0.55), residues: 91 sheet: 0.66 (0.15), residues: 1189 loop : -1.31 (0.17), residues: 1234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP Z 863 HIS 0.003 0.001 HIS B 268 PHE 0.015 0.001 PHE Z 848 TYR 0.015 0.001 TYR C 163 ARG 0.003 0.000 ARG J 790 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5028 Ramachandran restraints generated. 2514 Oldfield, 0 Emsley, 2514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5028 Ramachandran restraints generated. 2514 Oldfield, 0 Emsley, 2514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 141 time to evaluate : 2.241 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 11 ILE cc_start: 0.9185 (OUTLIER) cc_final: 0.8741 (tp) REVERT: A 95 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.8081 (mt) REVERT: A 340 ASN cc_start: 0.8845 (p0) cc_final: 0.8286 (p0) REVERT: A 355 ASP cc_start: 0.8472 (p0) cc_final: 0.8173 (p0) REVERT: A 375 LYS cc_start: 0.9180 (OUTLIER) cc_final: 0.8785 (mmtm) REVERT: A 417 MET cc_start: 0.9358 (pp-130) cc_final: 0.8866 (pp-130) REVERT: B 39 GLU cc_start: 0.8668 (OUTLIER) cc_final: 0.7368 (pp20) REVERT: B 116 ASP cc_start: 0.8751 (t0) cc_final: 0.8443 (t0) REVERT: Z 962 ILE cc_start: 0.8287 (OUTLIER) cc_final: 0.8015 (mt) REVERT: Z 1009 ARG cc_start: 0.9037 (OUTLIER) cc_final: 0.8011 (ptm-80) REVERT: J 809 ASP cc_start: 0.8582 (m-30) cc_final: 0.7891 (p0) REVERT: J 846 GLU cc_start: 0.6697 (OUTLIER) cc_final: 0.6162 (pp20) REVERT: J 954 LYS cc_start: 0.8923 (OUTLIER) cc_final: 0.8426 (tptp) REVERT: J 1009 ARG cc_start: 0.8947 (OUTLIER) cc_final: 0.7053 (ptm-80) REVERT: J 1032 ARG cc_start: 0.6653 (OUTLIER) cc_final: 0.6059 (mtp180) REVERT: J 1042 ARG cc_start: 0.8463 (OUTLIER) cc_final: 0.7821 (ttm170) REVERT: F 844 ARG cc_start: 0.7218 (ptm160) cc_final: 0.6410 (ptt180) REVERT: F 961 ASP cc_start: 0.8331 (OUTLIER) cc_final: 0.7924 (m-30) REVERT: F 1103 ARG cc_start: 0.8942 (OUTLIER) cc_final: 0.8454 (ptm160) outliers start: 110 outliers final: 90 residues processed: 245 average time/residue: 1.0932 time to fit residues: 311.3543 Evaluate side-chains 236 residues out of total 2073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 133 time to evaluate : 2.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 VAL Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 55 ASP Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 210 LYS Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 375 LYS Chi-restraints excluded: chain A residue 381 ASN Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 39 GLU Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 157 SER Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 360 ARG Chi-restraints excluded: chain C residue 1 VAL Chi-restraints excluded: chain C residue 89 LYS Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 209 SER Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain Z residue 800 PHE Chi-restraints excluded: chain Z residue 804 VAL Chi-restraints excluded: chain Z residue 835 VAL Chi-restraints excluded: chain Z residue 845 LEU Chi-restraints excluded: chain Z residue 862 MET Chi-restraints excluded: chain Z residue 877 VAL Chi-restraints excluded: chain Z residue 921 ASN Chi-restraints excluded: chain Z residue 956 THR Chi-restraints excluded: chain Z residue 962 ILE Chi-restraints excluded: chain Z residue 987 THR Chi-restraints excluded: chain Z residue 997 ILE Chi-restraints excluded: chain Z residue 1009 ARG Chi-restraints excluded: chain Z residue 1021 THR Chi-restraints excluded: chain Z residue 1052 THR Chi-restraints excluded: chain Z residue 1100 THR Chi-restraints excluded: chain Z residue 1102 THR Chi-restraints excluded: chain Z residue 1117 VAL Chi-restraints excluded: chain Z residue 1129 ILE Chi-restraints excluded: chain J residue 723 THR Chi-restraints excluded: chain J residue 804 VAL Chi-restraints excluded: chain J residue 810 ASP Chi-restraints excluded: chain J residue 824 GLU Chi-restraints excluded: chain J residue 846 GLU Chi-restraints excluded: chain J residue 854 ASP Chi-restraints excluded: chain J residue 867 ILE Chi-restraints excluded: chain J residue 870 THR Chi-restraints excluded: chain J residue 877 VAL Chi-restraints excluded: chain J residue 948 SER Chi-restraints excluded: chain J residue 954 LYS Chi-restraints excluded: chain J residue 955 LEU Chi-restraints excluded: chain J residue 956 THR Chi-restraints excluded: chain J residue 998 VAL Chi-restraints excluded: chain J residue 1009 ARG Chi-restraints excluded: chain J residue 1021 THR Chi-restraints excluded: chain J residue 1032 ARG Chi-restraints excluded: chain J residue 1042 ARG Chi-restraints excluded: chain J residue 1103 ARG Chi-restraints excluded: chain J residue 1117 VAL Chi-restraints excluded: chain J residue 1121 VAL Chi-restraints excluded: chain F residue 732 THR Chi-restraints excluded: chain F residue 776 SER Chi-restraints excluded: chain F residue 804 VAL Chi-restraints excluded: chain F residue 827 LEU Chi-restraints excluded: chain F residue 880 ILE Chi-restraints excluded: chain F residue 889 GLU Chi-restraints excluded: chain F residue 928 VAL Chi-restraints excluded: chain F residue 950 THR Chi-restraints excluded: chain F residue 955 LEU Chi-restraints excluded: chain F residue 961 ASP Chi-restraints excluded: chain F residue 973 LEU Chi-restraints excluded: chain F residue 977 THR Chi-restraints excluded: chain F residue 981 ASN Chi-restraints excluded: chain F residue 987 THR Chi-restraints excluded: chain F residue 1011 SER Chi-restraints excluded: chain F residue 1035 VAL Chi-restraints excluded: chain F residue 1052 THR Chi-restraints excluded: chain F residue 1099 LEU Chi-restraints excluded: chain F residue 1100 THR Chi-restraints excluded: chain F residue 1103 ARG Chi-restraints excluded: chain F residue 1117 VAL Chi-restraints excluded: chain F residue 1129 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 239 optimal weight: 1.9990 chunk 146 optimal weight: 0.0050 chunk 113 optimal weight: 1.9990 chunk 166 optimal weight: 3.9990 chunk 251 optimal weight: 2.9990 chunk 231 optimal weight: 0.8980 chunk 199 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 154 optimal weight: 0.8980 chunk 122 optimal weight: 2.9990 chunk 158 optimal weight: 0.6980 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 113 HIS ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 826 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.1103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 20301 Z= 0.179 Angle : 0.531 7.320 27564 Z= 0.291 Chirality : 0.045 0.227 2910 Planarity : 0.004 0.125 3603 Dihedral : 6.992 58.771 2795 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.40 % Allowed : 3.78 % Favored : 95.82 % Rotamer: Outliers : 4.68 % Allowed : 29.18 % Favored : 66.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.19 % 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: -0.41 (0.16), residues: 2514 helix: -1.01 (0.56), residues: 91 sheet: 0.72 (0.15), residues: 1188 loop : -1.24 (0.17), residues: 1235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP Z 863 HIS 0.002 0.000 HIS B 268 PHE 0.010 0.001 PHE J 817 TYR 0.017 0.001 TYR Z 765 ARG 0.002 0.000 ARG Z 844 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5028 Ramachandran restraints generated. 2514 Oldfield, 0 Emsley, 2514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5028 Ramachandran restraints generated. 2514 Oldfield, 0 Emsley, 2514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 144 time to evaluate : 2.466 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 11 ILE cc_start: 0.9120 (OUTLIER) cc_final: 0.8755 (tp) REVERT: A 95 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.8030 (mt) REVERT: A 340 ASN cc_start: 0.8674 (p0) cc_final: 0.8140 (p0) REVERT: A 355 ASP cc_start: 0.8449 (p0) cc_final: 0.8169 (p0) REVERT: A 375 LYS cc_start: 0.9157 (OUTLIER) cc_final: 0.8650 (mmtm) REVERT: A 417 MET cc_start: 0.9287 (pp-130) cc_final: 0.8842 (pp-130) REVERT: B 39 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.7276 (pp20) REVERT: B 116 ASP cc_start: 0.8702 (t0) cc_final: 0.8446 (t0) REVERT: B 179 MET cc_start: 0.9223 (OUTLIER) cc_final: 0.9009 (mtp) REVERT: Z 751 LYS cc_start: 0.8465 (tppp) cc_final: 0.7878 (tmmm) REVERT: Z 1009 ARG cc_start: 0.9009 (OUTLIER) cc_final: 0.8016 (ptm-80) REVERT: J 809 ASP cc_start: 0.8437 (m-30) cc_final: 0.8187 (m-30) REVERT: J 846 GLU cc_start: 0.6711 (OUTLIER) cc_final: 0.6138 (pp20) REVERT: J 954 LYS cc_start: 0.8863 (OUTLIER) cc_final: 0.8662 (tptp) REVERT: J 1032 ARG cc_start: 0.6509 (OUTLIER) cc_final: 0.5865 (mtp180) REVERT: J 1042 ARG cc_start: 0.8436 (OUTLIER) cc_final: 0.7809 (ttm170) REVERT: J 1103 ARG cc_start: 0.9005 (OUTLIER) cc_final: 0.7550 (ptm160) REVERT: F 844 ARG cc_start: 0.7259 (ptm160) cc_final: 0.6442 (ptt180) REVERT: F 1103 ARG cc_start: 0.8900 (OUTLIER) cc_final: 0.8411 (ptm160) outliers start: 97 outliers final: 76 residues processed: 234 average time/residue: 0.9965 time to fit residues: 275.4945 Evaluate side-chains 227 residues out of total 2073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 139 time to evaluate : 1.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 VAL Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 55 ASP Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 210 LYS Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 375 LYS Chi-restraints excluded: chain A residue 381 ASN Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 39 GLU Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 360 ARG Chi-restraints excluded: chain C residue 1 VAL Chi-restraints excluded: chain C residue 89 LYS Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 209 SER Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain Z residue 800 PHE Chi-restraints excluded: chain Z residue 835 VAL Chi-restraints excluded: chain Z residue 845 LEU Chi-restraints excluded: chain Z residue 862 MET Chi-restraints excluded: chain Z residue 877 VAL Chi-restraints excluded: chain Z residue 987 THR Chi-restraints excluded: chain Z residue 997 ILE Chi-restraints excluded: chain Z residue 1009 ARG Chi-restraints excluded: chain Z residue 1021 THR Chi-restraints excluded: chain Z residue 1100 THR Chi-restraints excluded: chain Z residue 1102 THR Chi-restraints excluded: chain Z residue 1117 VAL Chi-restraints excluded: chain Z residue 1129 ILE Chi-restraints excluded: chain J residue 804 VAL Chi-restraints excluded: chain J residue 810 ASP Chi-restraints excluded: chain J residue 824 GLU Chi-restraints excluded: chain J residue 846 GLU Chi-restraints excluded: chain J residue 854 ASP Chi-restraints excluded: chain J residue 867 ILE Chi-restraints excluded: chain J residue 870 THR Chi-restraints excluded: chain J residue 948 SER Chi-restraints excluded: chain J residue 954 LYS Chi-restraints excluded: chain J residue 955 LEU Chi-restraints excluded: chain J residue 1021 THR Chi-restraints excluded: chain J residue 1032 ARG Chi-restraints excluded: chain J residue 1042 ARG Chi-restraints excluded: chain J residue 1103 ARG Chi-restraints excluded: chain J residue 1117 VAL Chi-restraints excluded: chain J residue 1121 VAL Chi-restraints excluded: chain F residue 732 THR Chi-restraints excluded: chain F residue 776 SER Chi-restraints excluded: chain F residue 804 VAL Chi-restraints excluded: chain F residue 827 LEU Chi-restraints excluded: chain F residue 880 ILE Chi-restraints excluded: chain F residue 889 GLU Chi-restraints excluded: chain F residue 928 VAL Chi-restraints excluded: chain F residue 955 LEU Chi-restraints excluded: chain F residue 973 LEU Chi-restraints excluded: chain F residue 977 THR Chi-restraints excluded: chain F residue 981 ASN Chi-restraints excluded: chain F residue 987 THR Chi-restraints excluded: chain F residue 1011 SER Chi-restraints excluded: chain F residue 1025 THR Chi-restraints excluded: chain F residue 1035 VAL Chi-restraints excluded: chain F residue 1052 THR Chi-restraints excluded: chain F residue 1100 THR Chi-restraints excluded: chain F residue 1103 ARG Chi-restraints excluded: chain F residue 1129 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 212 optimal weight: 5.9990 chunk 61 optimal weight: 4.9990 chunk 184 optimal weight: 9.9990 chunk 29 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 200 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 205 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 175 optimal weight: 7.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.130140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.089826 restraints weight = 24765.626| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 1.75 r_work: 0.2770 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2665 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.1225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.083 20301 Z= 0.453 Angle : 0.648 7.737 27564 Z= 0.351 Chirality : 0.049 0.269 2910 Planarity : 0.005 0.128 3603 Dihedral : 7.509 59.897 2794 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.36 % Allowed : 4.49 % Favored : 95.15 % Rotamer: Outliers : 4.97 % Allowed : 28.94 % Favored : 66.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.38 % 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: -0.60 (0.16), residues: 2514 helix: -1.44 (0.53), residues: 91 sheet: 0.63 (0.14), residues: 1211 loop : -1.44 (0.16), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP Z 863 HIS 0.005 0.001 HIS A 4 PHE 0.032 0.002 PHE Z 848 TYR 0.022 0.002 TYR C 163 ARG 0.003 0.000 ARG Z 932 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6002.60 seconds wall clock time: 106 minutes 16.60 seconds (6376.60 seconds total)