Starting phenix.real_space_refine on Sun Aug 11 08:08:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yww_39645/08_2024/8yww_39645_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yww_39645/08_2024/8yww_39645.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yww_39645/08_2024/8yww_39645.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yww_39645/08_2024/8yww_39645.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yww_39645/08_2024/8yww_39645_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yww_39645/08_2024/8yww_39645_neut.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.097 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 136 5.16 5 C 20186 2.51 5 N 5300 2.21 5 O 6027 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 224": "OE1" <-> "OE2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 465": "OE1" <-> "OE2" Residue "A PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 574": "OD1" <-> "OD2" Residue "A TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 867": "OD1" <-> "OD2" Residue "A GLU 868": "OE1" <-> "OE2" Residue "A ASP 994": "OD1" <-> "OD2" Residue "B TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 224": "OE1" <-> "OE2" Residue "B ASP 287": "OD1" <-> "OD2" Residue "B GLU 298": "OE1" <-> "OE2" Residue "B GLU 309": "OE1" <-> "OE2" Residue "B PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 465": "OE1" <-> "OE2" Residue "B PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 574": "OD1" <-> "OD2" Residue "B GLU 583": "OE1" <-> "OE2" Residue "B TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 773": "OE1" <-> "OE2" Residue "B PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 950": "OD1" <-> "OD2" Residue "B ASP 979": "OD1" <-> "OD2" Residue "B ASP 994": "OD1" <-> "OD2" Residue "C PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 309": "OE1" <-> "OE2" Residue "C ASP 586": "OD1" <-> "OD2" Residue "C GLU 780": "OE1" <-> "OE2" Residue "C PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 994": "OD1" <-> "OD2" Residue "C ASP 1084": "OD1" <-> "OD2" Residue "C ASP 1146": "OD1" <-> "OD2" Residue "E GLU 46": "OE1" <-> "OE2" Residue "G GLU 46": "OE1" <-> "OE2" Residue "H PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 209": "OD1" <-> "OD2" Residue "H TYR 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 1.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 31649 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1024, 7754 Classifications: {'peptide': 1024} Incomplete info: {'truncation_to_alanine': 74} Link IDs: {'PTRANS': 56, 'TRANS': 967} Chain breaks: 9 Unresolved non-hydrogen bonds: 256 Unresolved non-hydrogen angles: 314 Unresolved non-hydrogen dihedrals: 208 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 9, 'TYR:plan': 2, 'ASN:plan1': 6, 'ASP:plan': 8, 'PHE:plan': 2, 'GLU:plan': 7, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 157 Chain: "B" Number of atoms: 7754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1024, 7754 Classifications: {'peptide': 1024} Incomplete info: {'truncation_to_alanine': 74} Link IDs: {'PTRANS': 56, 'TRANS': 967} Chain breaks: 8 Unresolved non-hydrogen bonds: 256 Unresolved non-hydrogen angles: 314 Unresolved non-hydrogen dihedrals: 208 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 9, 'TYR:plan': 2, 'ASN:plan1': 6, 'ASP:plan': 8, 'PHE:plan': 2, 'GLU:plan': 7, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 157 Chain: "C" Number of atoms: 7754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1024, 7754 Classifications: {'peptide': 1024} Incomplete info: {'truncation_to_alanine': 74} Link IDs: {'PTRANS': 56, 'TRANS': 967} Chain breaks: 8 Unresolved non-hydrogen bonds: 256 Unresolved non-hydrogen angles: 314 Unresolved non-hydrogen dihedrals: 208 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 9, 'TYR:plan': 2, 'ASN:plan1': 6, 'ASP:plan': 8, 'PHE:plan': 2, 'GLU:plan': 7, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 157 Chain: "E" Number of atoms: 1619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1619 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 205} Chain: "D" Number of atoms: 1646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1646 Classifications: {'peptide': 212} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 200} Chain: "F" Number of atoms: 1646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1646 Classifications: {'peptide': 212} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 200} Chain: "G" Number of atoms: 1619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1619 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 205} Chain: "H" Number of atoms: 1857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1857 Classifications: {'peptide': 245} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 235} Time building chain proxies: 15.91, per 1000 atoms: 0.50 Number of scatterers: 31649 At special positions: 0 Unit cell: (145.658, 145.658, 252.184, 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 136 16.00 O 6027 8.00 N 5300 7.00 C 20186 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=49, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.06 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.02 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.02 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.06 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.02 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.02 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 95 " distance=2.03 Simple disulfide: pdb=" SG CYS E 144 " - pdb=" SG CYS E 200 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.04 Simple disulfide: pdb=" SG CYS D 134 " - pdb=" SG CYS D 194 " distance=2.04 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.04 Simple disulfide: pdb=" SG CYS F 134 " - pdb=" SG CYS F 194 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 95 " distance=2.03 Simple disulfide: pdb=" SG CYS G 144 " - pdb=" SG CYS G 200 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 162 " - pdb=" SG CYS H 227 " 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: 10.25 Conformation dependent library (CDL) restraints added in 5.4 seconds 8206 Ramachandran restraints generated. 4103 Oldfield, 0 Emsley, 4103 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7758 Finding SS restraints... Secondary structure from input PDB file: 81 helices and 69 sheets defined 20.1% alpha, 29.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.30 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 385 through 390 removed outlier: 3.872A pdb=" N ASP A 389 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.235A pdb=" N SER A 408 " --> pdb=" O ASN A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.543A pdb=" N ASP A 442 " --> pdb=" O SER A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 571 No H-bonds generated for 'chain 'A' and resid 569 through 571' Processing helix chain 'A' and resid 616 through 620 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.532A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.120A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.916A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.516A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 983 removed outlier: 3.783A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.191A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 385 through 390 removed outlier: 3.872A pdb=" N ASP B 389 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.235A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.543A pdb=" N ASP B 442 " --> pdb=" O SER B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 571 No H-bonds generated for 'chain 'B' and resid 569 through 571' Processing helix chain 'B' and resid 616 through 620 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.590A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 918 removed outlier: 4.079A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.957A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.724A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG B 983 " --> pdb=" O ASP B 979 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU B 984 " --> pdb=" O ILE B 980 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.141A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1145 removed outlier: 4.006A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU B1145 " --> pdb=" O LEU B1141 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1140 through 1145' Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 removed outlier: 3.614A pdb=" N PHE C 342 " --> pdb=" O PHE C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 410 removed outlier: 3.517A pdb=" N GLU C 406 " --> pdb=" O ARG C 403 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N SER C 408 " --> pdb=" O ASN C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.644A pdb=" N ASN C 422 " --> pdb=" O ILE C 418 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 479 through 483 Processing helix chain 'C' and resid 502 through 506 Processing helix chain 'C' and resid 616 through 620 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 918 removed outlier: 4.105A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.876A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 983 removed outlier: 3.767A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.049A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.581A pdb=" N ASN E 32 " --> pdb=" O VAL E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 64 removed outlier: 3.580A pdb=" N LYS E 64 " --> pdb=" O GLY E 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 61 through 64' Processing helix chain 'E' and resid 160 through 162 No H-bonds generated for 'chain 'E' and resid 160 through 162' Processing helix chain 'E' and resid 189 through 193 Processing helix chain 'D' and resid 50 through 52 No H-bonds generated for 'chain 'D' and resid 50 through 52' Processing helix chain 'D' and resid 79 through 83 removed outlier: 4.163A pdb=" N ILE D 83 " --> pdb=" O PRO D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 126 Processing helix chain 'D' and resid 183 through 187 Processing helix chain 'F' and resid 50 through 52 No H-bonds generated for 'chain 'F' and resid 50 through 52' Processing helix chain 'F' and resid 79 through 83 removed outlier: 4.163A pdb=" N ILE F 83 " --> pdb=" O PRO F 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 121 through 126 Processing helix chain 'F' and resid 183 through 187 Processing helix chain 'G' and resid 28 through 32 removed outlier: 3.581A pdb=" N ASN G 32 " --> pdb=" O VAL G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 61 through 64 removed outlier: 3.580A pdb=" N LYS G 64 " --> pdb=" O GLY G 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 61 through 64' Processing helix chain 'G' and resid 160 through 162 No H-bonds generated for 'chain 'G' and resid 160 through 162' Processing helix chain 'G' and resid 189 through 193 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.729A pdb=" N ASP H 31 " --> pdb=" O LYS H 28 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.534A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.558A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.292A pdb=" N PHE A 43 " --> pdb=" O ARG B 567 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 8.481A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.924A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.722A pdb=" N ARG A 237 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N PHE A 106 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N GLN A 239 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N TRP A 104 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N LEU A 241 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 7.082A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 324 through 328 removed outlier: 5.125A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 357 through 358 removed outlier: 4.033A pdb=" N LEU A 513 " --> pdb=" O CYS A 432 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLY A 431 " --> pdb=" O TYR A 380 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 357 through 358 Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.220A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.635A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 702 through 703 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.721A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.721A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.315A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 788 through 789 removed outlier: 5.887A pdb=" N ILE A 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.790A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.653A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.810A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLU B 96 " --> pdb=" O ASN B 188 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.041A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.597A pdb=" N ILE B 105 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.363A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 357 through 358 removed outlier: 4.033A pdb=" N LEU B 513 " --> pdb=" O CYS B 432 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLY B 431 " --> pdb=" O TYR B 380 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 357 through 358 Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC7, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.102A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.544A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.700A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 733 through 735 removed outlier: 4.469A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 788 through 789 removed outlier: 5.852A pdb=" N ILE B 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.728A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD5, first strand: chain 'C' and resid 29 through 31 removed outlier: 3.556A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.765A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.972A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.933A pdb=" N ARG C 237 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N PHE C 106 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N GLN C 239 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N TRP C 104 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N LEU C 241 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.929A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 325 through 328 Processing sheet with id=AE1, first strand: chain 'C' and resid 356 through 358 removed outlier: 3.748A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AE3, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.093A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.549A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.628A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.628A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 733 through 735 removed outlier: 4.231A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.826A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'E' and resid 18 through 21 removed outlier: 3.628A pdb=" N LEU E 80 " --> pdb=" O LEU E 20 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 57 through 59 removed outlier: 5.173A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TYR E 94 " --> pdb=" O VAL E 37 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER E 106 " --> pdb=" O ARG E 97 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 57 through 59 removed outlier: 5.173A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TYR E 94 " --> pdb=" O VAL E 37 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 124 through 127 removed outlier: 5.226A pdb=" N ALA E 141 " --> pdb=" O VAL E 188 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N VAL E 188 " --> pdb=" O ALA E 141 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N GLY E 143 " --> pdb=" O VAL E 186 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N VAL E 186 " --> pdb=" O GLY E 143 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N LEU E 145 " --> pdb=" O SER E 184 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N SER E 184 " --> pdb=" O LEU E 145 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N LYS E 147 " --> pdb=" O LEU E 182 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N LEU E 182 " --> pdb=" O LYS E 147 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 124 through 127 removed outlier: 5.226A pdb=" N ALA E 141 " --> pdb=" O VAL E 188 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N VAL E 188 " --> pdb=" O ALA E 141 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N GLY E 143 " --> pdb=" O VAL E 186 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N VAL E 186 " --> pdb=" O GLY E 143 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N LEU E 145 " --> pdb=" O SER E 184 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N SER E 184 " --> pdb=" O LEU E 145 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N LYS E 147 " --> pdb=" O LEU E 182 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N LEU E 182 " --> pdb=" O LYS E 147 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER E 181 " --> pdb=" O VAL E 173 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL E 173 " --> pdb=" O SER E 181 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 154 through 158 removed outlier: 3.554A pdb=" N THR E 155 " --> pdb=" O ASN E 203 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N TYR E 198 " --> pdb=" O VAL E 215 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL E 211 " --> pdb=" O VAL E 202 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'D' and resid 5 through 6 removed outlier: 3.694A pdb=" N VAL D 19 " --> pdb=" O ILE D 75 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR D 72 " --> pdb=" O SER D 65 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'D' and resid 10 through 14 removed outlier: 6.743A pdb=" N LEU D 11 " --> pdb=" O GLU D 105 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N LYS D 107 " --> pdb=" O LEU D 11 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ALA D 13 " --> pdb=" O LYS D 107 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N TYR D 86 " --> pdb=" O THR D 102 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N LEU D 33 " --> pdb=" O TYR D 49 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N TYR D 49 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'D' and resid 114 through 118 removed outlier: 3.927A pdb=" N VAL D 133 " --> pdb=" O PHE D 118 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N CYS D 134 " --> pdb=" O SER D 177 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER D 176 " --> pdb=" O SER D 162 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLN D 160 " --> pdb=" O THR D 178 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'D' and resid 145 through 147 removed outlier: 4.210A pdb=" N LYS D 145 " --> pdb=" O THR D 197 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR D 197 " --> pdb=" O LYS D 145 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLN D 147 " --> pdb=" O GLU D 195 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N GLU D 195 " --> pdb=" O GLN D 147 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF8 Processing sheet with id=AF9, first strand: chain 'D' and resid 149 through 150 Processing sheet with id=AG1, first strand: chain 'F' and resid 5 through 6 removed outlier: 3.693A pdb=" N VAL F 19 " --> pdb=" O ILE F 75 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR F 72 " --> pdb=" O SER F 65 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'F' and resid 10 through 14 removed outlier: 6.743A pdb=" N LEU F 11 " --> pdb=" O GLU F 105 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N LYS F 107 " --> pdb=" O LEU F 11 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ALA F 13 " --> pdb=" O LYS F 107 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N TYR F 86 " --> pdb=" O THR F 102 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU F 33 " --> pdb=" O TYR F 49 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N TYR F 49 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'F' and resid 114 through 118 removed outlier: 3.927A pdb=" N VAL F 133 " --> pdb=" O PHE F 118 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N CYS F 134 " --> pdb=" O SER F 177 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER F 176 " --> pdb=" O SER F 162 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLN F 160 " --> pdb=" O THR F 178 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'F' and resid 145 through 147 removed outlier: 4.210A pdb=" N LYS F 145 " --> pdb=" O THR F 197 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR F 197 " --> pdb=" O LYS F 145 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLN F 147 " --> pdb=" O GLU F 195 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N GLU F 195 " --> pdb=" O GLN F 147 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG4 Processing sheet with id=AG5, first strand: chain 'F' and resid 149 through 150 Processing sheet with id=AG6, first strand: chain 'G' and resid 18 through 21 removed outlier: 3.628A pdb=" N LEU G 80 " --> pdb=" O LEU G 20 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'G' and resid 57 through 59 removed outlier: 5.173A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER G 49 " --> pdb=" O TRP G 36 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TYR G 94 " --> pdb=" O VAL G 37 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER G 106 " --> pdb=" O ARG G 97 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'G' and resid 57 through 59 removed outlier: 5.173A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER G 49 " --> pdb=" O TRP G 36 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TYR G 94 " --> pdb=" O VAL G 37 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'G' and resid 124 through 127 removed outlier: 5.226A pdb=" N ALA G 141 " --> pdb=" O VAL G 188 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N VAL G 188 " --> pdb=" O ALA G 141 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N GLY G 143 " --> pdb=" O VAL G 186 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N VAL G 186 " --> pdb=" O GLY G 143 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N LEU G 145 " --> pdb=" O SER G 184 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N SER G 184 " --> pdb=" O LEU G 145 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N LYS G 147 " --> pdb=" O LEU G 182 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N LEU G 182 " --> pdb=" O LYS G 147 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'G' and resid 124 through 127 removed outlier: 5.226A pdb=" N ALA G 141 " --> pdb=" O VAL G 188 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N VAL G 188 " --> pdb=" O ALA G 141 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N GLY G 143 " --> pdb=" O VAL G 186 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N VAL G 186 " --> pdb=" O GLY G 143 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N LEU G 145 " --> pdb=" O SER G 184 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N SER G 184 " --> pdb=" O LEU G 145 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N LYS G 147 " --> pdb=" O LEU G 182 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N LEU G 182 " --> pdb=" O LYS G 147 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER G 181 " --> pdb=" O VAL G 173 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL G 173 " --> pdb=" O SER G 181 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'G' and resid 154 through 158 removed outlier: 3.554A pdb=" N THR G 155 " --> pdb=" O ASN G 203 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N TYR G 198 " --> pdb=" O VAL G 215 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL G 211 " --> pdb=" O VAL G 202 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AH4, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.298A pdb=" N GLY H 10 " --> pdb=" O THR H 122 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N MET H 34 " --> pdb=" O GLY H 50 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N GLY H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'H' and resid 144 through 146 removed outlier: 3.524A pdb=" N ASP H 209 " --> pdb=" O SER H 206 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'H' and resid 184 through 187 removed outlier: 6.582A pdb=" N TRP H 174 " --> pdb=" O LEU H 186 " (cutoff:3.500A) 1246 hydrogen bonds defined for protein. 3291 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: 15.11 Time building geometry restraints manager: 11.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.71 - 1.17: 3 1.17 - 1.62: 32213 1.62 - 2.08: 172 2.08 - 2.53: 2 2.53 - 2.99: 2 Bond restraints: 32392 Sorted by residual: bond pdb=" C THR A 333 " pdb=" N ASN A 334 " ideal model delta sigma weight residual 1.330 2.986 -1.656 1.39e-02 5.18e+03 1.42e+04 bond pdb=" C GLY B 526 " pdb=" N PRO B 527 " ideal model delta sigma weight residual 1.333 2.754 -1.421 1.44e-02 4.82e+03 9.73e+03 bond pdb=" C PRO C 330 " pdb=" N ASN C 331 " ideal model delta sigma weight residual 1.334 1.977 -0.643 1.33e-02 5.65e+03 2.34e+03 bond pdb=" C PRO A 330 " pdb=" N ASN A 331 " ideal model delta sigma weight residual 1.333 2.114 -0.781 1.73e-02 3.34e+03 2.04e+03 bond pdb=" C LYS C 529 " pdb=" N SER C 530 " ideal model delta sigma weight residual 1.332 0.713 0.619 1.40e-02 5.10e+03 1.96e+03 ... (remaining 32387 not shown) Histogram of bond angle deviations from ideal: 4.33 - 35.54: 3 35.54 - 66.74: 2 66.74 - 97.95: 77 97.95 - 129.16: 43915 129.16 - 160.37: 172 Bond angle restraints: 44169 Sorted by residual: angle pdb=" O GLY B 526 " pdb=" C GLY B 526 " pdb=" N PRO B 527 " ideal model delta sigma weight residual 121.77 4.33 117.44 1.00e+00 1.00e+00 1.38e+04 angle pdb=" CA LYS C 529 " pdb=" C LYS C 529 " pdb=" N SER C 530 " ideal model delta sigma weight residual 116.84 13.09 103.75 1.71e+00 3.42e-01 3.68e+03 angle pdb=" C LYS C 529 " pdb=" N SER C 530 " pdb=" CA SER C 530 " ideal model delta sigma weight residual 121.54 24.66 96.88 1.91e+00 2.74e-01 2.57e+03 angle pdb=" O LYS B 529 " pdb=" C LYS B 529 " pdb=" N SER B 530 " ideal model delta sigma weight residual 122.59 64.13 58.46 1.33e+00 5.65e-01 1.93e+03 angle pdb=" O LYS A 529 " pdb=" C LYS A 529 " pdb=" N SER A 530 " ideal model delta sigma weight residual 122.59 70.63 51.96 1.33e+00 5.65e-01 1.53e+03 ... (remaining 44164 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 17582 17.95 - 35.90: 1310 35.90 - 53.85: 223 53.85 - 71.80: 64 71.80 - 89.75: 28 Dihedral angle restraints: 19207 sinusoidal: 7120 harmonic: 12087 Sorted by residual: dihedral pdb=" C LEU G 11 " pdb=" N LEU G 11 " pdb=" CA LEU G 11 " pdb=" CB LEU G 11 " ideal model delta harmonic sigma weight residual -122.60 -61.84 -60.76 0 2.50e+00 1.60e-01 5.91e+02 dihedral pdb=" C LEU E 11 " pdb=" N LEU E 11 " pdb=" CA LEU E 11 " pdb=" CB LEU E 11 " ideal model delta harmonic sigma weight residual -122.60 -61.86 -60.74 0 2.50e+00 1.60e-01 5.90e+02 dihedral pdb=" N LEU G 11 " pdb=" C LEU G 11 " pdb=" CA LEU G 11 " pdb=" CB LEU G 11 " ideal model delta harmonic sigma weight residual 122.80 62.54 60.26 0 2.50e+00 1.60e-01 5.81e+02 ... (remaining 19204 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.175: 4867 0.175 - 0.350: 127 0.350 - 0.525: 35 0.525 - 0.700: 6 0.700 - 0.875: 8 Chirality restraints: 5043 Sorted by residual: chirality pdb=" CA PHE A 338 " pdb=" N PHE A 338 " pdb=" C PHE A 338 " pdb=" CB PHE A 338 " both_signs ideal model delta sigma weight residual False 2.51 1.64 0.87 2.00e-01 2.50e+01 1.91e+01 chirality pdb=" CA PHE B 338 " pdb=" N PHE B 338 " pdb=" C PHE B 338 " pdb=" CB PHE B 338 " both_signs ideal model delta sigma weight residual False 2.51 1.64 0.87 2.00e-01 2.50e+01 1.91e+01 chirality pdb=" CA SER E 30 " pdb=" N SER E 30 " pdb=" C SER E 30 " pdb=" CB SER E 30 " both_signs ideal model delta sigma weight residual False 2.51 1.64 0.87 2.00e-01 2.50e+01 1.90e+01 ... (remaining 5040 not shown) Planarity restraints: 5728 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY C 526 " -0.112 2.00e-02 2.50e+03 2.04e-01 4.17e+02 pdb=" C GLY C 526 " 0.346 2.00e-02 2.50e+03 pdb=" O GLY C 526 " -0.175 2.00e-02 2.50e+03 pdb=" N PRO C 527 " -0.059 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 333 " -0.111 2.00e-02 2.50e+03 1.68e-01 2.83e+02 pdb=" C THR A 333 " 0.286 2.00e-02 2.50e+03 pdb=" O THR A 333 " -0.131 2.00e-02 2.50e+03 pdb=" N ASN A 334 " -0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 529 " -0.117 2.00e-02 2.50e+03 1.51e-01 2.29e+02 pdb=" C LYS B 529 " 0.255 2.00e-02 2.50e+03 pdb=" O LYS B 529 " -0.030 2.00e-02 2.50e+03 pdb=" N SER B 530 " -0.108 2.00e-02 2.50e+03 ... (remaining 5725 not shown) Histogram of nonbonded interaction distances: 0.60 - 1.46: 12 1.46 - 2.32: 123 2.32 - 3.18: 27076 3.18 - 4.04: 77222 4.04 - 4.90: 141908 Warning: very small nonbonded interaction distances. Nonbonded interactions: 246341 Sorted by model distance: nonbonded pdb=" OD2 ASP B 364 " pdb=" CG PRO B 527 " model vdw 0.602 3.440 nonbonded pdb=" CA THR C 333 " pdb=" ND2 ASN C 334 " model vdw 0.894 3.550 nonbonded pdb=" NH1 ARG A 357 " pdb=" CA THR C 167 " model vdw 0.896 3.550 nonbonded pdb=" OD2 ASP A 364 " pdb=" CD PRO A 527 " model vdw 0.909 3.440 nonbonded pdb=" OD2 ASP A 364 " pdb=" CG PRO A 527 " model vdw 1.062 3.440 ... (remaining 246336 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'E' selection = chain 'G' } 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: 3.130 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: 0.030 Extract box with map and model: 1.180 Check model and map are aligned: 0.230 Set scattering table: 0.290 Process input model: 81.580 Find NCS groups from input model: 0.980 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 101.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6378 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 : 0.016 1.656 32392 Z= 1.100 Angle : 1.900 117.442 44169 Z= 1.280 Chirality : 0.082 0.875 5043 Planarity : 0.009 0.204 5728 Dihedral : 13.250 89.750 11302 Min Nonbonded Distance : 0.602 Molprobity Statistics. All-atom Clashscore : 15.05 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.51 % Favored : 95.30 % Rotamer: Outliers : 0.77 % Allowed : 1.18 % Favored : 98.05 % Cbeta Deviations : 2.37 % Peptide Plane: Cis-proline : 3.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.39 (0.13), residues: 4103 helix: 2.34 (0.21), residues: 660 sheet: 0.15 (0.15), residues: 1079 loop : -1.28 (0.12), residues: 2364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP B 353 HIS 0.006 0.001 HIS E 102 PHE 0.020 0.002 PHE B 400 TYR 0.029 0.002 TYR B 453 ARG 0.005 0.001 ARG C 403 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8206 Ramachandran restraints generated. 4103 Oldfield, 0 Emsley, 4103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8206 Ramachandran restraints generated. 4103 Oldfield, 0 Emsley, 4103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 3613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 427 time to evaluate : 3.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 468 ILE cc_start: 0.2895 (OUTLIER) cc_final: 0.2506 (mp) REVERT: B 866 THR cc_start: 0.7407 (p) cc_final: 0.6795 (t) outliers start: 26 outliers final: 2 residues processed: 452 average time/residue: 0.9856 time to fit residues: 562.1346 Evaluate side-chains 207 residues out of total 3613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 204 time to evaluate : 3.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 1114 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 349 optimal weight: 0.1980 chunk 313 optimal weight: 8.9990 chunk 174 optimal weight: 0.6980 chunk 107 optimal weight: 3.9990 chunk 211 optimal weight: 0.8980 chunk 167 optimal weight: 6.9990 chunk 324 optimal weight: 30.0000 chunk 125 optimal weight: 2.9990 chunk 197 optimal weight: 0.3980 chunk 241 optimal weight: 0.8980 chunk 375 optimal weight: 20.0000 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 ASN A 360 ASN A 505 HIS A 751 ASN A 784 GLN A 856 ASN A1010 GLN ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 ASN B 784 GLN B 914 ASN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN C 49 HIS C 61 ASN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 334 ASN C 460 ASN C 901 GLN C1074 ASN ** E 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 27 GLN D 166 GLN F 24 GLN F 27 GLN F 166 GLN ** G 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6855 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.104 32392 Z= 0.219 Angle : 0.640 13.225 44169 Z= 0.340 Chirality : 0.048 0.302 5043 Planarity : 0.006 0.079 5728 Dihedral : 5.116 58.531 4472 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.86 % Favored : 94.99 % Rotamer: Outliers : 2.36 % Allowed : 9.20 % Favored : 88.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.35 (0.13), residues: 4111 helix: 2.46 (0.21), residues: 651 sheet: 0.25 (0.15), residues: 1105 loop : -1.33 (0.12), residues: 2355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP H 36 HIS 0.005 0.001 HIS H 35 PHE 0.034 0.002 PHE B 377 TYR 0.025 0.002 TYR B 265 ARG 0.006 0.001 ARG C 457 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8222 Ramachandran restraints generated. 4111 Oldfield, 0 Emsley, 4111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8222 Ramachandran restraints generated. 4111 Oldfield, 0 Emsley, 4111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 3613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 209 time to evaluate : 3.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 GLU cc_start: 0.6172 (OUTLIER) cc_final: 0.5822 (mp0) REVERT: A 468 ILE cc_start: 0.2466 (OUTLIER) cc_final: 0.2131 (mp) REVERT: A 720 ILE cc_start: 0.7596 (OUTLIER) cc_final: 0.6937 (pt) REVERT: C 58 PHE cc_start: 0.6464 (m-10) cc_final: 0.6145 (m-10) REVERT: C 119 ILE cc_start: 0.4014 (mt) cc_final: 0.3808 (mt) REVERT: D 4 MET cc_start: 0.0617 (OUTLIER) cc_final: -0.0184 (mtt) REVERT: D 29 ILE cc_start: 0.4544 (OUTLIER) cc_final: 0.3668 (mm) outliers start: 80 outliers final: 29 residues processed: 271 average time/residue: 0.9499 time to fit residues: 329.5733 Evaluate side-chains 209 residues out of total 3613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 175 time to evaluate : 3.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 964 LYS Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain D residue 4 MET Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 58 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 208 optimal weight: 10.0000 chunk 116 optimal weight: 0.9980 chunk 312 optimal weight: 20.0000 chunk 256 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 376 optimal weight: 20.0000 chunk 406 optimal weight: 40.0000 chunk 335 optimal weight: 20.0000 chunk 373 optimal weight: 30.0000 chunk 128 optimal weight: 4.9990 chunk 302 optimal weight: 2.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 ASN B 125 ASN ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 GLN C 751 ASN C 901 GLN C 965 GLN ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 201 ASN ** G 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 201 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.4471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.085 32392 Z= 0.468 Angle : 0.741 14.962 44169 Z= 0.396 Chirality : 0.053 0.299 5043 Planarity : 0.006 0.089 5728 Dihedral : 5.416 57.548 4470 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.45 % Favored : 94.48 % Rotamer: Outliers : 3.77 % Allowed : 11.41 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.73 (0.12), residues: 4111 helix: 1.73 (0.20), residues: 650 sheet: 0.12 (0.15), residues: 1093 loop : -1.49 (0.12), residues: 2368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 353 HIS 0.008 0.001 HIS A1064 PHE 0.026 0.003 PHE B 559 TYR 0.029 0.002 TYR C 265 ARG 0.021 0.001 ARG G 71 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8222 Ramachandran restraints generated. 4111 Oldfield, 0 Emsley, 4111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8222 Ramachandran restraints generated. 4111 Oldfield, 0 Emsley, 4111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 3613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 203 time to evaluate : 3.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 GLU cc_start: 0.6659 (OUTLIER) cc_final: 0.6413 (mp0) REVERT: A 756 TYR cc_start: 0.7873 (OUTLIER) cc_final: 0.7269 (t80) REVERT: B 488 CYS cc_start: 0.1727 (OUTLIER) cc_final: 0.0304 (p) REVERT: B 756 TYR cc_start: 0.7925 (m-80) cc_final: 0.7687 (m-80) REVERT: C 314 GLN cc_start: 0.8082 (OUTLIER) cc_final: 0.7369 (tt0) REVERT: C 512 VAL cc_start: 0.4436 (OUTLIER) cc_final: 0.4118 (m) REVERT: E 82 MET cc_start: -0.0767 (mtt) cc_final: -0.1117 (ttt) REVERT: D 4 MET cc_start: 0.0747 (mpp) cc_final: 0.0305 (mtt) outliers start: 128 outliers final: 56 residues processed: 305 average time/residue: 1.0192 time to fit residues: 393.4070 Evaluate side-chains 205 residues out of total 3613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 144 time to evaluate : 3.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 810 SER Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 964 LYS Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain F residue 129 THR Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 71 ARG Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 165 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 372 optimal weight: 7.9990 chunk 283 optimal weight: 0.7980 chunk 195 optimal weight: 0.8980 chunk 41 optimal weight: 6.9990 chunk 179 optimal weight: 0.9990 chunk 252 optimal weight: 4.9990 chunk 377 optimal weight: 0.6980 chunk 400 optimal weight: 3.9990 chunk 197 optimal weight: 0.9990 chunk 358 optimal weight: 10.0000 chunk 107 optimal weight: 5.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN B 314 GLN B 321 GLN B 784 GLN B 992 GLN C 901 GLN ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 32 ASN D 199 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.4654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 32392 Z= 0.189 Angle : 0.573 13.040 44169 Z= 0.302 Chirality : 0.046 0.234 5043 Planarity : 0.005 0.063 5728 Dihedral : 4.822 44.349 4468 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.82 % Favored : 95.14 % Rotamer: Outliers : 3.07 % Allowed : 13.65 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.13), residues: 4111 helix: 2.21 (0.21), residues: 647 sheet: 0.32 (0.15), residues: 1117 loop : -1.40 (0.12), residues: 2347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP B 353 HIS 0.003 0.001 HIS H 35 PHE 0.016 0.001 PHE A 377 TYR 0.024 0.001 TYR B 265 ARG 0.009 0.000 ARG B 995 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8222 Ramachandran restraints generated. 4111 Oldfield, 0 Emsley, 4111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8222 Ramachandran restraints generated. 4111 Oldfield, 0 Emsley, 4111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 3613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 165 time to evaluate : 3.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 GLU cc_start: 0.6562 (OUTLIER) cc_final: 0.6358 (mp0) REVERT: B 756 TYR cc_start: 0.7944 (m-80) cc_final: 0.7642 (m-80) REVERT: B 820 ASP cc_start: 0.7626 (OUTLIER) cc_final: 0.7190 (m-30) REVERT: E 82 MET cc_start: -0.0876 (mtt) cc_final: -0.1289 (ttt) REVERT: E 101 ARG cc_start: 0.3194 (OUTLIER) cc_final: 0.1931 (ttm-80) REVERT: D 4 MET cc_start: 0.0742 (mpp) cc_final: -0.0033 (mtt) outliers start: 104 outliers final: 48 residues processed: 249 average time/residue: 0.9906 time to fit residues: 312.0431 Evaluate side-chains 196 residues out of total 3613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 145 time to evaluate : 3.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 810 SER Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 101 ARG Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain F residue 129 THR Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain G residue 120 THR Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 121 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 333 optimal weight: 40.0000 chunk 227 optimal weight: 0.6980 chunk 5 optimal weight: 6.9990 chunk 297 optimal weight: 1.9990 chunk 165 optimal weight: 0.0470 chunk 341 optimal weight: 0.0570 chunk 276 optimal weight: 0.8980 chunk 0 optimal weight: 8.9990 chunk 204 optimal weight: 7.9990 chunk 359 optimal weight: 20.0000 chunk 100 optimal weight: 0.7980 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 196 ASN B 314 GLN B 784 GLN B 914 ASN B 992 GLN ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 moved from start: 0.4823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 32392 Z= 0.151 Angle : 0.530 8.587 44169 Z= 0.278 Chirality : 0.044 0.212 5043 Planarity : 0.004 0.065 5728 Dihedral : 4.484 42.140 4468 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.45 % Favored : 95.50 % Rotamer: Outliers : 2.89 % Allowed : 14.77 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.13), residues: 4111 helix: 2.67 (0.21), residues: 630 sheet: 0.46 (0.15), residues: 1120 loop : -1.26 (0.12), residues: 2361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 353 HIS 0.002 0.000 HIS E 102 PHE 0.012 0.001 PHE C1121 TYR 0.022 0.001 TYR B 265 ARG 0.010 0.000 ARG C 983 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8222 Ramachandran restraints generated. 4111 Oldfield, 0 Emsley, 4111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8222 Ramachandran restraints generated. 4111 Oldfield, 0 Emsley, 4111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 3613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 158 time to evaluate : 3.211 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 756 TYR cc_start: 0.7960 (m-80) cc_final: 0.7630 (m-80) REVERT: C 512 VAL cc_start: 0.4428 (OUTLIER) cc_final: 0.4159 (m) REVERT: C 513 LEU cc_start: 0.4246 (OUTLIER) cc_final: 0.3811 (tp) REVERT: E 82 MET cc_start: -0.0808 (mtt) cc_final: -0.1189 (ttt) REVERT: D 4 MET cc_start: 0.0454 (OUTLIER) cc_final: -0.0453 (mtt) outliers start: 98 outliers final: 46 residues processed: 238 average time/residue: 0.9237 time to fit residues: 284.0126 Evaluate side-chains 194 residues out of total 3613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 145 time to evaluate : 3.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 810 SER Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 176 SER Chi-restraints excluded: chain D residue 4 MET Chi-restraints excluded: chain F residue 129 THR Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 112 LEU Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain G residue 120 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 134 optimal weight: 30.0000 chunk 360 optimal weight: 8.9990 chunk 79 optimal weight: 0.6980 chunk 234 optimal weight: 9.9990 chunk 98 optimal weight: 2.9990 chunk 400 optimal weight: 10.0000 chunk 332 optimal weight: 30.0000 chunk 185 optimal weight: 3.9990 chunk 33 optimal weight: 20.0000 chunk 132 optimal weight: 9.9990 chunk 210 optimal weight: 6.9990 overall best weight: 4.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN A 422 ASN B 314 GLN B 505 HIS B 784 GLN B 992 GLN C 474 GLN C 901 GLN C 957 GLN ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN F 124 GLN ** G 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.5575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.096 32392 Z= 0.641 Angle : 0.799 12.740 44169 Z= 0.424 Chirality : 0.057 0.401 5043 Planarity : 0.006 0.088 5728 Dihedral : 5.500 46.099 4466 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.96 % Favored : 93.97 % Rotamer: Outliers : 4.22 % Allowed : 14.60 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.86 (0.12), residues: 4111 helix: 1.44 (0.20), residues: 638 sheet: 0.06 (0.15), residues: 1124 loop : -1.53 (0.12), residues: 2349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP B 64 HIS 0.015 0.002 HIS B1048 PHE 0.037 0.003 PHE A 32 TYR 0.038 0.003 TYR C 265 ARG 0.011 0.001 ARG C1039 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8222 Ramachandran restraints generated. 4111 Oldfield, 0 Emsley, 4111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8222 Ramachandran restraints generated. 4111 Oldfield, 0 Emsley, 4111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 3613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 155 time to evaluate : 3.157 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 489 TYR cc_start: -0.0312 (OUTLIER) cc_final: -0.1735 (p90) REVERT: B 588 THR cc_start: 0.7963 (OUTLIER) cc_final: 0.7731 (p) REVERT: B 756 TYR cc_start: 0.8047 (m-80) cc_final: 0.7706 (m-80) REVERT: B 820 ASP cc_start: 0.7805 (OUTLIER) cc_final: 0.7359 (m-30) REVERT: B 1122 VAL cc_start: 0.8892 (OUTLIER) cc_final: 0.8511 (t) REVERT: C 100 ILE cc_start: 0.7317 (OUTLIER) cc_final: 0.7066 (mm) REVERT: C 314 GLN cc_start: 0.8406 (OUTLIER) cc_final: 0.7854 (tm-30) REVERT: C 321 GLN cc_start: 0.7754 (OUTLIER) cc_final: 0.7033 (mp10) REVERT: C 512 VAL cc_start: 0.4435 (OUTLIER) cc_final: 0.4158 (m) REVERT: C 513 LEU cc_start: 0.4223 (OUTLIER) cc_final: 0.3866 (tp) REVERT: C 720 ILE cc_start: 0.8607 (OUTLIER) cc_final: 0.8174 (pp) REVERT: E 82 MET cc_start: -0.0673 (mtt) cc_final: -0.1093 (ttt) REVERT: F 4 MET cc_start: 0.2528 (OUTLIER) cc_final: 0.2131 (mmp) outliers start: 143 outliers final: 78 residues processed: 272 average time/residue: 0.9781 time to fit residues: 342.3143 Evaluate side-chains 225 residues out of total 3613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 136 time to evaluate : 3.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 810 SER Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 321 GLN Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 567 ARG Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain F residue 4 MET Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain G residue 120 THR Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 185 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 386 optimal weight: 0.9980 chunk 45 optimal weight: 5.9990 chunk 228 optimal weight: 0.9990 chunk 292 optimal weight: 0.9980 chunk 226 optimal weight: 1.9990 chunk 337 optimal weight: 20.0000 chunk 223 optimal weight: 5.9990 chunk 399 optimal weight: 0.8980 chunk 249 optimal weight: 9.9990 chunk 243 optimal weight: 20.0000 chunk 184 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 69 HIS ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN B 784 GLN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.5611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 32392 Z= 0.198 Angle : 0.563 8.512 44169 Z= 0.297 Chirality : 0.046 0.279 5043 Planarity : 0.005 0.066 5728 Dihedral : 4.754 44.600 4466 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.26 % Favored : 95.69 % Rotamer: Outliers : 2.36 % Allowed : 16.90 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.52 (0.13), residues: 4111 helix: 2.14 (0.20), residues: 640 sheet: 0.23 (0.15), residues: 1118 loop : -1.42 (0.12), residues: 2353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 353 HIS 0.004 0.001 HIS E 102 PHE 0.015 0.001 PHE C1121 TYR 0.025 0.001 TYR B 265 ARG 0.012 0.000 ARG C 983 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8222 Ramachandran restraints generated. 4111 Oldfield, 0 Emsley, 4111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8222 Ramachandran restraints generated. 4111 Oldfield, 0 Emsley, 4111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 3613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 152 time to evaluate : 3.269 Fit side-chains revert: symmetry clash REVERT: A 309 GLU cc_start: 0.6683 (OUTLIER) cc_final: 0.6456 (mp0) REVERT: A 565 PHE cc_start: 0.5926 (m-10) cc_final: 0.5689 (m-10) REVERT: B 329 PHE cc_start: 0.6361 (m-80) cc_final: 0.6031 (m-80) REVERT: B 489 TYR cc_start: -0.0397 (OUTLIER) cc_final: -0.1698 (p90) REVERT: B 756 TYR cc_start: 0.8032 (m-80) cc_final: 0.7658 (m-80) REVERT: C 512 VAL cc_start: 0.4413 (OUTLIER) cc_final: 0.4147 (m) REVERT: C 513 LEU cc_start: 0.4209 (OUTLIER) cc_final: 0.3779 (tp) REVERT: C 720 ILE cc_start: 0.8301 (OUTLIER) cc_final: 0.7849 (pt) REVERT: E 82 MET cc_start: -0.0945 (mtt) cc_final: -0.1248 (ttt) REVERT: D 4 MET cc_start: 0.0863 (OUTLIER) cc_final: 0.0152 (mtt) REVERT: H 185 LEU cc_start: -0.1164 (OUTLIER) cc_final: -0.1500 (mp) outliers start: 80 outliers final: 43 residues processed: 214 average time/residue: 0.9973 time to fit residues: 271.3532 Evaluate side-chains 178 residues out of total 3613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 128 time to evaluate : 3.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 755 GLN Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 810 SER Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain D residue 4 MET Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 185 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 246 optimal weight: 20.0000 chunk 159 optimal weight: 2.9990 chunk 238 optimal weight: 7.9990 chunk 120 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 chunk 253 optimal weight: 2.9990 chunk 271 optimal weight: 0.5980 chunk 197 optimal weight: 1.9990 chunk 37 optimal weight: 20.0000 chunk 313 optimal weight: 9.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 804 GLN A1010 GLN ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN B 784 GLN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.5749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 32392 Z= 0.243 Angle : 0.573 11.263 44169 Z= 0.302 Chirality : 0.046 0.248 5043 Planarity : 0.005 0.067 5728 Dihedral : 4.671 43.361 4466 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.16 % Favored : 94.79 % Rotamer: Outliers : 2.86 % Allowed : 16.78 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.45 (0.13), residues: 4111 helix: 2.29 (0.21), residues: 639 sheet: 0.26 (0.15), residues: 1119 loop : -1.38 (0.12), residues: 2353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 64 HIS 0.004 0.001 HIS A1064 PHE 0.016 0.002 PHE C1121 TYR 0.024 0.001 TYR B 265 ARG 0.012 0.000 ARG C 983 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8222 Ramachandran restraints generated. 4111 Oldfield, 0 Emsley, 4111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8222 Ramachandran restraints generated. 4111 Oldfield, 0 Emsley, 4111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 3613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 144 time to evaluate : 3.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 329 PHE cc_start: 0.6418 (m-80) cc_final: 0.6130 (m-80) REVERT: B 489 TYR cc_start: -0.0592 (OUTLIER) cc_final: -0.1783 (p90) REVERT: B 756 TYR cc_start: 0.8080 (m-80) cc_final: 0.7671 (m-80) REVERT: C 512 VAL cc_start: 0.4415 (OUTLIER) cc_final: 0.4142 (m) REVERT: C 513 LEU cc_start: 0.4249 (OUTLIER) cc_final: 0.3804 (tp) REVERT: C 720 ILE cc_start: 0.8358 (OUTLIER) cc_final: 0.7873 (pt) REVERT: E 82 MET cc_start: -0.1067 (mtt) cc_final: -0.1301 (ttt) REVERT: D 4 MET cc_start: 0.0900 (OUTLIER) cc_final: 0.0178 (mtt) outliers start: 97 outliers final: 60 residues processed: 225 average time/residue: 0.9464 time to fit residues: 273.7667 Evaluate side-chains 202 residues out of total 3613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 137 time to evaluate : 3.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 810 SER Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 464 PHE Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 176 SER Chi-restraints excluded: chain D residue 4 MET Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 185 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 362 optimal weight: 7.9990 chunk 382 optimal weight: 30.0000 chunk 348 optimal weight: 9.9990 chunk 371 optimal weight: 20.0000 chunk 223 optimal weight: 9.9990 chunk 161 optimal weight: 3.9990 chunk 291 optimal weight: 5.9990 chunk 114 optimal weight: 2.9990 chunk 336 optimal weight: 6.9990 chunk 351 optimal weight: 7.9990 chunk 370 optimal weight: 20.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 544 ASN A 613 GLN A1083 HIS ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN B 784 GLN B 954 HIS B 957 GLN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 ASN C 196 ASN C 417 ASN C 901 GLN E 32 ASN G 3 GLN ** G 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 175 GLN H 13 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.6302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.104 32392 Z= 0.761 Angle : 0.867 12.259 44169 Z= 0.462 Chirality : 0.061 0.305 5043 Planarity : 0.007 0.068 5728 Dihedral : 5.860 48.898 4466 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.74 % Favored : 93.19 % Rotamer: Outliers : 3.33 % Allowed : 16.57 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.12), residues: 4111 helix: 0.93 (0.19), residues: 651 sheet: -0.15 (0.15), residues: 1101 loop : -1.68 (0.12), residues: 2359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP B 64 HIS 0.015 0.003 HIS C1048 PHE 0.033 0.004 PHE C 65 TYR 0.039 0.003 TYR C 265 ARG 0.017 0.001 ARG C 983 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8222 Ramachandran restraints generated. 4111 Oldfield, 0 Emsley, 4111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8222 Ramachandran restraints generated. 4111 Oldfield, 0 Emsley, 4111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 3613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 144 time to evaluate : 3.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 489 TYR cc_start: -0.0453 (OUTLIER) cc_final: -0.1829 (p90) REVERT: B 619 GLU cc_start: 0.5693 (pt0) cc_final: 0.5397 (pt0) REVERT: B 756 TYR cc_start: 0.8099 (m-80) cc_final: 0.7722 (m-80) REVERT: B 820 ASP cc_start: 0.7831 (OUTLIER) cc_final: 0.7441 (m-30) REVERT: C 398 ASP cc_start: 0.3228 (OUTLIER) cc_final: 0.2454 (t70) REVERT: C 513 LEU cc_start: 0.4101 (OUTLIER) cc_final: 0.3732 (tp) REVERT: C 720 ILE cc_start: 0.8649 (OUTLIER) cc_final: 0.8314 (pp) REVERT: C 740 MET cc_start: 0.8181 (ttt) cc_final: 0.7749 (ttt) REVERT: C 751 ASN cc_start: 0.7902 (m110) cc_final: 0.7638 (m110) REVERT: C 977 LEU cc_start: 0.8193 (OUTLIER) cc_final: 0.7562 (mp) REVERT: H 83 MET cc_start: 0.0848 (OUTLIER) cc_final: -0.0336 (mpp) outliers start: 113 outliers final: 76 residues processed: 237 average time/residue: 0.9493 time to fit residues: 292.1912 Evaluate side-chains 216 residues out of total 3613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 133 time to evaluate : 3.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 810 SER Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 464 PHE Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 58 VAL Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 165 SER Chi-restraints excluded: chain H residue 185 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 244 optimal weight: 10.0000 chunk 393 optimal weight: 40.0000 chunk 239 optimal weight: 0.9990 chunk 186 optimal weight: 0.8980 chunk 273 optimal weight: 0.0870 chunk 412 optimal weight: 8.9990 chunk 379 optimal weight: 20.0000 chunk 328 optimal weight: 20.0000 chunk 34 optimal weight: 4.9990 chunk 253 optimal weight: 1.9990 chunk 201 optimal weight: 1.9990 overall best weight: 1.1964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN B 314 GLN B 388 ASN B 784 GLN B 954 HIS ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 ASN E 32 ASN G 102 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.6245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 32392 Z= 0.237 Angle : 0.609 14.897 44169 Z= 0.321 Chirality : 0.047 0.236 5043 Planarity : 0.005 0.067 5728 Dihedral : 5.086 46.810 4466 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.82 % Favored : 95.14 % Rotamer: Outliers : 1.92 % Allowed : 18.05 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.77 (0.13), residues: 4111 helix: 1.85 (0.20), residues: 633 sheet: 0.12 (0.15), residues: 1117 loop : -1.57 (0.12), residues: 2361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 64 HIS 0.004 0.001 HIS E 102 PHE 0.015 0.001 PHE C1121 TYR 0.026 0.001 TYR B 265 ARG 0.016 0.001 ARG C 983 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8222 Ramachandran restraints generated. 4111 Oldfield, 0 Emsley, 4111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8222 Ramachandran restraints generated. 4111 Oldfield, 0 Emsley, 4111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains ************Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 309 GLU cc_start: 0.6867 (OUTLIER) cc_final: 0.6656 (mp0) REVERT: A 569 ILE cc_start: 0.7611 (mp) cc_final: 0.7346 (mp) REVERT: B 489 TYR cc_start: -0.0481 (OUTLIER) cc_final: -0.1796 (p90) REVERT: B 619 GLU cc_start: 0.5687 (pt0) cc_final: 0.5372 (pt0) REVERT: B 756 TYR cc_start: 0.8062 (m-80) cc_final: 0.7684 (m-80) REVERT: C 274 THR cc_start: 0.8698 (t) cc_final: 0.8383 (m) REVERT: C 398 ASP cc_start: 0.2637 (OUTLIER) cc_final: 0.2243 (t70) REVERT: C 513 LEU cc_start: 0.3992 (OUTLIER) cc_final: 0.3708 (tp) REVERT: C 720 ILE cc_start: 0.8400 (OUTLIER) cc_final: 0.7952 (pt) REVERT: D 4 MET cc_start: 0.1265 (OUTLIER) cc_final: 0.0079 (ttt) REVERT: H 185 LEU cc_start: -0.1701 (OUTLIER) cc_final: -0.2144 (pt) outliers start: 65 outliers final: 47 residues processed: 202 average time/residue: 0.8605 time to fit residues: 219.4676 Evaluate side-chains 189 residues out of total 3613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 135 time to evaluate : 3.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 810 SER Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain D residue 4 MET Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 185 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 260 optimal weight: 0.6980 chunk 349 optimal weight: 8.9990 chunk 100 optimal weight: 3.9990 chunk 302 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 328 optimal weight: 10.0000 chunk 137 optimal weight: 20.0000 chunk 337 optimal weight: 7.9990 chunk 41 optimal weight: 40.0000 chunk 60 optimal weight: 4.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN B 784 GLN B 954 HIS B 957 GLN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 245 HIS C 978 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4684 r_free = 0.4684 target = 0.225723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.169270 restraints weight = 46343.242| |-----------------------------------------------------------------------------| r_work (start): 0.4088 rms_B_bonded: 3.06 r_work: 0.3536 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.6357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.121 32392 Z= 0.405 Angle : 0.675 11.784 44169 Z= 0.356 Chirality : 0.050 0.288 5043 Planarity : 0.006 0.068 5728 Dihedral : 5.192 46.901 4466 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.89 % Favored : 94.09 % Rotamer: Outliers : 2.54 % Allowed : 17.40 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.84 (0.13), residues: 4111 helix: 1.71 (0.20), residues: 643 sheet: 0.08 (0.15), residues: 1123 loop : -1.61 (0.12), residues: 2345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 64 HIS 0.010 0.002 HIS C 245 PHE 0.022 0.002 PHE C 65 TYR 0.027 0.002 TYR C 265 ARG 0.015 0.001 ARG C 983 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7890.52 seconds wall clock time: 206 minutes 56.61 seconds (12416.61 seconds total)