Starting phenix.real_space_refine on Thu Mar 21 23:12:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dk6_30704/03_2024/7dk6_30704.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dk6_30704/03_2024/7dk6_30704.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dk6_30704/03_2024/7dk6_30704.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dk6_30704/03_2024/7dk6_30704.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dk6_30704/03_2024/7dk6_30704.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dk6_30704/03_2024/7dk6_30704.pdb" } resolution = 4.3 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= 0.006 sd= 0.079 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 144 5.16 5 C 19977 2.51 5 N 5259 2.21 5 O 6068 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 190": "NH1" <-> "NH2" Residue "d TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 31448 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 8295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1060, 8295 Classifications: {'peptide': 1060} Link IDs: {'PTRANS': 51, 'TRANS': 1008} Chain breaks: 6 Chain: "B" Number of atoms: 8295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1060, 8295 Classifications: {'peptide': 1060} Link IDs: {'PTRANS': 51, 'TRANS': 1008} Chain breaks: 6 Chain: "C" Number of atoms: 8280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1058, 8280 Classifications: {'peptide': 1058} Link IDs: {'PTRANS': 51, 'TRANS': 1006} Chain breaks: 6 Chain: "a" Number of atoms: 1603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1603 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 200} Chain: "b" Number of atoms: 1686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1686 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 4, 'PTRANS': 8, 'TRANS': 204} Chain: "c" Number of atoms: 1603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1603 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 200} Chain: "d" Number of atoms: 1686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1686 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 4, 'PTRANS': 8, 'TRANS': 204} Time building chain proxies: 16.33, per 1000 atoms: 0.52 Number of scatterers: 31448 At special positions: 0 Unit cell: (143.82, 159.12, 237.66, 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 144 16.00 O 6068 8.00 N 5259 7.00 C 19977 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=46, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " 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=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS a 22 " - pdb=" SG CYS a 95 " distance=2.03 Simple disulfide: pdb=" SG CYS a 144 " - pdb=" SG CYS a 199 " distance=2.03 Simple disulfide: pdb=" SG CYS b 23 " - pdb=" SG CYS b 92 " distance=2.03 Simple disulfide: pdb=" SG CYS b 138 " - pdb=" SG CYS b 198 " distance=2.03 Simple disulfide: pdb=" SG CYS c 22 " - pdb=" SG CYS c 95 " distance=2.03 Simple disulfide: pdb=" SG CYS c 144 " - pdb=" SG CYS c 199 " distance=2.03 Simple disulfide: pdb=" SG CYS d 23 " - pdb=" SG CYS d 92 " distance=2.03 Simple disulfide: pdb=" SG CYS d 138 " - pdb=" SG CYS d 198 " 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: 12.27 Conformation dependent library (CDL) restraints added in 5.6 seconds 7984 Ramachandran restraints generated. 3992 Oldfield, 0 Emsley, 3992 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7566 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 66 sheets defined 19.8% alpha, 31.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.90 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.560A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 386 through 390 Processing helix chain 'A' and resid 403 through 410 removed outlier: 3.599A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 421 Processing helix chain 'A' and resid 616 through 620 removed outlier: 3.634A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.502A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 782 removed outlier: 4.499A pdb=" N THR A 761 " --> pdb=" O GLY A 757 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.539A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.043A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.662A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1031 removed outlier: 3.978A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLN A1002 " --> pdb=" O THR A 998 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 386 through 390 removed outlier: 3.553A pdb=" N ASP B 389 " --> pdb=" O LYS B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 421 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.698A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 620 removed outlier: 3.606A pdb=" N VAL B 620 " --> pdb=" O CYS B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 removed outlier: 4.162A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) 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 782 removed outlier: 3.533A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 897 through 908 removed outlier: 3.668A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.250A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 966 removed outlier: 3.904A pdb=" N LEU B 966 " --> pdb=" O LEU B 962 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.231A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 3.697A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 365 through 370 removed outlier: 3.542A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 390 Processing helix chain 'C' and resid 403 through 410 removed outlier: 3.625A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 421 removed outlier: 3.738A pdb=" N TYR C 421 " --> pdb=" O LYS C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.782A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 782 removed outlier: 3.524A pdb=" N GLN C 774 " --> pdb=" O ILE C 770 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 825 removed outlier: 3.637A pdb=" N LEU C 821 " --> pdb=" O PHE C 817 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 removed outlier: 3.639A pdb=" N GLN C 872 " --> pdb=" O GLU C 868 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 891 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 968 removed outlier: 4.027A pdb=" N LEU C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N SER C 967 " --> pdb=" O VAL C 963 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER C 968 " --> pdb=" O LYS C 964 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.663A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 3.849A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'a' and resid 28 through 32 removed outlier: 3.667A pdb=" N TYR a 32 " --> pdb=" O LEU a 29 " (cutoff:3.500A) Processing helix chain 'a' and resid 86 through 90 removed outlier: 3.762A pdb=" N THR a 90 " --> pdb=" O THR a 87 " (cutoff:3.500A) Processing helix chain 'a' and resid 190 through 192 No H-bonds generated for 'chain 'a' and resid 190 through 192' Processing helix chain 'b' and resid 125 through 132 removed outlier: 3.650A pdb=" N GLY b 132 " --> pdb=" O GLN b 128 " (cutoff:3.500A) Processing helix chain 'b' and resid 187 through 191 Processing helix chain 'c' and resid 86 through 90 removed outlier: 3.738A pdb=" N THR c 90 " --> pdb=" O THR c 87 " (cutoff:3.500A) Processing helix chain 'd' and resid 125 through 132 Processing helix chain 'd' and resid 187 through 191 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 37 removed outlier: 7.066A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.895A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N LYS A 202 " --> pdb=" O ASN A 196 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N ASN A 196 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N TYR A 204 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N PHE A 194 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N LYS A 206 " --> pdb=" O PHE A 192 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N PHE A 192 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N THR A 208 " --> pdb=" O ARG A 190 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N ARG A 190 " --> pdb=" O THR A 208 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ILE A 210 " --> pdb=" O ASN A 188 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N ASN A 188 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL A 90 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA A 263 " --> pdb=" O ALA A 67 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 43 removed outlier: 4.655A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ILE B 587 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.517A pdb=" N VAL A 289 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.333A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ARG A 246 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N VAL A 143 " --> pdb=" O ARG A 246 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N PHE A 140 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N PHE A 157 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N GLY A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 84 through 85 removed outlier: 4.397A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.380A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 326 through 327 removed outlier: 5.200A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.600A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.683A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.024A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N TYR A 660 " --> pdb=" O SER A 698 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.024A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER A 673 " --> pdb=" O ILE A 693 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 701 through 703 removed outlier: 6.203A pdb=" N ALA A 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 728 removed outlier: 3.503A pdb=" N LYS A1073 " --> pdb=" O ILE A 714 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.246A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1094 through 1097 removed outlier: 5.117A pdb=" N GLN A1106 " --> pdb=" O GLU A1111 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N GLU A1111 " --> pdb=" O GLN A1106 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 27 through 30 removed outlier: 3.966A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA B 93 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL B 90 " --> pdb=" O PHE B 194 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LYS B 187 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL B 193 " --> pdb=" O TYR B 204 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 42 through 43 removed outlier: 6.384A pdb=" N PHE B 43 " --> pdb=" O ARG C 567 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE C 543 " --> pdb=" O LEU C 546 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.532A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG B 273 " --> pdb=" O ASP B 53 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 4.331A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 154 through 157 removed outlier: 6.483A pdb=" N GLY B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N THR B 259 " --> pdb=" O HIS B 245 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 314 removed outlier: 3.501A pdb=" N THR B 599 " --> pdb=" O GLY B 311 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.551A pdb=" N TRP B 436 " --> pdb=" O ARG B 509 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.539A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 452 through 454 removed outlier: 3.537A pdb=" N TYR B 453 " --> pdb=" O GLN B 493 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.945A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER B 673 " --> pdb=" O ILE B 693 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.415A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL B1068 " --> pdb=" O THR B 719 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.415A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL B1068 " --> pdb=" O THR B 719 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD4, first strand: chain 'B' and resid 788 through 790 removed outlier: 5.983A pdb=" N ILE B 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD6, first strand: chain 'C' and resid 27 through 30 removed outlier: 4.121A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA C 263 " --> pdb=" O ALA C 67 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA C 93 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N ASN C 188 " --> pdb=" O ILE C 210 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N ILE C 210 " --> pdb=" O ASN C 188 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N ARG C 190 " --> pdb=" O THR C 208 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N THR C 208 " --> pdb=" O ARG C 190 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N PHE C 192 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N LYS C 206 " --> pdb=" O PHE C 192 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N PHE C 194 " --> pdb=" O TYR C 204 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N TYR C 204 " --> pdb=" O PHE C 194 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N ASN C 196 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N LYS C 202 " --> pdb=" O ASN C 196 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.514A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ARG C 273 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.424A pdb=" N GLY C 142 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TYR C 144 " --> pdb=" O MET C 153 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N MET C 153 " --> pdb=" O TYR C 144 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 84 through 85 removed outlier: 4.415A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.488A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.624A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE4, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.965A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.588A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLN C 675 " --> pdb=" O SER C 691 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.339A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 734 through 736 removed outlier: 3.527A pdb=" N THR C 859 " --> pdb=" O SER C 735 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.573A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AE9, first strand: chain 'a' and resid 6 through 7 Processing sheet with id=AF1, first strand: chain 'a' and resid 57 through 59 removed outlier: 5.828A pdb=" N TRP a 47 " --> pdb=" O ARG a 38 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ARG a 38 " --> pdb=" O TRP a 47 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL a 34 " --> pdb=" O MET a 51 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA a 96 " --> pdb=" O HIS a 35 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N PHE a 106 " --> pdb=" O LYS a 97 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'a' and resid 57 through 59 removed outlier: 5.828A pdb=" N TRP a 47 " --> pdb=" O ARG a 38 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ARG a 38 " --> pdb=" O TRP a 47 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL a 34 " --> pdb=" O MET a 51 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA a 96 " --> pdb=" O HIS a 35 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL a 113 " --> pdb=" O ALA a 91 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR a 111 " --> pdb=" O TYR a 93 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'a' and resid 124 through 128 removed outlier: 5.907A pdb=" N TYR a 179 " --> pdb=" O GLY a 148 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'a' and resid 124 through 128 removed outlier: 5.907A pdb=" N TYR a 179 " --> pdb=" O GLY a 148 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'a' and resid 155 through 158 Processing sheet with id=AF6, first strand: chain 'b' and resid 5 through 7 Processing sheet with id=AF7, first strand: chain 'b' and resid 10 through 14 removed outlier: 6.360A pdb=" N LEU b 11 " --> pdb=" O GLU b 109 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N LYS b 111 " --> pdb=" O LEU b 11 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N VAL b 13 " --> pdb=" O LYS b 111 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N HIS b 38 " --> pdb=" O GLN b 93 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ILE b 52 " --> pdb=" O TRP b 39 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N GLN b 41 " --> pdb=" O LEU b 50 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N LEU b 50 " --> pdb=" O GLN b 41 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'b' and resid 120 through 122 removed outlier: 5.124A pdb=" N SER b 135 " --> pdb=" O LEU b 185 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N LEU b 185 " --> pdb=" O SER b 135 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N VAL b 137 " --> pdb=" O LEU b 183 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N LEU b 183 " --> pdb=" O VAL b 137 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N PHE b 139 " --> pdb=" O SER b 181 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N SER b 181 " --> pdb=" O PHE b 139 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ASN b 141 " --> pdb=" O MET b 179 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N MET b 179 " --> pdb=" O ASN b 141 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU b 164 " --> pdb=" O THR b 182 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'b' and resid 120 through 122 removed outlier: 5.124A pdb=" N SER b 135 " --> pdb=" O LEU b 185 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N LEU b 185 " --> pdb=" O SER b 135 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N VAL b 137 " --> pdb=" O LEU b 183 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N LEU b 183 " --> pdb=" O VAL b 137 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N PHE b 139 " --> pdb=" O SER b 181 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N SER b 181 " --> pdb=" O PHE b 139 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ASN b 141 " --> pdb=" O MET b 179 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N MET b 179 " --> pdb=" O ASN b 141 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER b 178 " --> pdb=" O THR b 168 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'b' and resid 148 through 150 Processing sheet with id=AG2, first strand: chain 'b' and resid 195 through 197 Processing sheet with id=AG3, first strand: chain 'c' and resid 6 through 7 removed outlier: 3.815A pdb=" N VAL c 78 " --> pdb=" O CYS c 22 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'c' and resid 57 through 59 removed outlier: 4.014A pdb=" N GLU c 46 " --> pdb=" O ARG c 38 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N TRP c 36 " --> pdb=" O LEU c 48 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA c 96 " --> pdb=" O HIS c 35 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N PHE c 106 " --> pdb=" O LYS c 97 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'c' and resid 57 through 59 removed outlier: 4.014A pdb=" N GLU c 46 " --> pdb=" O ARG c 38 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N TRP c 36 " --> pdb=" O LEU c 48 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA c 96 " --> pdb=" O HIS c 35 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'c' and resid 124 through 128 removed outlier: 4.025A pdb=" N LYS c 147 " --> pdb=" O SER c 124 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'c' and resid 124 through 128 removed outlier: 4.025A pdb=" N LYS c 147 " --> pdb=" O SER c 124 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU c 178 " --> pdb=" O GLN c 175 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N THR c 180 " --> pdb=" O VAL c 173 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'c' and resid 155 through 158 Processing sheet with id=AG9, first strand: chain 'd' and resid 6 through 7 Processing sheet with id=AH1, first strand: chain 'd' and resid 10 through 13 removed outlier: 3.505A pdb=" N HIS d 38 " --> pdb=" O GLN d 93 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ILE d 52 " --> pdb=" O TRP d 39 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N GLN d 41 " --> pdb=" O LEU d 50 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N LEU d 50 " --> pdb=" O GLN d 41 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'd' and resid 120 through 122 removed outlier: 3.602A pdb=" N SER d 120 " --> pdb=" O PHE d 139 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N TYR d 177 " --> pdb=" O ASN d 142 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N SER d 178 " --> pdb=" O THR d 168 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'd' and resid 148 through 154 removed outlier: 3.546A pdb=" N THR d 197 " --> pdb=" O LYS d 153 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS d 211 " --> pdb=" O CYS d 198 " (cutoff:3.500A) 1188 hydrogen bonds defined for protein. 3246 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: 14.69 Time building geometry restraints manager: 13.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10134 1.34 - 1.46: 7634 1.46 - 1.58: 14224 1.58 - 1.70: 0 1.70 - 1.82: 186 Bond restraints: 32178 Sorted by residual: bond pdb=" C PHE B 497 " pdb=" N GLN B 498 " ideal model delta sigma weight residual 1.329 1.364 -0.036 1.35e-02 5.49e+03 6.95e+00 bond pdb=" C THR B 599 " pdb=" N PRO B 600 " ideal model delta sigma weight residual 1.326 1.353 -0.027 1.44e-02 4.82e+03 3.59e+00 bond pdb=" N GLN c 1 " pdb=" CA GLN c 1 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.18e+00 bond pdb=" N ASN b 1 " pdb=" CA ASN b 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.02e+00 bond pdb=" N GLN B 14 " pdb=" CA GLN B 14 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.97e+00 ... (remaining 32173 not shown) Histogram of bond angle deviations from ideal: 100.49 - 107.19: 1055 107.19 - 113.89: 17691 113.89 - 120.59: 12035 120.59 - 127.29: 12669 127.29 - 133.99: 348 Bond angle restraints: 43798 Sorted by residual: angle pdb=" C GLU b 27 " pdb=" N SER b 28 " pdb=" CA SER b 28 " ideal model delta sigma weight residual 121.70 128.33 -6.63 1.80e+00 3.09e-01 1.36e+01 angle pdb=" C GLU d 27 " pdb=" N SER d 28 " pdb=" CA SER d 28 " ideal model delta sigma weight residual 121.70 127.62 -5.92 1.80e+00 3.09e-01 1.08e+01 angle pdb=" C ILE B 326 " pdb=" N VAL B 327 " pdb=" CA VAL B 327 " ideal model delta sigma weight residual 120.49 124.17 -3.68 1.38e+00 5.25e-01 7.12e+00 angle pdb=" C GLY A 482 " pdb=" N VAL A 483 " pdb=" CA VAL A 483 " ideal model delta sigma weight residual 120.35 124.05 -3.70 1.39e+00 5.18e-01 7.10e+00 angle pdb=" C GLU c 152 " pdb=" N PRO c 153 " pdb=" CA PRO c 153 " ideal model delta sigma weight residual 127.00 132.97 -5.97 2.40e+00 1.74e-01 6.19e+00 ... (remaining 43793 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 18737 17.99 - 35.99: 368 35.99 - 53.98: 66 53.98 - 71.97: 11 71.97 - 89.96: 10 Dihedral angle restraints: 19192 sinusoidal: 7439 harmonic: 11753 Sorted by residual: dihedral pdb=" CB CYS C1032 " pdb=" SG CYS C1032 " pdb=" SG CYS C1043 " pdb=" CB CYS C1043 " ideal model delta sinusoidal sigma weight residual 93.00 142.84 -49.84 1 1.00e+01 1.00e-02 3.41e+01 dihedral pdb=" CB CYS A1032 " pdb=" SG CYS A1032 " pdb=" SG CYS A1043 " pdb=" CB CYS A1043 " ideal model delta sinusoidal sigma weight residual 93.00 142.74 -49.74 1 1.00e+01 1.00e-02 3.40e+01 dihedral pdb=" CA ASN C 149 " pdb=" C ASN C 149 " pdb=" N LYS C 150 " pdb=" CA LYS C 150 " ideal model delta harmonic sigma weight residual 180.00 -158.77 -21.23 0 5.00e+00 4.00e-02 1.80e+01 ... (remaining 19189 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 3299 0.034 - 0.067: 1126 0.067 - 0.101: 234 0.101 - 0.135: 285 0.135 - 0.168: 13 Chirality restraints: 4957 Sorted by residual: chirality pdb=" CA ILE B 714 " pdb=" N ILE B 714 " pdb=" C ILE B 714 " pdb=" CB ILE B 714 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.07e-01 chirality pdb=" CA ILE C 714 " pdb=" N ILE C 714 " pdb=" C ILE C 714 " pdb=" CB ILE C 714 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.91e-01 chirality pdb=" CA ILE B 896 " pdb=" N ILE B 896 " pdb=" C ILE B 896 " pdb=" CB ILE B 896 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.27e-01 ... (remaining 4954 not shown) Planarity restraints: 5679 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY a 8 " 0.025 5.00e-02 4.00e+02 3.72e-02 2.21e+00 pdb=" N PRO a 9 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO a 9 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO a 9 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU a 152 " 0.023 5.00e-02 4.00e+02 3.47e-02 1.92e+00 pdb=" N PRO a 153 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO a 153 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO a 153 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 578 " -0.020 5.00e-02 4.00e+02 3.01e-02 1.45e+00 pdb=" N PRO B 579 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO B 579 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO B 579 " -0.017 5.00e-02 4.00e+02 ... (remaining 5676 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 444 2.66 - 3.22: 28974 3.22 - 3.78: 47414 3.78 - 4.34: 69447 4.34 - 4.90: 113094 Nonbonded interactions: 259373 Sorted by model distance: nonbonded pdb=" O GLN B 755 " pdb=" OG SER C 968 " model vdw 2.096 2.440 nonbonded pdb=" OG1 THR a 136 " pdb=" O MET a 139 " model vdw 2.101 2.440 nonbonded pdb=" O ASN C 439 " pdb=" OG SER C 443 " model vdw 2.102 2.440 nonbonded pdb=" OD2 ASP B 398 " pdb=" OH TYR B 423 " model vdw 2.111 2.440 nonbonded pdb=" OG1 THR C 912 " pdb=" OD1 ASN C 914 " model vdw 2.115 2.440 ... (remaining 259368 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 676 or resid 690 through 827 or resid 855 throu \ gh 1147)) selection = (chain 'B' and (resid 14 through 676 or resid 690 through 827 or resid 855 throu \ gh 1147)) selection = chain 'C' } ncs_group { reference = chain 'a' selection = chain 'c' } ncs_group { reference = chain 'b' selection = chain 'd' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 14.780 Check model and map are aligned: 0.500 Set scattering table: 0.290 Process input model: 83.890 Find NCS groups from input model: 1.970 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 107.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4535 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 : 0.003 0.039 32178 Z= 0.188 Angle : 0.542 6.626 43798 Z= 0.294 Chirality : 0.043 0.168 4957 Planarity : 0.002 0.037 5679 Dihedral : 7.786 89.963 11488 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 1.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 0.06 % Allowed : 0.74 % Favored : 99.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.17 (0.11), residues: 3992 helix: -1.48 (0.14), residues: 701 sheet: -1.92 (0.14), residues: 1066 loop : -2.44 (0.11), residues: 2225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 152 HIS 0.003 0.001 HIS A1048 PHE 0.014 0.001 PHE C 490 TYR 0.013 0.001 TYR C 873 ARG 0.003 0.000 ARG C 78 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7984 Ramachandran restraints generated. 3992 Oldfield, 0 Emsley, 3992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7984 Ramachandran restraints generated. 3992 Oldfield, 0 Emsley, 3992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1116 residues out of total 3531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1114 time to evaluate : 3.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 ASN cc_start: 0.3413 (t0) cc_final: 0.2865 (t0) REVERT: A 224 GLU cc_start: 0.5963 (mt-10) cc_final: 0.5561 (mt-10) REVERT: A 353 TRP cc_start: 0.3667 (p90) cc_final: 0.3351 (p90) REVERT: A 395 VAL cc_start: 0.6867 (t) cc_final: 0.6631 (t) REVERT: A 449 TYR cc_start: 0.2946 (m-80) cc_final: 0.2691 (m-80) REVERT: A 612 TYR cc_start: 0.6968 (m-80) cc_final: 0.6500 (m-80) REVERT: A 724 THR cc_start: 0.6869 (m) cc_final: 0.6014 (t) REVERT: A 736 VAL cc_start: 0.7880 (t) cc_final: 0.7544 (p) REVERT: A 805 ILE cc_start: 0.9427 (pt) cc_final: 0.9221 (pt) REVERT: A 901 GLN cc_start: 0.7896 (mt0) cc_final: 0.7512 (tt0) REVERT: A 907 ASN cc_start: 0.7780 (m-40) cc_final: 0.6953 (m-40) REVERT: A 960 ASN cc_start: 0.6634 (m-40) cc_final: 0.6431 (m-40) REVERT: A 998 THR cc_start: 0.8323 (p) cc_final: 0.8023 (t) REVERT: A 1007 TYR cc_start: 0.7768 (t80) cc_final: 0.6999 (t80) REVERT: A 1033 VAL cc_start: 0.8787 (t) cc_final: 0.8293 (t) REVERT: A 1041 ASP cc_start: 0.7022 (t0) cc_final: 0.6802 (t0) REVERT: A 1081 ILE cc_start: 0.8031 (pp) cc_final: 0.7693 (pp) REVERT: A 1115 ILE cc_start: 0.7269 (mt) cc_final: 0.6967 (mt) REVERT: B 141 LEU cc_start: 0.7347 (mt) cc_final: 0.7098 (mp) REVERT: B 572 THR cc_start: 0.7209 (p) cc_final: 0.6710 (m) REVERT: B 592 PHE cc_start: 0.5979 (t80) cc_final: 0.5177 (t80) REVERT: B 645 THR cc_start: 0.7829 (p) cc_final: 0.7117 (p) REVERT: B 736 VAL cc_start: 0.7747 (t) cc_final: 0.7373 (t) REVERT: B 753 LEU cc_start: 0.7413 (tp) cc_final: 0.6669 (tp) REVERT: B 803 SER cc_start: 0.7276 (p) cc_final: 0.7062 (m) REVERT: B 822 LEU cc_start: 0.8577 (mt) cc_final: 0.7706 (mt) REVERT: B 888 PHE cc_start: 0.8014 (p90) cc_final: 0.7796 (p90) REVERT: B 1027 THR cc_start: 0.8362 (m) cc_final: 0.7972 (t) REVERT: B 1051 SER cc_start: 0.8008 (m) cc_final: 0.7793 (p) REVERT: B 1054 GLN cc_start: 0.8099 (mm-40) cc_final: 0.7539 (mm-40) REVERT: B 1061 VAL cc_start: 0.9041 (t) cc_final: 0.8703 (p) REVERT: B 1141 LEU cc_start: 0.5650 (mp) cc_final: 0.4580 (mp) REVERT: C 64 TRP cc_start: 0.3613 (t60) cc_final: 0.3401 (t60) REVERT: C 196 ASN cc_start: 0.7477 (t0) cc_final: 0.6742 (m-40) REVERT: C 197 ILE cc_start: 0.6720 (mt) cc_final: 0.6494 (pt) REVERT: C 805 ILE cc_start: 0.9104 (pt) cc_final: 0.8894 (pt) REVERT: C 864 LEU cc_start: 0.8152 (tp) cc_final: 0.7611 (tp) REVERT: C 882 ILE cc_start: 0.8570 (mt) cc_final: 0.7896 (mt) REVERT: C 907 ASN cc_start: 0.8030 (m-40) cc_final: 0.7763 (m-40) REVERT: C 916 LEU cc_start: 0.7437 (tt) cc_final: 0.7166 (tt) REVERT: C 993 ILE cc_start: 0.7259 (mt) cc_final: 0.6995 (mt) REVERT: C 1023 ASN cc_start: 0.7040 (m-40) cc_final: 0.6617 (t0) REVERT: a 52 TRP cc_start: 0.3491 (m-10) cc_final: 0.3274 (m-10) REVERT: a 90 THR cc_start: 0.2614 (m) cc_final: 0.2397 (t) REVERT: a 139 MET cc_start: -0.1767 (mmm) cc_final: -0.3345 (tmm) REVERT: a 159 ASN cc_start: 0.2313 (m-40) cc_final: 0.1459 (t0) REVERT: b 110 ILE cc_start: 0.6098 (mm) cc_final: 0.5591 (mm) REVERT: c 113 VAL cc_start: 0.4807 (t) cc_final: 0.4571 (t) REVERT: c 144 CYS cc_start: -0.0627 (OUTLIER) cc_final: -0.2179 (p) REVERT: d 218 CYS cc_start: 0.5939 (t) cc_final: 0.5571 (t) outliers start: 2 outliers final: 0 residues processed: 1115 average time/residue: 0.4323 time to fit residues: 758.2702 Evaluate side-chains 533 residues out of total 3531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 532 time to evaluate : 3.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 338 optimal weight: 1.9990 chunk 303 optimal weight: 0.9990 chunk 168 optimal weight: 10.0000 chunk 103 optimal weight: 0.0370 chunk 205 optimal weight: 0.9980 chunk 162 optimal weight: 0.8980 chunk 314 optimal weight: 1.9990 chunk 121 optimal weight: 5.9990 chunk 191 optimal weight: 0.0170 chunk 233 optimal weight: 1.9990 chunk 364 optimal weight: 8.9990 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN A 540 ASN A 955 ASN A 969 ASN A1058 HIS B 125 ASN B 149 ASN B 188 ASN B 388 ASN B 606 ASN B 751 ASN ** B 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN ** C 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 ASN C 544 ASN C 779 GLN ** C 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 GLN C 953 ASN C1005 GLN C1011 GLN C1023 ASN a 73 ASN a 102 HIS a 200 ASN b 93 GLN b 160 GLN c 98 ASN d 41 GLN d 57 ASN d 94 GLN ** d 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4854 moved from start: 0.3293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 32178 Z= 0.185 Angle : 0.560 12.533 43798 Z= 0.290 Chirality : 0.045 0.232 4957 Planarity : 0.004 0.075 5679 Dihedral : 3.655 20.202 4321 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 0.25 % Allowed : 2.01 % Favored : 97.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.12), residues: 3992 helix: 0.26 (0.18), residues: 711 sheet: -1.00 (0.15), residues: 1018 loop : -1.87 (0.12), residues: 2263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 64 HIS 0.005 0.001 HIS d 202 PHE 0.031 0.002 PHE B 823 TYR 0.020 0.001 TYR d 32 ARG 0.005 0.001 ARG C 577 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7984 Ramachandran restraints generated. 3992 Oldfield, 0 Emsley, 3992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7984 Ramachandran restraints generated. 3992 Oldfield, 0 Emsley, 3992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 763 residues out of total 3531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 754 time to evaluate : 3.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.6295 (mtt-85) cc_final: 0.6035 (mtt-85) REVERT: A 196 ASN cc_start: 0.3294 (t0) cc_final: 0.3071 (t0) REVERT: A 224 GLU cc_start: 0.6054 (mt-10) cc_final: 0.5853 (mt-10) REVERT: A 724 THR cc_start: 0.6511 (m) cc_final: 0.6259 (t) REVERT: A 901 GLN cc_start: 0.7853 (mt0) cc_final: 0.7438 (tt0) REVERT: A 969 ASN cc_start: 0.6488 (m-40) cc_final: 0.6215 (m110) REVERT: A 1009 THR cc_start: 0.8786 (m) cc_final: 0.8510 (m) REVERT: B 572 THR cc_start: 0.7022 (p) cc_final: 0.6520 (m) REVERT: B 753 LEU cc_start: 0.7699 (tp) cc_final: 0.7462 (tp) REVERT: B 803 SER cc_start: 0.6955 (p) cc_final: 0.6675 (m) REVERT: B 822 LEU cc_start: 0.8495 (mt) cc_final: 0.7827 (mt) REVERT: B 867 ASP cc_start: 0.6367 (p0) cc_final: 0.5968 (p0) REVERT: B 921 LYS cc_start: 0.7337 (ptmt) cc_final: 0.7087 (ptmm) REVERT: B 1004 LEU cc_start: 0.8399 (mt) cc_final: 0.7985 (tp) REVERT: B 1054 GLN cc_start: 0.8441 (mm-40) cc_final: 0.7934 (mm-40) REVERT: B 1061 VAL cc_start: 0.8930 (t) cc_final: 0.8568 (p) REVERT: C 196 ASN cc_start: 0.7315 (t0) cc_final: 0.6509 (m-40) REVERT: C 197 ILE cc_start: 0.6736 (mt) cc_final: 0.6474 (mt) REVERT: C 238 PHE cc_start: 0.6237 (p90) cc_final: 0.6000 (p90) REVERT: C 710 ASN cc_start: 0.5648 (p0) cc_final: 0.5422 (p0) REVERT: C 901 GLN cc_start: 0.8291 (tt0) cc_final: 0.7941 (tt0) REVERT: C 933 LYS cc_start: 0.8450 (ttpt) cc_final: 0.8191 (tppt) REVERT: C 952 VAL cc_start: 0.7881 (m) cc_final: 0.7591 (t) REVERT: C 1023 ASN cc_start: 0.7705 (m110) cc_final: 0.7161 (t0) REVERT: C 1042 PHE cc_start: 0.8120 (t80) cc_final: 0.7481 (t80) REVERT: C 1092 GLU cc_start: 0.6588 (pp20) cc_final: 0.6293 (pp20) REVERT: C 1112 PRO cc_start: 0.7241 (Cg_exo) cc_final: 0.6916 (Cg_endo) REVERT: a 106 PHE cc_start: -0.0458 (m-80) cc_final: -0.0789 (m-80) REVERT: a 139 MET cc_start: -0.1163 (mmm) cc_final: -0.3081 (tmm) REVERT: a 159 ASN cc_start: 0.2207 (m-40) cc_final: 0.1380 (m-40) REVERT: a 160 SER cc_start: 0.4634 (m) cc_final: 0.4330 (t) REVERT: c 94 TYR cc_start: 0.2176 (m-80) cc_final: 0.1524 (m-10) REVERT: d 178 SER cc_start: 0.2181 (t) cc_final: 0.1462 (m) outliers start: 9 outliers final: 1 residues processed: 759 average time/residue: 0.4169 time to fit residues: 510.7505 Evaluate side-chains 470 residues out of total 3531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 469 time to evaluate : 3.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 202 optimal weight: 3.9990 chunk 113 optimal weight: 7.9990 chunk 303 optimal weight: 1.9990 chunk 247 optimal weight: 0.9980 chunk 100 optimal weight: 0.5980 chunk 364 optimal weight: 0.8980 chunk 394 optimal weight: 2.9990 chunk 324 optimal weight: 5.9990 chunk 361 optimal weight: 7.9990 chunk 124 optimal weight: 0.9990 chunk 292 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1058 HIS B 81 ASN B 317 ASN B 774 GLN ** B 779 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 784 GLN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 954 GLN B1005 GLN ** C 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 ASN ** C 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 409 GLN C 777 ASN ** C 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 953 ASN C 955 ASN ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1101 HIS a 200 ASN b 41 GLN b 46 GLN b 160 GLN b 214 ASN c 39 GLN c 200 ASN ** d 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4975 moved from start: 0.4177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 32178 Z= 0.197 Angle : 0.548 11.886 43798 Z= 0.282 Chirality : 0.044 0.246 4957 Planarity : 0.004 0.115 5679 Dihedral : 3.884 25.762 4321 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 0.08 % Allowed : 2.18 % Favored : 97.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.12), residues: 3992 helix: 0.61 (0.19), residues: 717 sheet: -0.71 (0.15), residues: 1026 loop : -1.66 (0.12), residues: 2249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 258 HIS 0.006 0.001 HIS d 202 PHE 0.037 0.002 PHE c 80 TYR 0.018 0.002 TYR d 32 ARG 0.021 0.001 ARG C 273 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7984 Ramachandran restraints generated. 3992 Oldfield, 0 Emsley, 3992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7984 Ramachandran restraints generated. 3992 Oldfield, 0 Emsley, 3992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 655 residues out of total 3531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 652 time to evaluate : 3.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 LEU cc_start: 0.5349 (mm) cc_final: 0.4947 (mm) REVERT: A 724 THR cc_start: 0.6879 (m) cc_final: 0.6665 (t) REVERT: A 758 SER cc_start: 0.7138 (t) cc_final: 0.6745 (t) REVERT: A 867 ASP cc_start: 0.6013 (t0) cc_final: 0.5698 (t0) REVERT: A 901 GLN cc_start: 0.7911 (mt0) cc_final: 0.7678 (tt0) REVERT: A 959 LEU cc_start: 0.7699 (tt) cc_final: 0.7486 (tt) REVERT: A 969 ASN cc_start: 0.6554 (m-40) cc_final: 0.6128 (m110) REVERT: A 1013 ILE cc_start: 0.8894 (mt) cc_final: 0.8594 (mt) REVERT: A 1128 VAL cc_start: 0.7285 (m) cc_final: 0.6797 (t) REVERT: B 303 LEU cc_start: 0.7669 (mt) cc_final: 0.7300 (mt) REVERT: B 572 THR cc_start: 0.7036 (p) cc_final: 0.6737 (m) REVERT: B 645 THR cc_start: 0.7946 (p) cc_final: 0.7687 (p) REVERT: B 753 LEU cc_start: 0.7707 (tp) cc_final: 0.7457 (tp) REVERT: B 820 ASP cc_start: 0.5179 (t0) cc_final: 0.4766 (t0) REVERT: B 822 LEU cc_start: 0.8285 (mt) cc_final: 0.7664 (mt) REVERT: B 867 ASP cc_start: 0.6121 (p0) cc_final: 0.5764 (p0) REVERT: B 1054 GLN cc_start: 0.8594 (mm-40) cc_final: 0.8313 (mm-40) REVERT: B 1061 VAL cc_start: 0.8882 (t) cc_final: 0.8630 (p) REVERT: C 196 ASN cc_start: 0.7424 (t0) cc_final: 0.6597 (m-40) REVERT: C 197 ILE cc_start: 0.6662 (mt) cc_final: 0.6397 (mt) REVERT: C 238 PHE cc_start: 0.6223 (p90) cc_final: 0.5873 (p90) REVERT: C 569 ILE cc_start: 0.7071 (pt) cc_final: 0.6768 (pt) REVERT: C 901 GLN cc_start: 0.8293 (tt0) cc_final: 0.7838 (tt0) REVERT: C 917 TYR cc_start: 0.8048 (m-80) cc_final: 0.7822 (m-80) REVERT: C 961 THR cc_start: 0.8885 (p) cc_final: 0.8626 (p) REVERT: C 962 LEU cc_start: 0.9006 (tp) cc_final: 0.8795 (tp) REVERT: C 977 LEU cc_start: 0.7589 (mm) cc_final: 0.7334 (mm) REVERT: C 1023 ASN cc_start: 0.7414 (m110) cc_final: 0.7068 (t0) REVERT: C 1063 LEU cc_start: 0.8330 (mt) cc_final: 0.7949 (mt) REVERT: C 1092 GLU cc_start: 0.6760 (pp20) cc_final: 0.6381 (pp20) REVERT: C 1112 PRO cc_start: 0.7229 (Cg_exo) cc_final: 0.7002 (Cg_endo) REVERT: a 106 PHE cc_start: 0.0012 (m-80) cc_final: -0.0590 (m-80) REVERT: a 139 MET cc_start: -0.1093 (mmm) cc_final: -0.3131 (tmm) REVERT: d 178 SER cc_start: 0.2464 (t) cc_final: 0.2041 (m) outliers start: 3 outliers final: 0 residues processed: 654 average time/residue: 0.4069 time to fit residues: 437.9600 Evaluate side-chains 429 residues out of total 3531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 429 time to evaluate : 3.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 360 optimal weight: 5.9990 chunk 274 optimal weight: 0.0980 chunk 189 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 174 optimal weight: 0.9990 chunk 244 optimal weight: 5.9990 chunk 366 optimal weight: 5.9990 chunk 387 optimal weight: 4.9990 chunk 191 optimal weight: 10.0000 chunk 346 optimal weight: 4.9990 chunk 104 optimal weight: 0.2980 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 ASN ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 540 ASN A 907 ASN A 953 ASN A1058 HIS B 343 ASN B 388 ASN ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 GLN ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 920 GLN ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 544 ASN C 655 HIS C 804 GLN C 907 ASN C 953 ASN C 955 ASN ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1054 GLN ** a 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 159 ASN b 41 GLN b 160 GLN ** d 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5267 moved from start: 0.5454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 32178 Z= 0.330 Angle : 0.680 13.791 43798 Z= 0.355 Chirality : 0.047 0.369 4957 Planarity : 0.005 0.078 5679 Dihedral : 4.811 36.027 4321 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 18.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 0.03 % Allowed : 3.00 % Favored : 96.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.12), residues: 3992 helix: 0.28 (0.18), residues: 728 sheet: -0.72 (0.15), residues: 1024 loop : -1.75 (0.12), residues: 2240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 886 HIS 0.010 0.002 HIS c 203 PHE 0.035 0.003 PHE C 559 TYR 0.027 0.002 TYR B 365 ARG 0.018 0.001 ARG B 246 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7984 Ramachandran restraints generated. 3992 Oldfield, 0 Emsley, 3992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7984 Ramachandran restraints generated. 3992 Oldfield, 0 Emsley, 3992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 611 residues out of total 3531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 610 time to evaluate : 3.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 LEU cc_start: 0.5856 (mm) cc_final: 0.5604 (mm) REVERT: A 867 ASP cc_start: 0.5934 (t0) cc_final: 0.5632 (t0) REVERT: A 907 ASN cc_start: 0.7349 (m110) cc_final: 0.6646 (m-40) REVERT: A 955 ASN cc_start: 0.8086 (m-40) cc_final: 0.7817 (t0) REVERT: A 962 LEU cc_start: 0.7945 (tp) cc_final: 0.7685 (tp) REVERT: A 969 ASN cc_start: 0.6648 (m-40) cc_final: 0.6191 (m110) REVERT: A 1055 SER cc_start: 0.8681 (t) cc_final: 0.8459 (p) REVERT: A 1128 VAL cc_start: 0.7553 (m) cc_final: 0.7052 (t) REVERT: B 101 ILE cc_start: 0.6291 (tt) cc_final: 0.6068 (tt) REVERT: B 572 THR cc_start: 0.7365 (p) cc_final: 0.6517 (m) REVERT: B 797 PHE cc_start: 0.6850 (m-80) cc_final: 0.6535 (m-80) REVERT: B 822 LEU cc_start: 0.8236 (mt) cc_final: 0.7995 (mt) REVERT: B 881 THR cc_start: 0.7418 (p) cc_final: 0.7201 (p) REVERT: B 882 ILE cc_start: 0.8804 (mt) cc_final: 0.8315 (mp) REVERT: B 921 LYS cc_start: 0.7329 (ptmt) cc_final: 0.7045 (ttpp) REVERT: B 1061 VAL cc_start: 0.8941 (t) cc_final: 0.8644 (p) REVERT: C 135 PHE cc_start: 0.3891 (m-80) cc_final: 0.3681 (m-80) REVERT: C 170 TYR cc_start: 0.5538 (t80) cc_final: 0.5098 (t80) REVERT: C 197 ILE cc_start: 0.6669 (mt) cc_final: 0.6437 (mt) REVERT: C 592 PHE cc_start: 0.6217 (t80) cc_final: 0.5688 (t80) REVERT: C 961 THR cc_start: 0.8790 (p) cc_final: 0.8539 (p) REVERT: C 1023 ASN cc_start: 0.7316 (m110) cc_final: 0.7080 (t0) REVERT: C 1092 GLU cc_start: 0.6964 (pp20) cc_final: 0.6278 (pp20) REVERT: C 1112 PRO cc_start: 0.7413 (Cg_exo) cc_final: 0.7045 (Cg_endo) REVERT: a 87 THR cc_start: 0.2494 (p) cc_final: 0.2192 (p) REVERT: a 106 PHE cc_start: -0.0002 (m-80) cc_final: -0.0462 (m-80) REVERT: a 139 MET cc_start: -0.1083 (mmm) cc_final: -0.3203 (tmm) REVERT: a 211 ASP cc_start: 0.4654 (m-30) cc_final: 0.2894 (p0) REVERT: b 179 MET cc_start: 0.0817 (tmm) cc_final: 0.0372 (tmm) REVERT: d 218 CYS cc_start: 0.5886 (t) cc_final: 0.5396 (t) outliers start: 1 outliers final: 0 residues processed: 611 average time/residue: 0.4006 time to fit residues: 402.6719 Evaluate side-chains 400 residues out of total 3531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 400 time to evaluate : 3.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 322 optimal weight: 2.9990 chunk 220 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 288 optimal weight: 4.9990 chunk 159 optimal weight: 5.9990 chunk 330 optimal weight: 7.9990 chunk 267 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 197 optimal weight: 0.5980 chunk 347 optimal weight: 5.9990 chunk 97 optimal weight: 0.7980 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 540 ASN A 919 ASN ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 388 ASN ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN C 450 ASN C 544 ASN ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 39 GLN a 159 ASN a 175 GLN ** b 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 160 GLN d 41 GLN ** d 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5364 moved from start: 0.6315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 32178 Z= 0.314 Angle : 0.671 14.434 43798 Z= 0.352 Chirality : 0.048 0.450 4957 Planarity : 0.005 0.083 5679 Dihedral : 5.159 34.045 4321 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 19.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 0.03 % Allowed : 2.27 % Favored : 97.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.12), residues: 3992 helix: 0.17 (0.19), residues: 733 sheet: -0.81 (0.16), residues: 1025 loop : -1.85 (0.12), residues: 2234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP a 158 HIS 0.007 0.002 HIS c 203 PHE 0.031 0.003 PHE C 559 TYR 0.029 0.002 TYR C1047 ARG 0.014 0.001 ARG A 44 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7984 Ramachandran restraints generated. 3992 Oldfield, 0 Emsley, 3992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7984 Ramachandran restraints generated. 3992 Oldfield, 0 Emsley, 3992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 576 residues out of total 3531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 575 time to evaluate : 3.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 LEU cc_start: 0.5995 (mm) cc_final: 0.5455 (mm) REVERT: A 274 THR cc_start: 0.6152 (m) cc_final: 0.5746 (m) REVERT: A 741 TYR cc_start: 0.7559 (t80) cc_final: 0.7173 (t80) REVERT: A 805 ILE cc_start: 0.9278 (pt) cc_final: 0.9077 (pt) REVERT: A 955 ASN cc_start: 0.8125 (m-40) cc_final: 0.7880 (t0) REVERT: A 962 LEU cc_start: 0.8040 (tp) cc_final: 0.7327 (tp) REVERT: A 969 ASN cc_start: 0.6996 (m-40) cc_final: 0.6746 (m110) REVERT: A 1128 VAL cc_start: 0.7646 (m) cc_final: 0.7088 (t) REVERT: B 736 VAL cc_start: 0.7516 (t) cc_final: 0.7303 (p) REVERT: B 874 THR cc_start: 0.7619 (p) cc_final: 0.7174 (p) REVERT: B 921 LYS cc_start: 0.7451 (ptmt) cc_final: 0.7091 (ttpp) REVERT: B 1050 MET cc_start: 0.6312 (ptt) cc_final: 0.5956 (ptt) REVERT: C 38 TYR cc_start: 0.8282 (m-80) cc_final: 0.8025 (m-80) REVERT: C 170 TYR cc_start: 0.5747 (t80) cc_final: 0.5437 (t80) REVERT: C 238 PHE cc_start: 0.6242 (p90) cc_final: 0.5935 (p90) REVERT: C 275 PHE cc_start: 0.7530 (m-80) cc_final: 0.7045 (m-80) REVERT: C 592 PHE cc_start: 0.6621 (t80) cc_final: 0.6024 (t80) REVERT: C 882 ILE cc_start: 0.8678 (OUTLIER) cc_final: 0.8261 (mp) REVERT: C 933 LYS cc_start: 0.8681 (ttpt) cc_final: 0.8386 (tptt) REVERT: C 1050 MET cc_start: 0.6857 (ptp) cc_final: 0.6454 (ptm) REVERT: C 1092 GLU cc_start: 0.6687 (pp20) cc_final: 0.6467 (pp20) REVERT: C 1112 PRO cc_start: 0.7496 (Cg_exo) cc_final: 0.7176 (Cg_endo) REVERT: a 87 THR cc_start: 0.3264 (p) cc_final: 0.2982 (p) REVERT: a 106 PHE cc_start: 0.0732 (m-80) cc_final: 0.0010 (m-80) REVERT: d 144 TYR cc_start: 0.2663 (t80) cc_final: 0.2432 (t80) outliers start: 1 outliers final: 0 residues processed: 575 average time/residue: 0.4221 time to fit residues: 401.4581 Evaluate side-chains 392 residues out of total 3531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 391 time to evaluate : 3.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 130 optimal weight: 4.9990 chunk 349 optimal weight: 5.9990 chunk 76 optimal weight: 5.9990 chunk 227 optimal weight: 7.9990 chunk 95 optimal weight: 1.9990 chunk 387 optimal weight: 2.9990 chunk 322 optimal weight: 1.9990 chunk 179 optimal weight: 0.7980 chunk 32 optimal weight: 6.9990 chunk 128 optimal weight: 8.9990 chunk 203 optimal weight: 0.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 HIS ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 388 ASN ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 784 GLN B 920 GLN B1002 GLN ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 GLN ** C 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN C 953 ASN C 955 ASN ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1054 GLN ** b 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 193 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5386 moved from start: 0.6678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 32178 Z= 0.284 Angle : 0.633 13.227 43798 Z= 0.332 Chirality : 0.046 0.275 4957 Planarity : 0.005 0.084 5679 Dihedral : 5.120 29.990 4321 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 19.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 0.03 % Allowed : 1.93 % Favored : 98.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.13), residues: 3992 helix: 0.19 (0.19), residues: 734 sheet: -0.77 (0.16), residues: 1046 loop : -1.82 (0.12), residues: 2212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 64 HIS 0.018 0.002 HIS C1048 PHE 0.042 0.002 PHE C 559 TYR 0.024 0.002 TYR B 266 ARG 0.008 0.001 ARG B 34 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7984 Ramachandran restraints generated. 3992 Oldfield, 0 Emsley, 3992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7984 Ramachandran restraints generated. 3992 Oldfield, 0 Emsley, 3992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 3531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 566 time to evaluate : 3.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 LEU cc_start: 0.5937 (mm) cc_final: 0.5469 (mm) REVERT: A 741 TYR cc_start: 0.7586 (t80) cc_final: 0.7274 (t80) REVERT: A 955 ASN cc_start: 0.8166 (m-40) cc_final: 0.7867 (t0) REVERT: A 959 LEU cc_start: 0.8267 (tt) cc_final: 0.8063 (tt) REVERT: A 962 LEU cc_start: 0.7885 (tp) cc_final: 0.7257 (tp) REVERT: A 969 ASN cc_start: 0.6819 (m-40) cc_final: 0.6222 (m110) REVERT: B 867 ASP cc_start: 0.6716 (p0) cc_final: 0.6504 (p0) REVERT: B 921 LYS cc_start: 0.7366 (ptmt) cc_final: 0.7142 (ttpp) REVERT: B 1050 MET cc_start: 0.6363 (ptt) cc_final: 0.5595 (ptt) REVERT: C 38 TYR cc_start: 0.8270 (m-80) cc_final: 0.7993 (m-80) REVERT: C 170 TYR cc_start: 0.5772 (t80) cc_final: 0.5531 (t80) REVERT: C 275 PHE cc_start: 0.7564 (m-80) cc_final: 0.7083 (m-80) REVERT: C 592 PHE cc_start: 0.6620 (t80) cc_final: 0.6022 (t80) REVERT: C 735 SER cc_start: 0.8140 (m) cc_final: 0.7922 (m) REVERT: C 877 LEU cc_start: 0.9145 (mp) cc_final: 0.8915 (mt) REVERT: C 906 PHE cc_start: 0.7588 (m-80) cc_final: 0.7296 (m-80) REVERT: C 933 LYS cc_start: 0.8728 (ttpt) cc_final: 0.8372 (tptt) REVERT: C 977 LEU cc_start: 0.7601 (mm) cc_final: 0.7387 (mm) REVERT: C 1010 GLN cc_start: 0.6700 (tm-30) cc_final: 0.6287 (tm-30) REVERT: C 1018 ILE cc_start: 0.9251 (tt) cc_final: 0.8766 (tt) REVERT: C 1055 SER cc_start: 0.8760 (t) cc_final: 0.8525 (t) REVERT: C 1112 PRO cc_start: 0.7488 (Cg_exo) cc_final: 0.7075 (Cg_endo) REVERT: a 87 THR cc_start: 0.3255 (p) cc_final: 0.3044 (p) outliers start: 1 outliers final: 0 residues processed: 567 average time/residue: 0.3955 time to fit residues: 370.8743 Evaluate side-chains 409 residues out of total 3531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 409 time to evaluate : 3.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 374 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 chunk 221 optimal weight: 5.9990 chunk 283 optimal weight: 3.9990 chunk 219 optimal weight: 6.9990 chunk 326 optimal weight: 10.0000 chunk 216 optimal weight: 0.0870 chunk 386 optimal weight: 10.0000 chunk 241 optimal weight: 0.6980 chunk 235 optimal weight: 0.9990 chunk 178 optimal weight: 0.7980 overall best weight: 1.3162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1058 HIS ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 388 ASN ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 556 ASN ** C 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1135 ASN b 41 GLN b 46 GLN ** c 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 193 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5365 moved from start: 0.6844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 32178 Z= 0.241 Angle : 0.610 12.888 43798 Z= 0.318 Chirality : 0.045 0.284 4957 Planarity : 0.005 0.085 5679 Dihedral : 4.997 28.340 4321 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 18.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 0.08 % Allowed : 1.19 % Favored : 98.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.13), residues: 3992 helix: 0.44 (0.19), residues: 721 sheet: -0.74 (0.16), residues: 1041 loop : -1.76 (0.12), residues: 2230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C 64 HIS 0.012 0.001 HIS C1048 PHE 0.024 0.002 PHE C 559 TYR 0.021 0.002 TYR B 904 ARG 0.013 0.001 ARG B 905 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7984 Ramachandran restraints generated. 3992 Oldfield, 0 Emsley, 3992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7984 Ramachandran restraints generated. 3992 Oldfield, 0 Emsley, 3992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 568 residues out of total 3531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 565 time to evaluate : 4.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 LEU cc_start: 0.5880 (mm) cc_final: 0.5422 (mm) REVERT: A 309 GLU cc_start: 0.7296 (tp30) cc_final: 0.7074 (tp30) REVERT: A 568 ASP cc_start: 0.7973 (p0) cc_final: 0.7690 (p0) REVERT: A 598 ILE cc_start: 0.8759 (mp) cc_final: 0.8475 (mm) REVERT: A 699 LEU cc_start: 0.8450 (mt) cc_final: 0.8233 (mt) REVERT: A 741 TYR cc_start: 0.7553 (t80) cc_final: 0.7222 (t80) REVERT: A 907 ASN cc_start: 0.7402 (m-40) cc_final: 0.7059 (m-40) REVERT: A 955 ASN cc_start: 0.8113 (m-40) cc_final: 0.7887 (t0) REVERT: A 959 LEU cc_start: 0.8227 (tt) cc_final: 0.8017 (tt) REVERT: A 962 LEU cc_start: 0.7895 (tp) cc_final: 0.7188 (tp) REVERT: A 969 ASN cc_start: 0.6870 (m-40) cc_final: 0.6293 (m110) REVERT: B 819 GLU cc_start: 0.5538 (mm-30) cc_final: 0.5249 (mm-30) REVERT: B 921 LYS cc_start: 0.7425 (ptmt) cc_final: 0.7134 (ttpp) REVERT: C 38 TYR cc_start: 0.8263 (m-80) cc_final: 0.7982 (m-80) REVERT: C 170 TYR cc_start: 0.5785 (t80) cc_final: 0.5582 (t80) REVERT: C 238 PHE cc_start: 0.6094 (p90) cc_final: 0.5802 (p90) REVERT: C 275 PHE cc_start: 0.7606 (m-80) cc_final: 0.7132 (m-80) REVERT: C 584 ILE cc_start: 0.3238 (tp) cc_final: 0.2898 (mm) REVERT: C 592 PHE cc_start: 0.6671 (t80) cc_final: 0.6050 (t80) REVERT: C 735 SER cc_start: 0.8065 (m) cc_final: 0.7612 (t) REVERT: C 864 LEU cc_start: 0.8760 (tp) cc_final: 0.8485 (tp) REVERT: C 906 PHE cc_start: 0.7691 (m-80) cc_final: 0.7323 (m-80) REVERT: C 916 LEU cc_start: 0.7684 (tp) cc_final: 0.7410 (tp) REVERT: C 933 LYS cc_start: 0.8600 (ttpt) cc_final: 0.8334 (tptt) REVERT: C 977 LEU cc_start: 0.7524 (mm) cc_final: 0.7288 (mm) REVERT: C 1055 SER cc_start: 0.8619 (t) cc_final: 0.8417 (t) REVERT: C 1112 PRO cc_start: 0.7614 (Cg_exo) cc_final: 0.7232 (Cg_endo) REVERT: a 139 MET cc_start: -0.0515 (tpt) cc_final: -0.2629 (tmm) outliers start: 3 outliers final: 0 residues processed: 568 average time/residue: 0.4036 time to fit residues: 377.3079 Evaluate side-chains 410 residues out of total 3531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 410 time to evaluate : 3.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 239 optimal weight: 0.6980 chunk 154 optimal weight: 7.9990 chunk 230 optimal weight: 5.9990 chunk 116 optimal weight: 1.9990 chunk 75 optimal weight: 5.9990 chunk 74 optimal weight: 0.6980 chunk 245 optimal weight: 0.9990 chunk 263 optimal weight: 5.9990 chunk 191 optimal weight: 8.9990 chunk 36 optimal weight: 4.9990 chunk 303 optimal weight: 1.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 ASN ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 774 GLN ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1058 HIS B 81 ASN ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN B1135 ASN ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1135 ASN ** b 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 128 GLN ** d 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5373 moved from start: 0.7066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 32178 Z= 0.232 Angle : 0.609 11.916 43798 Z= 0.317 Chirality : 0.045 0.279 4957 Planarity : 0.005 0.089 5679 Dihedral : 4.978 32.708 4321 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 18.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.05 % Twisted Proline : 0.49 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.13), residues: 3992 helix: 0.55 (0.19), residues: 713 sheet: -0.68 (0.16), residues: 1034 loop : -1.74 (0.12), residues: 2245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 64 HIS 0.016 0.001 HIS d 193 PHE 0.033 0.002 PHE B 32 TYR 0.025 0.002 TYR B 266 ARG 0.008 0.001 ARG B 34 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7984 Ramachandran restraints generated. 3992 Oldfield, 0 Emsley, 3992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7984 Ramachandran restraints generated. 3992 Oldfield, 0 Emsley, 3992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 3531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 552 time to evaluate : 3.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 LEU cc_start: 0.6012 (mm) cc_final: 0.5626 (mm) REVERT: A 58 PHE cc_start: 0.5742 (m-80) cc_final: 0.5402 (m-10) REVERT: A 297 SER cc_start: 0.8901 (m) cc_final: 0.8688 (m) REVERT: A 301 CYS cc_start: 0.7205 (m) cc_final: 0.6886 (t) REVERT: A 309 GLU cc_start: 0.7227 (tp30) cc_final: 0.6946 (tp30) REVERT: A 598 ILE cc_start: 0.8688 (mp) cc_final: 0.8401 (mm) REVERT: A 699 LEU cc_start: 0.8520 (mt) cc_final: 0.8239 (mt) REVERT: A 741 TYR cc_start: 0.7554 (t80) cc_final: 0.7283 (t80) REVERT: A 907 ASN cc_start: 0.7370 (m-40) cc_final: 0.7034 (m-40) REVERT: A 955 ASN cc_start: 0.8157 (m-40) cc_final: 0.7923 (t0) REVERT: A 959 LEU cc_start: 0.8232 (tt) cc_final: 0.8008 (tt) REVERT: A 962 LEU cc_start: 0.7945 (tp) cc_final: 0.7349 (tp) REVERT: B 568 ASP cc_start: 0.6107 (m-30) cc_final: 0.5801 (m-30) REVERT: B 712 ILE cc_start: 0.8669 (tt) cc_final: 0.8431 (tt) REVERT: B 736 VAL cc_start: 0.7473 (t) cc_final: 0.7251 (p) REVERT: B 819 GLU cc_start: 0.5599 (mm-30) cc_final: 0.5258 (mm-30) REVERT: B 869 MET cc_start: 0.7663 (mtm) cc_final: 0.7428 (mtp) REVERT: B 921 LYS cc_start: 0.7420 (ptmt) cc_final: 0.7009 (ttpp) REVERT: C 275 PHE cc_start: 0.7676 (m-80) cc_final: 0.7181 (m-80) REVERT: C 584 ILE cc_start: 0.3236 (tp) cc_final: 0.2625 (mt) REVERT: C 592 PHE cc_start: 0.6640 (t80) cc_final: 0.6089 (t80) REVERT: C 735 SER cc_start: 0.8265 (m) cc_final: 0.7822 (t) REVERT: C 864 LEU cc_start: 0.8674 (tp) cc_final: 0.8322 (tp) REVERT: C 933 LYS cc_start: 0.8677 (ttpt) cc_final: 0.8411 (tptt) REVERT: C 977 LEU cc_start: 0.7505 (mm) cc_final: 0.7199 (mm) REVERT: C 1006 THR cc_start: 0.8126 (m) cc_final: 0.7860 (m) REVERT: C 1055 SER cc_start: 0.8557 (t) cc_final: 0.8354 (t) REVERT: C 1112 PRO cc_start: 0.7430 (Cg_exo) cc_final: 0.7136 (Cg_endo) REVERT: a 139 MET cc_start: 0.0428 (tpt) cc_final: -0.2890 (tmm) outliers start: 0 outliers final: 0 residues processed: 552 average time/residue: 0.3909 time to fit residues: 359.1496 Evaluate side-chains 409 residues out of total 3531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 409 time to evaluate : 3.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 351 optimal weight: 9.9990 chunk 370 optimal weight: 3.9990 chunk 337 optimal weight: 0.0270 chunk 360 optimal weight: 9.9990 chunk 216 optimal weight: 0.4980 chunk 156 optimal weight: 4.9990 chunk 282 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 chunk 325 optimal weight: 5.9990 chunk 340 optimal weight: 1.9990 chunk 358 optimal weight: 0.0040 overall best weight: 0.9054 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1058 HIS ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 556 ASN ** C 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1106 GLN C1135 ASN b 41 GLN b 214 ASN c 102 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5332 moved from start: 0.7149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 32178 Z= 0.200 Angle : 0.589 11.169 43798 Z= 0.306 Chirality : 0.045 0.321 4957 Planarity : 0.004 0.090 5679 Dihedral : 4.804 26.143 4321 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 16.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 0.08 % Allowed : 0.40 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.13), residues: 3992 helix: 0.65 (0.20), residues: 714 sheet: -0.60 (0.16), residues: 1036 loop : -1.72 (0.12), residues: 2242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP a 52 HIS 0.011 0.001 HIS C1048 PHE 0.019 0.002 PHE A 377 TYR 0.025 0.002 TYR B 266 ARG 0.012 0.001 ARG d 65 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7984 Ramachandran restraints generated. 3992 Oldfield, 0 Emsley, 3992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7984 Ramachandran restraints generated. 3992 Oldfield, 0 Emsley, 3992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 556 residues out of total 3531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 553 time to evaluate : 3.972 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 44 ARG cc_start: 0.6122 (mtt-85) cc_final: 0.5830 (mtt-85) REVERT: A 54 LEU cc_start: 0.6003 (mm) cc_final: 0.5666 (mm) REVERT: A 301 CYS cc_start: 0.7106 (m) cc_final: 0.6780 (t) REVERT: A 309 GLU cc_start: 0.7227 (tp30) cc_final: 0.6944 (tp30) REVERT: A 598 ILE cc_start: 0.8718 (mp) cc_final: 0.8387 (mm) REVERT: A 699 LEU cc_start: 0.8519 (mt) cc_final: 0.8276 (mt) REVERT: A 741 TYR cc_start: 0.7509 (t80) cc_final: 0.7270 (t80) REVERT: A 907 ASN cc_start: 0.7297 (m-40) cc_final: 0.6707 (m-40) REVERT: A 959 LEU cc_start: 0.8211 (tt) cc_final: 0.7957 (tt) REVERT: A 962 LEU cc_start: 0.7908 (tp) cc_final: 0.7344 (tp) REVERT: B 101 ILE cc_start: 0.6090 (tt) cc_final: 0.5758 (tt) REVERT: B 568 ASP cc_start: 0.6091 (m-30) cc_final: 0.5806 (m-30) REVERT: B 736 VAL cc_start: 0.7518 (t) cc_final: 0.7300 (p) REVERT: B 819 GLU cc_start: 0.5564 (mm-30) cc_final: 0.5194 (mm-30) REVERT: B 869 MET cc_start: 0.7577 (mtm) cc_final: 0.7341 (mtp) REVERT: B 921 LYS cc_start: 0.7324 (ptmt) cc_final: 0.6968 (ttpp) REVERT: B 997 ILE cc_start: 0.9067 (tp) cc_final: 0.8707 (tp) REVERT: B 1029 MET cc_start: 0.7910 (tpp) cc_final: 0.7696 (tpp) REVERT: C 238 PHE cc_start: 0.5962 (p90) cc_final: 0.5734 (p90) REVERT: C 275 PHE cc_start: 0.7596 (m-80) cc_final: 0.7207 (m-80) REVERT: C 293 LEU cc_start: 0.8456 (tp) cc_final: 0.8028 (tt) REVERT: C 592 PHE cc_start: 0.6556 (t80) cc_final: 0.6038 (t80) REVERT: C 735 SER cc_start: 0.8283 (m) cc_final: 0.7866 (t) REVERT: C 977 LEU cc_start: 0.7422 (mm) cc_final: 0.7079 (mm) REVERT: C 1006 THR cc_start: 0.7777 (m) cc_final: 0.7572 (m) REVERT: C 1055 SER cc_start: 0.8464 (t) cc_final: 0.8262 (t) REVERT: C 1112 PRO cc_start: 0.7487 (Cg_exo) cc_final: 0.7123 (Cg_endo) outliers start: 3 outliers final: 1 residues processed: 556 average time/residue: 0.3931 time to fit residues: 364.7803 Evaluate side-chains 418 residues out of total 3531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 417 time to evaluate : 3.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 236 optimal weight: 2.9990 chunk 380 optimal weight: 9.9990 chunk 232 optimal weight: 0.0170 chunk 180 optimal weight: 0.3980 chunk 264 optimal weight: 4.9990 chunk 399 optimal weight: 8.9990 chunk 367 optimal weight: 4.9990 chunk 318 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 245 optimal weight: 0.9980 chunk 195 optimal weight: 0.5980 overall best weight: 1.0020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 ASN ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN A1011 GLN A1058 HIS B 188 ASN ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1106 GLN C1135 ASN ** b 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 102 HIS d 193 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5343 moved from start: 0.7296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 32178 Z= 0.210 Angle : 0.595 10.967 43798 Z= 0.309 Chirality : 0.045 0.257 4957 Planarity : 0.005 0.092 5679 Dihedral : 4.839 26.050 4321 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 16.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 0.03 % Allowed : 0.25 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.13), residues: 3992 helix: 0.68 (0.20), residues: 714 sheet: -0.59 (0.16), residues: 1049 loop : -1.68 (0.13), residues: 2229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP a 52 HIS 0.011 0.001 HIS C1048 PHE 0.032 0.002 PHE c 80 TYR 0.025 0.002 TYR B 266 ARG 0.010 0.001 ARG d 65 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7984 Ramachandran restraints generated. 3992 Oldfield, 0 Emsley, 3992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7984 Ramachandran restraints generated. 3992 Oldfield, 0 Emsley, 3992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 559 residues out of total 3531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 558 time to evaluate : 3.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 LEU cc_start: 0.6020 (mm) cc_final: 0.5577 (mm) REVERT: A 301 CYS cc_start: 0.7119 (m) cc_final: 0.6780 (t) REVERT: A 309 GLU cc_start: 0.7276 (tp30) cc_final: 0.7016 (tp30) REVERT: A 598 ILE cc_start: 0.8751 (mp) cc_final: 0.8389 (mm) REVERT: A 699 LEU cc_start: 0.8526 (mt) cc_final: 0.8273 (mt) REVERT: A 905 ARG cc_start: 0.8117 (mmt180) cc_final: 0.7860 (mtt-85) REVERT: A 962 LEU cc_start: 0.8045 (tp) cc_final: 0.7465 (tp) REVERT: A 969 ASN cc_start: 0.7202 (m-40) cc_final: 0.6617 (m-40) REVERT: B 101 ILE cc_start: 0.5881 (tt) cc_final: 0.5666 (tt) REVERT: B 819 GLU cc_start: 0.5630 (mm-30) cc_final: 0.5114 (mm-30) REVERT: B 869 MET cc_start: 0.7596 (mtm) cc_final: 0.7339 (mtp) REVERT: B 921 LYS cc_start: 0.7306 (ptmt) cc_final: 0.7018 (ttpp) REVERT: C 238 PHE cc_start: 0.5977 (p90) cc_final: 0.5710 (p90) REVERT: C 275 PHE cc_start: 0.7640 (m-80) cc_final: 0.7215 (m-80) REVERT: C 293 LEU cc_start: 0.8439 (tp) cc_final: 0.8135 (tt) REVERT: C 592 PHE cc_start: 0.6509 (t80) cc_final: 0.6062 (t80) REVERT: C 735 SER cc_start: 0.8316 (m) cc_final: 0.7790 (t) REVERT: C 864 LEU cc_start: 0.8691 (tp) cc_final: 0.8428 (tp) REVERT: C 901 GLN cc_start: 0.8303 (tt0) cc_final: 0.8060 (tp40) REVERT: C 977 LEU cc_start: 0.7375 (mm) cc_final: 0.7150 (mm) REVERT: C 1006 THR cc_start: 0.7815 (m) cc_final: 0.7535 (m) REVERT: C 1055 SER cc_start: 0.8488 (t) cc_final: 0.8283 (t) REVERT: C 1112 PRO cc_start: 0.7544 (Cg_exo) cc_final: 0.7256 (Cg_endo) outliers start: 1 outliers final: 0 residues processed: 559 average time/residue: 0.3797 time to fit residues: 355.0186 Evaluate side-chains 420 residues out of total 3531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 420 time to evaluate : 3.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 252 optimal weight: 4.9990 chunk 338 optimal weight: 0.0870 chunk 97 optimal weight: 2.9990 chunk 293 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 88 optimal weight: 0.6980 chunk 318 optimal weight: 5.9990 chunk 133 optimal weight: 4.9990 chunk 327 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 overall best weight: 1.3162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS A 185 ASN ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 ASN ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1058 HIS ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN ** C 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 556 ASN ** C 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 953 ASN C 957 GLN C1106 GLN ** b 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.119814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.099295 restraints weight = 134051.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.100847 restraints weight = 78945.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.101832 restraints weight = 51865.855| |-----------------------------------------------------------------------------| r_work (final): 0.3776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6528 moved from start: 0.7500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 32178 Z= 0.241 Angle : 0.616 11.296 43798 Z= 0.321 Chirality : 0.045 0.241 4957 Planarity : 0.005 0.093 5679 Dihedral : 4.952 25.974 4321 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 18.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 0.11 % Allowed : 0.37 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.13), residues: 3992 helix: 0.63 (0.20), residues: 712 sheet: -0.65 (0.16), residues: 1031 loop : -1.71 (0.12), residues: 2249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP c 36 HIS 0.011 0.001 HIS C1048 PHE 0.024 0.002 PHE B 823 TYR 0.025 0.002 TYR B 266 ARG 0.010 0.001 ARG d 65 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8214.67 seconds wall clock time: 151 minutes 19.74 seconds (9079.74 seconds total)