Starting phenix.real_space_refine on Thu Mar 21 12:27:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vxf_32178/03_2024/7vxf_32178.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vxf_32178/03_2024/7vxf_32178.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vxf_32178/03_2024/7vxf_32178.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vxf_32178/03_2024/7vxf_32178.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vxf_32178/03_2024/7vxf_32178.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vxf_32178/03_2024/7vxf_32178.pdb" } resolution = 3.6 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= -0.003 sd= 0.164 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 19214 2.51 5 N 5012 2.21 5 O 5709 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 169": "NH1" <-> "NH2" Residue "C ARG 245": "NH1" <-> "NH2" Residue "C PHE 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 357": "NH1" <-> "NH2" Residue "B TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 888": "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: 30079 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 8454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1079, 8454 Classifications: {'peptide': 1079} Link IDs: {'PTRANS': 52, 'TRANS': 1026} Chain breaks: 5 Chain: "C" Number of atoms: 4870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 569} Chain: "B" Number of atoms: 8301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1059, 8301 Classifications: {'peptide': 1059} Link IDs: {'PTRANS': 51, 'TRANS': 1007} Chain breaks: 6 Chain: "D" Number of atoms: 8454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1079, 8454 Classifications: {'peptide': 1079} Link IDs: {'CIS': 1, 'PTRANS': 52, 'TRANS': 1025} Chain breaks: 5 Time building chain proxies: 14.82, per 1000 atoms: 0.49 Number of scatterers: 30079 At special positions: 0 Unit cell: (161.764, 150.834, 263.413, 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 5709 8.00 N 5012 7.00 C 19214 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 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 C 133 " - pdb=" SG CYS C 141 " distance=2.03 Simple disulfide: pdb=" SG CYS C 344 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 530 " - pdb=" SG CYS C 542 " 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=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 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 D 131 " - pdb=" SG CYS D 166 " distance=2.03 Simple disulfide: pdb=" SG CYS D 291 " - pdb=" SG CYS D 301 " distance=2.03 Simple disulfide: pdb=" SG CYS D 379 " - pdb=" SG CYS D 432 " distance=2.03 Simple disulfide: pdb=" SG CYS D 480 " - pdb=" SG CYS D 488 " distance=2.03 Simple disulfide: pdb=" SG CYS D 538 " - pdb=" SG CYS D 590 " distance=2.03 Simple disulfide: pdb=" SG CYS D 617 " - pdb=" SG CYS D 649 " distance=2.03 Simple disulfide: pdb=" SG CYS D 662 " - pdb=" SG CYS D 671 " distance=2.03 Simple disulfide: pdb=" SG CYS D 738 " - pdb=" SG CYS D 760 " distance=2.03 Simple disulfide: pdb=" SG CYS D 743 " - pdb=" SG CYS D 749 " distance=2.03 Simple disulfide: pdb=" SG CYS D1032 " - pdb=" SG CYS D1043 " distance=2.03 Simple disulfide: pdb=" SG CYS D1082 " - pdb=" SG CYS D1126 " 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: 11.63 Conformation dependent library (CDL) restraints added in 5.8 seconds 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7156 Finding SS restraints... Secondary structure from input PDB file: 97 helices and 46 sheets defined 31.3% alpha, 17.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.44 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.584A pdb=" N LYS A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 343 removed outlier: 3.941A pdb=" N PHE A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 386 through 389 Processing helix chain 'A' and resid 403 through 407 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 737 through 743 removed outlier: 3.636A pdb=" N TYR A 741 " --> pdb=" O ASP A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.763A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ASN A 751 " --> pdb=" O THR A 747 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 780 removed outlier: 3.543A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLN A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU A 780 " --> pdb=" O LYS A 776 " (cutoff:3.500A) Processing helix chain 'A' and resid 818 through 825 Processing helix chain 'A' and resid 849 through 854 Processing helix chain 'A' and resid 866 through 884 removed outlier: 3.590A pdb=" N ILE A 870 " --> pdb=" O THR A 866 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA A 871 " --> pdb=" O ASP A 867 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLN A 872 " --> pdb=" O GLU A 868 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N THR A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.801A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 919 removed outlier: 4.177A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLU A 918 " --> pdb=" O ASN A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.689A pdb=" N ASN A 925 " --> pdb=" O LYS A 921 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) 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 removed outlier: 3.941A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLN A 965 " --> pdb=" O THR A 961 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 982 removed outlier: 3.583A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.561A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLN A1002 " --> pdb=" O THR A 998 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1154 removed outlier: 4.116A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LYS A1154 " --> pdb=" O GLU A1150 " (cutoff:3.500A) Processing helix chain 'A' and resid 1155 through 1160 Processing helix chain 'C' and resid 20 through 53 removed outlier: 4.041A pdb=" N HIS C 34 " --> pdb=" O ASP C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 81 removed outlier: 3.742A pdb=" N GLN C 60 " --> pdb=" O GLU C 56 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASN C 63 " --> pdb=" O VAL C 59 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS C 74 " --> pdb=" O SER C 70 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N THR C 78 " --> pdb=" O LYS C 74 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N LEU C 79 " --> pdb=" O GLU C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 88 removed outlier: 3.947A pdb=" N GLU C 87 " --> pdb=" O PRO C 84 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE C 88 " --> pdb=" O LEU C 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 84 through 88' Processing helix chain 'C' and resid 90 through 102 removed outlier: 4.071A pdb=" N ALA C 99 " --> pdb=" O LEU C 95 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LEU C 100 " --> pdb=" O GLN C 96 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLN C 102 " --> pdb=" O GLN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 108 removed outlier: 3.929A pdb=" N VAL C 107 " --> pdb=" O GLY C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 130 removed outlier: 3.849A pdb=" N ASN C 117 " --> pdb=" O SER C 113 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR C 118 " --> pdb=" O LYS C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 155 removed outlier: 3.796A pdb=" N ALA C 153 " --> pdb=" O ASN C 149 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ASN C 154 " --> pdb=" O GLU C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 172 removed outlier: 3.611A pdb=" N ARG C 161 " --> pdb=" O ASP C 157 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA C 164 " --> pdb=" O GLU C 160 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N TRP C 168 " --> pdb=" O ALA C 164 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ARG C 169 " --> pdb=" O TRP C 165 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N SER C 170 " --> pdb=" O GLU C 166 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLU C 171 " --> pdb=" O SER C 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 194 removed outlier: 3.674A pdb=" N MET C 190 " --> pdb=" O LEU C 186 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA C 191 " --> pdb=" O LYS C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 205 removed outlier: 3.545A pdb=" N TYR C 202 " --> pdb=" O ASP C 198 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N TRP C 203 " --> pdb=" O TYR C 199 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ARG C 204 " --> pdb=" O GLY C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 208 No H-bonds generated for 'chain 'C' and resid 206 through 208' Processing helix chain 'C' and resid 220 through 250 removed outlier: 4.000A pdb=" N GLU C 224 " --> pdb=" O GLY C 220 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU C 231 " --> pdb=" O GLU C 227 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLU C 232 " --> pdb=" O HIS C 228 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE C 233 " --> pdb=" O THR C 229 " (cutoff:3.500A) Proline residue: C 235 - end of helix removed outlier: 3.802A pdb=" N HIS C 239 " --> pdb=" O PRO C 235 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU C 240 " --> pdb=" O LEU C 236 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ASN C 250 " --> pdb=" O ALA C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 279 Processing helix chain 'C' and resid 293 through 301 removed outlier: 3.738A pdb=" N ASP C 299 " --> pdb=" O ASP C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 318 removed outlier: 4.072A pdb=" N PHE C 308 " --> pdb=" O ALA C 304 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS C 309 " --> pdb=" O GLN C 305 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N PHE C 314 " --> pdb=" O GLU C 310 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N PHE C 315 " --> pdb=" O ALA C 311 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL C 318 " --> pdb=" O PHE C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 330 removed outlier: 3.610A pdb=" N TRP C 328 " --> pdb=" O THR C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 385 removed outlier: 3.671A pdb=" N PHE C 369 " --> pdb=" O THR C 365 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU C 370 " --> pdb=" O MET C 366 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N HIS C 373 " --> pdb=" O PHE C 369 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE C 379 " --> pdb=" O GLU C 375 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ALA C 384 " --> pdb=" O GLN C 380 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N TYR C 385 " --> pdb=" O TYR C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 388 No H-bonds generated for 'chain 'C' and resid 386 through 388' Processing helix chain 'C' and resid 389 through 393 Processing helix chain 'C' and resid 399 through 413 removed outlier: 3.568A pdb=" N VAL C 404 " --> pdb=" O PHE C 400 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N GLY C 405 " --> pdb=" O HIS C 401 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N MET C 408 " --> pdb=" O VAL C 404 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER C 409 " --> pdb=" O GLY C 405 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER C 411 " --> pdb=" O ILE C 407 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA C 412 " --> pdb=" O MET C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 421 removed outlier: 3.744A pdb=" N ILE C 421 " --> pdb=" O HIS C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 447 removed outlier: 3.640A pdb=" N ASN C 437 " --> pdb=" O GLU C 433 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LYS C 441 " --> pdb=" O ASN C 437 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N THR C 445 " --> pdb=" O LYS C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 466 removed outlier: 3.999A pdb=" N PHE C 452 " --> pdb=" O GLY C 448 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 471 No H-bonds generated for 'chain 'C' and resid 469 through 471' Processing helix chain 'C' and resid 472 through 485 removed outlier: 3.881A pdb=" N GLU C 483 " --> pdb=" O GLU C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 498 through 503 removed outlier: 4.127A pdb=" N SER C 502 " --> pdb=" O CYS C 498 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU C 503 " --> pdb=" O ASP C 499 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 498 through 503' Processing helix chain 'C' and resid 503 through 508 Processing helix chain 'C' and resid 513 through 533 removed outlier: 3.513A pdb=" N THR C 517 " --> pdb=" O ILE C 513 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N THR C 519 " --> pdb=" O TYR C 515 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LEU C 520 " --> pdb=" O TYR C 516 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N CYS C 530 " --> pdb=" O GLN C 526 " (cutoff:3.500A) Processing helix chain 'C' and resid 538 through 542 Processing helix chain 'C' and resid 548 through 559 removed outlier: 3.656A pdb=" N GLN C 552 " --> pdb=" O THR C 548 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LYS C 553 " --> pdb=" O GLU C 549 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASN C 556 " --> pdb=" O GLN C 552 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N MET C 557 " --> pdb=" O LYS C 553 " (cutoff:3.500A) Processing helix chain 'C' and resid 565 through 572 removed outlier: 3.519A pdb=" N ASN C 572 " --> pdb=" O LEU C 568 " (cutoff:3.500A) Processing helix chain 'C' and resid 581 through 588 removed outlier: 3.588A pdb=" N PHE C 588 " --> pdb=" O LEU C 584 " (cutoff:3.500A) Processing helix chain 'C' and resid 588 through 599 removed outlier: 3.693A pdb=" N TRP C 594 " --> pdb=" O PRO C 590 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASP C 597 " --> pdb=" O THR C 593 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 removed outlier: 3.590A pdb=" N LYS B 300 " --> pdb=" O LEU B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 344 removed outlier: 4.009A pdb=" N PHE B 342 " --> pdb=" O PHE B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 371 Processing helix chain 'B' and resid 386 through 389 Processing helix chain 'B' and resid 403 through 410 removed outlier: 4.128A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLN B 409 " --> pdb=" O GLU B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 737 through 743 removed outlier: 3.688A pdb=" N TYR B 741 " --> pdb=" O ASP B 737 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.776A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ASN B 751 " --> pdb=" O THR B 747 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 780 removed outlier: 3.553A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLN B 779 " --> pdb=" O ASP B 775 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLU B 780 " --> pdb=" O LYS B 776 " (cutoff:3.500A) Processing helix chain 'B' and resid 818 through 825 Processing helix chain 'B' and resid 849 through 854 Processing helix chain 'B' and resid 866 through 884 removed outlier: 3.582A pdb=" N ILE B 870 " --> pdb=" O THR B 866 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA B 871 " --> pdb=" O ASP B 867 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLN B 872 " --> pdb=" O GLU B 868 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 891 removed outlier: 4.072A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.608A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 removed outlier: 4.173A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLU B 918 " --> pdb=" O ASN B 914 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.657A pdb=" N ASN B 925 " --> pdb=" O LYS B 921 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) 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 965 removed outlier: 3.939A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLN B 965 " --> pdb=" O THR B 961 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 982 removed outlier: 3.639A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.522A pdb=" N GLU B 990 " --> pdb=" O PRO B 986 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLN B1002 " --> pdb=" O THR B 998 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER B1003 " --> pdb=" O GLY B 999 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1154 removed outlier: 4.050A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LYS B1154 " --> pdb=" O GLU B1150 " (cutoff:3.500A) Processing helix chain 'B' and resid 1155 through 1161 removed outlier: 3.588A pdb=" N HIS B1159 " --> pdb=" O TYR B1155 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR B1160 " --> pdb=" O PHE B1156 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 304 removed outlier: 3.526A pdb=" N THR D 299 " --> pdb=" O PRO D 295 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 390 removed outlier: 4.111A pdb=" N ASN D 388 " --> pdb=" O THR D 385 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 422 Processing helix chain 'D' and resid 502 through 506 Processing helix chain 'D' and resid 737 through 743 removed outlier: 4.054A pdb=" N ILE D 742 " --> pdb=" O CYS D 738 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N CYS D 743 " --> pdb=" O THR D 739 " (cutoff:3.500A) Processing helix chain 'D' and resid 747 through 755 removed outlier: 3.721A pdb=" N LEU D 752 " --> pdb=" O GLU D 748 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLN D 755 " --> pdb=" O ASN D 751 " (cutoff:3.500A) Processing helix chain 'D' and resid 758 through 780 removed outlier: 3.597A pdb=" N ASP D 775 " --> pdb=" O ALA D 771 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N THR D 778 " --> pdb=" O GLN D 774 " (cutoff:3.500A) Processing helix chain 'D' and resid 818 through 825 Processing helix chain 'D' and resid 849 through 854 Processing helix chain 'D' and resid 866 through 884 Processing helix chain 'D' and resid 886 through 891 removed outlier: 4.025A pdb=" N ALA D 890 " --> pdb=" O TRP D 886 " (cutoff:3.500A) Processing helix chain 'D' and resid 897 through 899 No H-bonds generated for 'chain 'D' and resid 897 through 899' Processing helix chain 'D' and resid 900 through 909 removed outlier: 4.043A pdb=" N TYR D 904 " --> pdb=" O MET D 900 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE D 909 " --> pdb=" O ARG D 905 " (cutoff:3.500A) Processing helix chain 'D' and resid 913 through 941 removed outlier: 3.899A pdb=" N TYR D 917 " --> pdb=" O GLN D 913 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N LYS D 921 " --> pdb=" O TYR D 917 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N LEU D 922 " --> pdb=" O GLU D 918 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASN D 925 " --> pdb=" O LYS D 921 " (cutoff:3.500A) Processing helix chain 'D' and resid 945 through 965 removed outlier: 3.678A pdb=" N VAL D 951 " --> pdb=" O LYS D 947 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL D 963 " --> pdb=" O LEU D 959 " (cutoff:3.500A) Processing helix chain 'D' and resid 966 through 968 No H-bonds generated for 'chain 'D' and resid 966 through 968' Processing helix chain 'D' and resid 976 through 982 removed outlier: 3.715A pdb=" N ILE D 980 " --> pdb=" O VAL D 976 " (cutoff:3.500A) Processing helix chain 'D' and resid 985 through 1032 removed outlier: 4.092A pdb=" N VAL D 991 " --> pdb=" O PRO D 987 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLN D 992 " --> pdb=" O GLU D 988 " (cutoff:3.500A) Processing helix chain 'D' and resid 1140 through 1157 removed outlier: 4.269A pdb=" N GLU D1144 " --> pdb=" O PRO D1140 " (cutoff:3.500A) Processing helix chain 'D' and resid 1158 through 1161 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 3.770A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N VAL A 90 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N PHE A 194 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL A 193 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR A 204 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLU A 224 " --> pdb=" O SER A 205 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 4.475A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.778A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE A 238 " --> pdb=" O LEU A 84 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG A 237 " --> pdb=" O GLY A 107 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLN A 239 " --> pdb=" O ILE A 105 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ILE A 105 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N CYS A 131 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU A 118 " --> pdb=" O LYS A 129 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LYS A 129 " --> pdb=" O LEU A 118 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 141 through 142 removed outlier: 3.516A pdb=" N GLU A 156 " --> pdb=" O GLY A 142 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 318 removed outlier: 3.771A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N CYS A 649 " --> pdb=" O TYR A 612 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 327 removed outlier: 4.024A pdb=" N ASN A 542 " --> pdb=" O ILE A 326 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLY A 548 " --> pdb=" O PHE A 541 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU A 585 " --> pdb=" O VAL A 576 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLY A 566 " --> pdb=" O ALA A 575 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 355 through 358 removed outlier: 3.747A pdb=" N LYS A 356 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU A 513 " --> pdb=" O CYS A 432 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA A 435 " --> pdb=" O THR A 376 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'A' and resid 653 through 655 removed outlier: 5.683A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA A 672 " --> pdb=" O ILE A 664 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ILE A 664 " --> pdb=" O ALA A 672 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.681A pdb=" N ILE A 714 " --> pdb=" O LYS A1073 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LYS A1073 " --> pdb=" O ILE A 714 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 718 through 728 removed outlier: 3.624A pdb=" N SER A 721 " --> pdb=" O THR A1066 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 735 through 736 Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1122 removed outlier: 3.528A pdb=" N ILE A1081 " --> pdb=" O HIS A1088 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 131 through 133 removed outlier: 3.561A pdb=" N LEU C 142 " --> pdb=" O VAL C 132 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 262 through 263 removed outlier: 6.093A pdb=" N LEU C 262 " --> pdb=" O VAL C 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'C' and resid 347 through 352 removed outlier: 3.595A pdb=" N THR C 347 " --> pdb=" O LEU C 359 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ASP C 355 " --> pdb=" O LEU C 351 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 27 through 30 removed outlier: 3.748A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA B 93 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N VAL B 90 " --> pdb=" O PHE B 194 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N PHE B 194 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL B 193 " --> pdb=" O TYR B 204 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TYR B 204 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLU B 224 " --> pdb=" O SER B 205 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 48 through 55 removed outlier: 4.369A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 83 through 85 removed outlier: 3.578A pdb=" N ARG B 237 " --> pdb=" O GLY B 107 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLN B 239 " --> pdb=" O ILE B 105 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ILE B 105 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N CYS B 131 " --> pdb=" O SER B 116 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU B 118 " --> pdb=" O LYS B 129 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LYS B 129 " --> pdb=" O LEU B 118 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE B 128 " --> pdb=" O TYR B 170 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 141 through 142 removed outlier: 3.694A pdb=" N GLU B 156 " --> pdb=" O GLY B 142 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 318 removed outlier: 3.549A pdb=" N GLY B 311 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N THR B 599 " --> pdb=" O GLY B 311 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N CYS B 649 " --> pdb=" O TYR B 612 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 325 through 327 removed outlier: 4.036A pdb=" N ASN B 542 " --> pdb=" O ILE B 326 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLY B 548 " --> pdb=" O PHE B 541 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU B 585 " --> pdb=" O VAL B 576 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLY B 566 " --> pdb=" O ALA B 575 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 355 through 358 removed outlier: 3.792A pdb=" N LYS B 356 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU B 513 " --> pdb=" O CYS B 432 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA B 435 " --> pdb=" O THR B 376 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR B 376 " --> pdb=" O ALA B 435 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AC9, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD1, first strand: chain 'B' and resid 653 through 655 removed outlier: 5.616A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA B 672 " --> pdb=" O ILE B 664 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ILE B 664 " --> pdb=" O ALA B 672 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.549A pdb=" N ILE B 714 " --> pdb=" O LYS B1073 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS B1073 " --> pdb=" O ILE B 714 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 718 through 728 removed outlier: 3.641A pdb=" N SER B 721 " --> pdb=" O THR B1066 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA B1056 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 735 through 736 Processing sheet with id=AD5, first strand: chain 'B' and resid 1120 through 1122 removed outlier: 3.562A pdb=" N ILE B1081 " --> pdb=" O HIS B1088 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 27 through 30 removed outlier: 3.816A pdb=" N ALA D 27 " --> pdb=" O TRP D 64 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N ASN D 61 " --> pdb=" O TYR D 269 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N TYR D 269 " --> pdb=" O ASN D 61 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N VAL D 267 " --> pdb=" O THR D 63 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ALA D 264 " --> pdb=" O THR D 95 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL D 90 " --> pdb=" O PHE D 194 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N PHE D 194 " --> pdb=" O VAL D 90 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LYS D 195 " --> pdb=" O LYS D 202 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL D 227 " --> pdb=" O ILE D 203 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N SER D 205 " --> pdb=" O PRO D 225 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 48 through 55 removed outlier: 3.644A pdb=" N THR D 51 " --> pdb=" O PHE D 275 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N PHE D 275 " --> pdb=" O THR D 51 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ASP D 287 " --> pdb=" O LYS D 278 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 84 through 85 removed outlier: 3.842A pdb=" N LEU D 84 " --> pdb=" O PHE D 238 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU D 241 " --> pdb=" O GLY D 103 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N GLY D 103 " --> pdb=" O LEU D 241 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N CYS D 131 " --> pdb=" O SER D 116 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N VAL D 126 " --> pdb=" O SER D 172 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE D 168 " --> pdb=" O VAL D 130 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N GLU D 132 " --> pdb=" O CYS D 166 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N CYS D 166 " --> pdb=" O GLU D 132 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 141 through 142 Processing sheet with id=AE1, first strand: chain 'D' and resid 311 through 319 removed outlier: 5.836A pdb=" N ILE D 312 " --> pdb=" O THR D 599 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N THR D 599 " --> pdb=" O ILE D 312 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N GLN D 314 " --> pdb=" O VAL D 597 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N VAL D 597 " --> pdb=" O GLN D 314 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N SER D 316 " --> pdb=" O VAL D 595 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 324 through 327 removed outlier: 6.939A pdb=" N GLU D 324 " --> pdb=" O ASN D 540 " (cutoff:3.500A) removed outlier: 8.720A pdb=" N ASN D 542 " --> pdb=" O GLU D 324 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N ILE D 326 " --> pdb=" O ASN D 542 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N ASP D 574 " --> pdb=" O ILE D 587 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA D 575 " --> pdb=" O GLY D 566 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 354 through 357 removed outlier: 4.368A pdb=" N ASN D 354 " --> pdb=" O SER D 399 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N SER D 399 " --> pdb=" O ASN D 354 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA D 397 " --> pdb=" O LYS D 356 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N LEU D 513 " --> pdb=" O CYS D 432 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N CYS D 432 " --> pdb=" O LEU D 513 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS D 378 " --> pdb=" O VAL D 433 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ALA D 435 " --> pdb=" O THR D 376 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N THR D 376 " --> pdb=" O ALA D 435 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 452 through 454 Processing sheet with id=AE5, first strand: chain 'D' and resid 654 through 655 removed outlier: 6.037A pdb=" N GLU D 654 " --> pdb=" O ALA D 694 " (cutoff:3.500A) removed outlier: 8.329A pdb=" N THR D 696 " --> pdb=" O GLU D 654 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 711 through 715 removed outlier: 3.826A pdb=" N ILE D 714 " --> pdb=" O LYS D1073 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS D1073 " --> pdb=" O ILE D 714 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 718 through 728 removed outlier: 3.650A pdb=" N SER D 721 " --> pdb=" O THR D1066 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ALA D1056 " --> pdb=" O GLY D1059 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N TYR D1067 " --> pdb=" O HIS D1048 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N HIS D1048 " --> pdb=" O TYR D1067 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 733 through 736 removed outlier: 4.375A pdb=" N LYS D 733 " --> pdb=" O LEU D 861 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 1120 through 1122 removed outlier: 3.650A pdb=" N ILE D1081 " --> pdb=" O HIS D1088 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 1094 through 1097 1030 hydrogen bonds defined for protein. 2898 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: 12.65 Time building geometry restraints manager: 12.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 9715 1.35 - 1.46: 7584 1.46 - 1.58: 13310 1.58 - 1.70: 0 1.70 - 1.82: 195 Bond restraints: 30804 Sorted by residual: bond pdb=" C LEU D 229 " pdb=" N PRO D 230 " ideal model delta sigma weight residual 1.334 1.437 -0.103 2.34e-02 1.83e+03 1.92e+01 bond pdb=" C PRO D 25 " pdb=" N PRO D 26 " ideal model delta sigma weight residual 1.334 1.433 -0.100 2.34e-02 1.83e+03 1.81e+01 bond pdb=" C CYS D 336 " pdb=" N PRO D 337 " ideal model delta sigma weight residual 1.334 1.423 -0.089 2.34e-02 1.83e+03 1.44e+01 bond pdb=" C PRO B 25 " pdb=" N PRO B 26 " ideal model delta sigma weight residual 1.334 1.403 -0.069 2.34e-02 1.83e+03 8.71e+00 bond pdb=" C PRO A 25 " pdb=" N PRO A 26 " ideal model delta sigma weight residual 1.334 1.392 -0.059 2.34e-02 1.83e+03 6.25e+00 ... (remaining 30799 not shown) Histogram of bond angle deviations from ideal: 99.08 - 106.06: 770 106.06 - 113.05: 16330 113.05 - 120.04: 10324 120.04 - 127.02: 14144 127.02 - 134.01: 321 Bond angle restraints: 41889 Sorted by residual: angle pdb=" C LYS A 790 " pdb=" N THR A 791 " pdb=" CA THR A 791 " ideal model delta sigma weight residual 120.94 132.07 -11.13 1.90e+00 2.77e-01 3.43e+01 angle pdb=" N ALA A 292 " pdb=" CA ALA A 292 " pdb=" C ALA A 292 " ideal model delta sigma weight residual 110.80 99.08 11.72 2.13e+00 2.20e-01 3.03e+01 angle pdb=" N ALA B 292 " pdb=" CA ALA B 292 " pdb=" C ALA B 292 " ideal model delta sigma weight residual 110.80 100.34 10.46 2.13e+00 2.20e-01 2.41e+01 angle pdb=" N CYS A 291 " pdb=" CA CYS A 291 " pdb=" C CYS A 291 " ideal model delta sigma weight residual 108.73 116.16 -7.43 1.63e+00 3.76e-01 2.08e+01 angle pdb=" CA CYS D 361 " pdb=" C CYS D 361 " pdb=" N VAL D 362 " ideal model delta sigma weight residual 115.79 120.51 -4.72 1.34e+00 5.57e-01 1.24e+01 ... (remaining 41884 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.99: 17855 15.99 - 31.97: 307 31.97 - 47.96: 112 47.96 - 63.94: 28 63.94 - 79.93: 15 Dihedral angle restraints: 18317 sinusoidal: 7197 harmonic: 11120 Sorted by residual: dihedral pdb=" CA THR D 531 " pdb=" C THR D 531 " pdb=" N ASN D 532 " pdb=" CA ASN D 532 " ideal model delta harmonic sigma weight residual -180.00 -153.12 -26.88 0 5.00e+00 4.00e-02 2.89e+01 dihedral pdb=" CB CYS A 662 " pdb=" SG CYS A 662 " pdb=" SG CYS A 671 " pdb=" CB CYS A 671 " ideal model delta sinusoidal sigma weight residual 93.00 56.40 36.60 1 1.00e+01 1.00e-02 1.89e+01 dihedral pdb=" CA LEU A 241 " pdb=" C LEU A 241 " pdb=" N HIS A 242 " pdb=" CA HIS A 242 " ideal model delta harmonic sigma weight residual -180.00 -158.44 -21.56 0 5.00e+00 4.00e-02 1.86e+01 ... (remaining 18314 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 3861 0.049 - 0.098: 571 0.098 - 0.147: 233 0.147 - 0.196: 3 0.196 - 0.245: 3 Chirality restraints: 4671 Sorted by residual: chirality pdb=" CA CYS A 291 " pdb=" N CYS A 291 " pdb=" C CYS A 291 " pdb=" CB CYS A 291 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.49e+00 chirality pdb=" CA ALA A 292 " pdb=" N ALA A 292 " pdb=" C ALA A 292 " pdb=" CB ALA A 292 " both_signs ideal model delta sigma weight residual False 2.48 2.72 -0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CA ALA B 292 " pdb=" N ALA B 292 " pdb=" C ALA B 292 " pdb=" CB ALA B 292 " both_signs ideal model delta sigma weight residual False 2.48 2.72 -0.23 2.00e-01 2.50e+01 1.36e+00 ... (remaining 4668 not shown) Planarity restraints: 5431 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP A 290 " -0.014 2.00e-02 2.50e+03 2.86e-02 8.21e+00 pdb=" C ASP A 290 " 0.050 2.00e-02 2.50e+03 pdb=" O ASP A 290 " -0.019 2.00e-02 2.50e+03 pdb=" N CYS A 291 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP B 294 " 0.036 5.00e-02 4.00e+02 5.51e-02 4.86e+00 pdb=" N PRO B 295 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO B 295 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 295 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 294 " 0.036 5.00e-02 4.00e+02 5.51e-02 4.85e+00 pdb=" N PRO A 295 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 295 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 295 " 0.031 5.00e-02 4.00e+02 ... (remaining 5428 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.40: 85 2.40 - 3.03: 16361 3.03 - 3.65: 42558 3.65 - 4.28: 64323 4.28 - 4.90: 107518 Nonbonded interactions: 230845 Sorted by model distance: nonbonded pdb=" O GLY A 103 " pdb=" CE1 HIS A 242 " model vdw 1.780 3.260 nonbonded pdb=" OG1 THR D 108 " pdb=" O ASN D 234 " model vdw 2.197 2.440 nonbonded pdb=" OG SER D 746 " pdb=" OE1 GLU D 748 " model vdw 2.205 2.440 nonbonded pdb=" OG1 THR D 33 " pdb=" O GLY D 219 " model vdw 2.250 2.440 nonbonded pdb=" OG1 THR A 912 " pdb=" NE2 GLN A1106 " model vdw 2.262 2.520 ... (remaining 230840 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 470 or resid 491 through 1161)) selection = chain 'B' selection = (chain 'D' and (resid 14 through 470 or resid 491 through 1161)) } 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: 2.070 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: 11.370 Check model and map are aligned: 0.470 Set scattering table: 0.290 Process input model: 79.440 Find NCS groups from input model: 2.200 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 98.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4765 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 : 0.002 0.103 30804 Z= 0.128 Angle : 0.479 11.725 41889 Z= 0.276 Chirality : 0.041 0.245 4671 Planarity : 0.003 0.055 5431 Dihedral : 8.026 79.929 11044 Min Nonbonded Distance : 1.780 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.97 % Favored : 95.89 % Rotamer: Outliers : 0.03 % Allowed : 0.27 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.43 (0.11), residues: 3774 helix: -3.28 (0.10), residues: 946 sheet: -0.51 (0.17), residues: 655 loop : -1.11 (0.12), residues: 2173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 436 HIS 0.006 0.001 HIS B 242 PHE 0.017 0.001 PHE D 59 TYR 0.016 0.001 TYR A 495 ARG 0.002 0.000 ARG D 102 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 859 residues out of total 3343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 858 time to evaluate : 3.708 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: A 88 ASP cc_start: 0.4327 (p0) cc_final: 0.4045 (p0) REVERT: A 574 ASP cc_start: 0.7620 (p0) cc_final: 0.7346 (p0) REVERT: A 584 ILE cc_start: 0.7384 (mt) cc_final: 0.7055 (mp) REVERT: A 693 ILE cc_start: 0.8623 (pt) cc_final: 0.8299 (pt) REVERT: A 714 ILE cc_start: 0.8527 (mp) cc_final: 0.8257 (mt) REVERT: B 305 SER cc_start: 0.8401 (t) cc_final: 0.8178 (t) REVERT: B 1033 VAL cc_start: 0.8081 (t) cc_final: 0.7687 (t) REVERT: D 159 VAL cc_start: 0.3726 (t) cc_final: 0.3426 (t) REVERT: D 710 ASN cc_start: 0.6325 (p0) cc_final: 0.6093 (p0) REVERT: D 1102 TRP cc_start: 0.6782 (m100) cc_final: 0.6483 (m100) outliers start: 1 outliers final: 0 residues processed: 859 average time/residue: 0.4144 time to fit residues: 557.7234 Evaluate side-chains 407 residues out of total 3343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 407 time to evaluate : 3.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 319 optimal weight: 3.9990 chunk 286 optimal weight: 0.8980 chunk 158 optimal weight: 4.9990 chunk 97 optimal weight: 0.9990 chunk 193 optimal weight: 6.9990 chunk 153 optimal weight: 7.9990 chunk 296 optimal weight: 9.9990 chunk 114 optimal weight: 7.9990 chunk 180 optimal weight: 20.0000 chunk 220 optimal weight: 1.9990 chunk 343 optimal weight: 6.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN A 394 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 544 ASN A 690 GLN A 787 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN A1054 GLN A1088 HIS ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN C 60 GLN C 61 ASN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 241 HIS C 380 GLN C 401 HIS C 417 HIS C 505 HIS B 30 ASN B 66 HIS B 211 ASN B 563 GLN ** B 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN B1005 GLN B1088 HIS ** B1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 30 ASN D 121 ASN ** D 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 360 ASN D 655 HIS D 787 GLN D 824 ASN D 914 ASN D1005 GLN ** D1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1088 HIS D1106 GLN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5411 moved from start: 0.3871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.115 30804 Z= 0.285 Angle : 0.658 10.098 41889 Z= 0.345 Chirality : 0.047 0.326 4671 Planarity : 0.005 0.056 5431 Dihedral : 4.082 27.661 4087 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.78 % Favored : 98.20 % Rotamer: Outliers : 2.48 % Allowed : 8.50 % Favored : 89.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.12), residues: 3774 helix: -0.50 (0.15), residues: 966 sheet: -0.29 (0.17), residues: 689 loop : -0.88 (0.12), residues: 2119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 477 HIS 0.016 0.002 HIS C 505 PHE 0.038 0.002 PHE A 55 TYR 0.027 0.002 TYR D 741 ARG 0.007 0.001 ARG A1107 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 541 residues out of total 3343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 458 time to evaluate : 3.330 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 305 SER cc_start: 0.7270 (t) cc_final: 0.6857 (p) REVERT: A 559 PHE cc_start: 0.5145 (m-10) cc_final: 0.4421 (m-10) REVERT: A 902 MET cc_start: 0.8341 (mmm) cc_final: 0.7797 (mmt) REVERT: A 962 LEU cc_start: 0.8853 (tp) cc_final: 0.8556 (tt) REVERT: A 992 GLN cc_start: 0.8564 (mm110) cc_final: 0.8293 (mm110) REVERT: C 85 LEU cc_start: 0.1148 (mp) cc_final: 0.0631 (pp) REVERT: C 323 MET cc_start: -0.1169 (mmm) cc_final: -0.1426 (mtm) REVERT: C 408 MET cc_start: 0.1057 (mtt) cc_final: 0.0651 (mtp) REVERT: C 455 MET cc_start: -0.2214 (tmm) cc_final: -0.3080 (tmm) REVERT: B 46 SER cc_start: 0.7453 (m) cc_final: 0.7048 (p) REVERT: B 365 TYR cc_start: 0.4437 (m-80) cc_final: 0.1999 (t80) REVERT: D 858 LEU cc_start: 0.7508 (mt) cc_final: 0.7248 (mt) REVERT: D 918 GLU cc_start: 0.6824 (OUTLIER) cc_final: 0.6174 (mp0) outliers start: 83 outliers final: 46 residues processed: 518 average time/residue: 0.4020 time to fit residues: 336.7395 Evaluate side-chains 369 residues out of total 3343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 322 time to evaluate : 3.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 941 THR Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1148 PHE Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 438 PHE Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 737 ASP Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain D residue 301 CYS Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 572 THR Chi-restraints excluded: chain D residue 709 ASN Chi-restraints excluded: chain D residue 875 SER Chi-restraints excluded: chain D residue 884 SER Chi-restraints excluded: chain D residue 918 GLU Chi-restraints excluded: chain D residue 929 SER Chi-restraints excluded: chain D residue 967 SER Chi-restraints excluded: chain D residue 974 SER Chi-restraints excluded: chain D residue 1077 THR Chi-restraints excluded: chain D residue 1136 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 190 optimal weight: 7.9990 chunk 106 optimal weight: 0.7980 chunk 285 optimal weight: 6.9990 chunk 233 optimal weight: 7.9990 chunk 94 optimal weight: 5.9990 chunk 343 optimal weight: 4.9990 chunk 371 optimal weight: 0.9990 chunk 306 optimal weight: 5.9990 chunk 341 optimal weight: 0.9980 chunk 117 optimal weight: 7.9990 chunk 275 optimal weight: 10.0000 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 GLN A 49 HIS ** A 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 GLN A 955 ASN A1088 HIS A1106 GLN A1159 HIS ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 524 GLN ** B 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS B 498 GLN B 913 GLN ** B 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 978 ASN B1010 GLN B1088 HIS D 148 ASN ** D 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 321 GLN D 703 ASN D 779 GLN D 856 ASN D 955 ASN ** D1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5674 moved from start: 0.5289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 30804 Z= 0.278 Angle : 0.618 10.791 41889 Z= 0.319 Chirality : 0.045 0.182 4671 Planarity : 0.005 0.050 5431 Dihedral : 4.244 29.059 4087 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.54 % Favored : 97.43 % Rotamer: Outliers : 2.87 % Allowed : 10.26 % Favored : 86.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.13), residues: 3774 helix: 0.43 (0.16), residues: 986 sheet: -0.14 (0.18), residues: 679 loop : -0.87 (0.12), residues: 2109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 104 HIS 0.006 0.001 HIS A 207 PHE 0.028 0.002 PHE A 797 TYR 0.030 0.002 TYR C 252 ARG 0.008 0.001 ARG B1107 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 3343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 365 time to evaluate : 3.732 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: A 241 LEU cc_start: 0.5192 (pp) cc_final: 0.4978 (pp) REVERT: A 305 SER cc_start: 0.7788 (t) cc_final: 0.7568 (p) REVERT: A 568 ASP cc_start: 0.7587 (p0) cc_final: 0.7353 (p0) REVERT: A 697 MET cc_start: 0.6623 (tpt) cc_final: 0.6209 (tpt) REVERT: A 699 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8145 (mm) REVERT: A 737 ASP cc_start: 0.8679 (OUTLIER) cc_final: 0.8454 (p0) REVERT: A 978 ASN cc_start: 0.7666 (m110) cc_final: 0.7372 (m-40) REVERT: A 992 GLN cc_start: 0.8466 (mm110) cc_final: 0.8259 (mm110) REVERT: C 85 LEU cc_start: 0.1535 (mp) cc_final: 0.1106 (pp) REVERT: C 323 MET cc_start: -0.0929 (mmm) cc_final: -0.1281 (mtm) REVERT: C 383 MET cc_start: 0.4046 (tmm) cc_final: 0.3620 (tmm) REVERT: C 408 MET cc_start: 0.1080 (mtt) cc_final: 0.0846 (mtp) REVERT: C 536 GLU cc_start: 0.6311 (OUTLIER) cc_final: 0.5606 (pt0) REVERT: B 266 TYR cc_start: 0.6711 (OUTLIER) cc_final: 0.6240 (m-80) REVERT: B 365 TYR cc_start: 0.4515 (m-80) cc_final: 0.1880 (t80) REVERT: B 904 TYR cc_start: 0.7118 (t80) cc_final: 0.6713 (t80) REVERT: B 992 GLN cc_start: 0.8656 (mm-40) cc_final: 0.8433 (mm-40) REVERT: D 779 GLN cc_start: 0.7128 (OUTLIER) cc_final: 0.6725 (mp10) outliers start: 96 outliers final: 60 residues processed: 425 average time/residue: 0.3737 time to fit residues: 263.6177 Evaluate side-chains 362 residues out of total 3343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 297 time to evaluate : 3.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 872 GLN Chi-restraints excluded: chain A residue 941 THR Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1148 PHE Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 328 TRP Chi-restraints excluded: chain C residue 438 PHE Chi-restraints excluded: chain C residue 536 GLU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 737 ASP Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 104 TRP Chi-restraints excluded: chain D residue 301 CYS Chi-restraints excluded: chain D residue 318 PHE Chi-restraints excluded: chain D residue 517 LEU Chi-restraints excluded: chain D residue 529 LYS Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 572 THR Chi-restraints excluded: chain D residue 611 LEU Chi-restraints excluded: chain D residue 709 ASN Chi-restraints excluded: chain D residue 732 THR Chi-restraints excluded: chain D residue 743 CYS Chi-restraints excluded: chain D residue 779 GLN Chi-restraints excluded: chain D residue 874 THR Chi-restraints excluded: chain D residue 929 SER Chi-restraints excluded: chain D residue 945 LEU Chi-restraints excluded: chain D residue 959 LEU Chi-restraints excluded: chain D residue 967 SER Chi-restraints excluded: chain D residue 974 SER Chi-restraints excluded: chain D residue 1031 GLU Chi-restraints excluded: chain D residue 1077 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 339 optimal weight: 4.9990 chunk 258 optimal weight: 5.9990 chunk 178 optimal weight: 6.9990 chunk 38 optimal weight: 0.2980 chunk 164 optimal weight: 9.9990 chunk 230 optimal weight: 2.9990 chunk 345 optimal weight: 0.7980 chunk 365 optimal weight: 5.9990 chunk 180 optimal weight: 20.0000 chunk 327 optimal weight: 8.9990 chunk 98 optimal weight: 5.9990 overall best weight: 3.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 498 GLN A 954 GLN A1083 HIS C 42 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 330 ASN C 556 ASN B 14 GLN B 394 ASN B 655 HIS B 856 ASN ** B 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 949 GLN B 955 ASN B 957 GLN B 969 ASN B 978 ASN B1048 HIS ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 498 GLN D 755 GLN D 762 GLN ** D 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1002 GLN ** D1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1125 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5846 moved from start: 0.6387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 30804 Z= 0.291 Angle : 0.625 10.284 41889 Z= 0.322 Chirality : 0.046 0.209 4671 Planarity : 0.004 0.064 5431 Dihedral : 4.390 26.471 4087 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.68 % Favored : 97.30 % Rotamer: Outliers : 2.90 % Allowed : 11.88 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.13), residues: 3774 helix: 0.66 (0.16), residues: 1014 sheet: -0.07 (0.18), residues: 696 loop : -0.98 (0.13), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 436 HIS 0.009 0.001 HIS B 242 PHE 0.033 0.002 PHE B 275 TYR 0.030 0.002 TYR A 160 ARG 0.018 0.001 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 3343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 335 time to evaluate : 3.460 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: A 697 MET cc_start: 0.6480 (tpt) cc_final: 0.6226 (tpt) REVERT: A 699 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8272 (mm) REVERT: A 731 MET cc_start: 0.7886 (ttt) cc_final: 0.7657 (ttt) REVERT: A 900 MET cc_start: 0.8307 (mmm) cc_final: 0.7765 (mtp) REVERT: A 918 GLU cc_start: 0.7363 (OUTLIER) cc_final: 0.6652 (mp0) REVERT: A 978 ASN cc_start: 0.8019 (m110) cc_final: 0.7748 (m-40) REVERT: C 54 ILE cc_start: 0.5638 (OUTLIER) cc_final: 0.5102 (pt) REVERT: C 85 LEU cc_start: 0.1775 (mp) cc_final: 0.1333 (pp) REVERT: C 408 MET cc_start: 0.1315 (mtt) cc_final: 0.1097 (mtp) REVERT: C 536 GLU cc_start: 0.6308 (OUTLIER) cc_final: 0.5556 (pt0) REVERT: B 796 ASP cc_start: 0.6250 (p0) cc_final: 0.6036 (p0) REVERT: B 904 TYR cc_start: 0.7340 (t80) cc_final: 0.6997 (t80) REVERT: B 992 GLN cc_start: 0.8582 (mm-40) cc_final: 0.8374 (mm-40) outliers start: 97 outliers final: 51 residues processed: 407 average time/residue: 0.3990 time to fit residues: 269.3778 Evaluate side-chains 331 residues out of total 3343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 276 time to evaluate : 3.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 265 TYR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 872 GLN Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1148 PHE Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 438 PHE Chi-restraints excluded: chain C residue 536 GLU Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 874 THR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 301 CYS Chi-restraints excluded: chain D residue 318 PHE Chi-restraints excluded: chain D residue 529 LYS Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 572 THR Chi-restraints excluded: chain D residue 604 THR Chi-restraints excluded: chain D residue 658 ASN Chi-restraints excluded: chain D residue 743 CYS Chi-restraints excluded: chain D residue 874 THR Chi-restraints excluded: chain D residue 884 SER Chi-restraints excluded: chain D residue 929 SER Chi-restraints excluded: chain D residue 1077 THR Chi-restraints excluded: chain D residue 1116 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 304 optimal weight: 20.0000 chunk 207 optimal weight: 0.0060 chunk 5 optimal weight: 0.8980 chunk 272 optimal weight: 8.9990 chunk 150 optimal weight: 9.9990 chunk 311 optimal weight: 9.9990 chunk 252 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 186 optimal weight: 0.9980 chunk 327 optimal weight: 5.9990 chunk 92 optimal weight: 0.8980 overall best weight: 1.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 439 ASN ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 ASN ** B 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 ASN ** D 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 762 GLN D 779 GLN D 954 GLN ** D 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1005 GLN ** D1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5840 moved from start: 0.6733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 30804 Z= 0.193 Angle : 0.558 13.814 41889 Z= 0.283 Chirality : 0.043 0.166 4671 Planarity : 0.004 0.051 5431 Dihedral : 4.186 27.171 4087 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.76 % Favored : 97.22 % Rotamer: Outliers : 2.48 % Allowed : 13.34 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.13), residues: 3774 helix: 0.91 (0.16), residues: 1018 sheet: -0.00 (0.18), residues: 687 loop : -0.93 (0.13), residues: 2069 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 477 HIS 0.005 0.001 HIS D 207 PHE 0.042 0.002 PHE B 275 TYR 0.020 0.001 TYR D 495 ARG 0.006 0.000 ARG D 102 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 3343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 303 time to evaluate : 3.899 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: A 900 MET cc_start: 0.8230 (mmm) cc_final: 0.7755 (mtp) REVERT: C 536 GLU cc_start: 0.6247 (OUTLIER) cc_final: 0.4812 (pm20) REVERT: B 759 PHE cc_start: 0.8055 (OUTLIER) cc_final: 0.7797 (t80) REVERT: B 900 MET cc_start: 0.8117 (OUTLIER) cc_final: 0.7267 (mtm) REVERT: B 904 TYR cc_start: 0.7305 (t80) cc_final: 0.6913 (t80) REVERT: B 992 GLN cc_start: 0.8385 (mm-40) cc_final: 0.8112 (mt0) REVERT: D 563 GLN cc_start: 0.4030 (OUTLIER) cc_final: 0.2818 (mt0) outliers start: 83 outliers final: 53 residues processed: 361 average time/residue: 0.3727 time to fit residues: 224.9694 Evaluate side-chains 323 residues out of total 3343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 266 time to evaluate : 3.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 872 GLN Chi-restraints excluded: chain A residue 941 THR Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 438 PHE Chi-restraints excluded: chain C residue 536 GLU Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain B residue 737 ASP Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain D residue 104 TRP Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 301 CYS Chi-restraints excluded: chain D residue 318 PHE Chi-restraints excluded: chain D residue 517 LEU Chi-restraints excluded: chain D residue 529 LYS Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 563 GLN Chi-restraints excluded: chain D residue 572 THR Chi-restraints excluded: chain D residue 607 GLN Chi-restraints excluded: chain D residue 743 CYS Chi-restraints excluded: chain D residue 874 THR Chi-restraints excluded: chain D residue 929 SER Chi-restraints excluded: chain D residue 959 LEU Chi-restraints excluded: chain D residue 969 ASN Chi-restraints excluded: chain D residue 996 LEU Chi-restraints excluded: chain D residue 1146 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 122 optimal weight: 40.0000 chunk 329 optimal weight: 0.9990 chunk 72 optimal weight: 0.1980 chunk 214 optimal weight: 6.9990 chunk 90 optimal weight: 0.8980 chunk 365 optimal weight: 6.9990 chunk 303 optimal weight: 5.9990 chunk 169 optimal weight: 10.0000 chunk 30 optimal weight: 0.7980 chunk 120 optimal weight: 30.0000 chunk 192 optimal weight: 7.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 556 ASN ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 ASN ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 755 GLN D 762 GLN D1005 GLN ** D1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5877 moved from start: 0.7063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 30804 Z= 0.194 Angle : 0.550 12.411 41889 Z= 0.279 Chirality : 0.043 0.203 4671 Planarity : 0.004 0.060 5431 Dihedral : 4.100 25.833 4087 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.99 % Favored : 96.98 % Rotamer: Outliers : 2.81 % Allowed : 13.49 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.13), residues: 3774 helix: 1.11 (0.16), residues: 1020 sheet: 0.04 (0.18), residues: 674 loop : -0.91 (0.13), residues: 2080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 104 HIS 0.005 0.001 HIS A 242 PHE 0.050 0.002 PHE B 275 TYR 0.018 0.001 TYR D 495 ARG 0.008 0.000 ARG A 319 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 3343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 291 time to evaluate : 3.992 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: A 86 PHE cc_start: 0.7023 (OUTLIER) cc_final: 0.6654 (m-80) REVERT: A 205 SER cc_start: 0.7477 (t) cc_final: 0.7136 (p) REVERT: A 918 GLU cc_start: 0.7307 (OUTLIER) cc_final: 0.6485 (mp0) REVERT: C 455 MET cc_start: -0.1863 (tmm) cc_final: -0.2336 (tmm) REVERT: C 536 GLU cc_start: 0.6212 (OUTLIER) cc_final: 0.4660 (pm20) REVERT: B 900 MET cc_start: 0.8114 (OUTLIER) cc_final: 0.7256 (mtm) REVERT: B 904 TYR cc_start: 0.7304 (t80) cc_final: 0.6865 (t80) REVERT: D 563 GLN cc_start: 0.3853 (OUTLIER) cc_final: 0.2632 (mt0) outliers start: 94 outliers final: 69 residues processed: 366 average time/residue: 0.3824 time to fit residues: 234.7592 Evaluate side-chains 341 residues out of total 3343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 267 time to evaluate : 3.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 941 THR Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 438 PHE Chi-restraints excluded: chain C residue 515 TYR Chi-restraints excluded: chain C residue 536 GLU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 737 ASP Chi-restraints excluded: chain B residue 764 ASN Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 874 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain D residue 104 TRP Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 301 CYS Chi-restraints excluded: chain D residue 307 THR Chi-restraints excluded: chain D residue 318 PHE Chi-restraints excluded: chain D residue 517 LEU Chi-restraints excluded: chain D residue 529 LYS Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 563 GLN Chi-restraints excluded: chain D residue 572 THR Chi-restraints excluded: chain D residue 607 GLN Chi-restraints excluded: chain D residue 617 CYS Chi-restraints excluded: chain D residue 658 ASN Chi-restraints excluded: chain D residue 732 THR Chi-restraints excluded: chain D residue 743 CYS Chi-restraints excluded: chain D residue 808 ASP Chi-restraints excluded: chain D residue 874 THR Chi-restraints excluded: chain D residue 881 THR Chi-restraints excluded: chain D residue 884 SER Chi-restraints excluded: chain D residue 929 SER Chi-restraints excluded: chain D residue 959 LEU Chi-restraints excluded: chain D residue 1040 VAL Chi-restraints excluded: chain D residue 1074 ASN Chi-restraints excluded: chain D residue 1146 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 352 optimal weight: 4.9990 chunk 41 optimal weight: 0.8980 chunk 208 optimal weight: 20.0000 chunk 267 optimal weight: 1.9990 chunk 206 optimal weight: 20.0000 chunk 307 optimal weight: 9.9990 chunk 204 optimal weight: 10.0000 chunk 364 optimal weight: 0.8980 chunk 228 optimal weight: 5.9990 chunk 222 optimal weight: 7.9990 chunk 168 optimal weight: 2.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 544 ASN ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 505 HIS B 762 GLN B 856 ASN D 165 ASN ** D 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 242 HIS D 751 ASN D 774 GLN D 787 GLN D1048 HIS ** D1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5961 moved from start: 0.7635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 30804 Z= 0.233 Angle : 0.579 12.778 41889 Z= 0.295 Chirality : 0.044 0.176 4671 Planarity : 0.004 0.045 5431 Dihedral : 4.256 27.361 4087 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.60 % Favored : 96.37 % Rotamer: Outliers : 3.11 % Allowed : 13.97 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.13), residues: 3774 helix: 1.04 (0.16), residues: 1022 sheet: -0.15 (0.18), residues: 697 loop : -0.95 (0.13), residues: 2055 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP B 104 HIS 0.005 0.001 HIS A 242 PHE 0.020 0.002 PHE A 275 TYR 0.029 0.002 TYR D 495 ARG 0.007 0.000 ARG B 765 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 3343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 302 time to evaluate : 3.756 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 205 SER cc_start: 0.7375 (t) cc_final: 0.7106 (p) REVERT: A 697 MET cc_start: 0.7180 (mmm) cc_final: 0.6835 (mmm) REVERT: A 918 GLU cc_start: 0.7356 (OUTLIER) cc_final: 0.6473 (mp0) REVERT: C 536 GLU cc_start: 0.6144 (OUTLIER) cc_final: 0.5294 (pt0) REVERT: B 745 ASP cc_start: 0.6268 (OUTLIER) cc_final: 0.5934 (m-30) REVERT: B 904 TYR cc_start: 0.7383 (t80) cc_final: 0.6933 (t80) REVERT: D 242 HIS cc_start: 0.1983 (OUTLIER) cc_final: 0.1576 (m170) REVERT: D 563 GLN cc_start: 0.4243 (OUTLIER) cc_final: 0.3073 (mt0) REVERT: D 750 SER cc_start: 0.6979 (OUTLIER) cc_final: 0.6715 (m) outliers start: 104 outliers final: 73 residues processed: 379 average time/residue: 0.3741 time to fit residues: 236.4366 Evaluate side-chains 347 residues out of total 3343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 268 time to evaluate : 3.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 941 THR Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 438 PHE Chi-restraints excluded: chain C residue 515 TYR Chi-restraints excluded: chain C residue 536 GLU Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain B residue 737 ASP Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 874 THR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 104 TRP Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 242 HIS Chi-restraints excluded: chain D residue 301 CYS Chi-restraints excluded: chain D residue 307 THR Chi-restraints excluded: chain D residue 318 PHE Chi-restraints excluded: chain D residue 517 LEU Chi-restraints excluded: chain D residue 529 LYS Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 563 GLN Chi-restraints excluded: chain D residue 572 THR Chi-restraints excluded: chain D residue 658 ASN Chi-restraints excluded: chain D residue 701 VAL Chi-restraints excluded: chain D residue 729 VAL Chi-restraints excluded: chain D residue 732 THR Chi-restraints excluded: chain D residue 750 SER Chi-restraints excluded: chain D residue 874 THR Chi-restraints excluded: chain D residue 881 THR Chi-restraints excluded: chain D residue 929 SER Chi-restraints excluded: chain D residue 959 LEU Chi-restraints excluded: chain D residue 996 LEU Chi-restraints excluded: chain D residue 1040 VAL Chi-restraints excluded: chain D residue 1074 ASN Chi-restraints excluded: chain D residue 1123 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 225 optimal weight: 0.1980 chunk 145 optimal weight: 9.9990 chunk 217 optimal weight: 3.9990 chunk 109 optimal weight: 5.9990 chunk 71 optimal weight: 5.9990 chunk 70 optimal weight: 0.9980 chunk 231 optimal weight: 4.9990 chunk 248 optimal weight: 2.9990 chunk 180 optimal weight: 20.0000 chunk 33 optimal weight: 6.9990 chunk 286 optimal weight: 5.9990 overall best weight: 2.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1048 HIS ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 ASN B 762 GLN B 856 ASN B 955 ASN ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6006 moved from start: 0.8010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 30804 Z= 0.253 Angle : 0.582 12.785 41889 Z= 0.298 Chirality : 0.044 0.179 4671 Planarity : 0.004 0.045 5431 Dihedral : 4.316 21.669 4087 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.92 % Favored : 96.05 % Rotamer: Outliers : 2.78 % Allowed : 14.87 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.13), residues: 3774 helix: 0.95 (0.16), residues: 1047 sheet: -0.25 (0.18), residues: 687 loop : -0.98 (0.13), residues: 2040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP B 104 HIS 0.015 0.001 HIS D 242 PHE 0.024 0.002 PHE B 759 TYR 0.020 0.002 TYR D 495 ARG 0.006 0.000 ARG A 319 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 3343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 292 time to evaluate : 3.585 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 205 SER cc_start: 0.7427 (t) cc_final: 0.7165 (p) REVERT: A 900 MET cc_start: 0.8115 (mmm) cc_final: 0.7892 (mtt) REVERT: A 918 GLU cc_start: 0.7343 (OUTLIER) cc_final: 0.6506 (mp0) REVERT: A 979 ASP cc_start: 0.8156 (m-30) cc_final: 0.7894 (m-30) REVERT: A 1034 LEU cc_start: 0.9019 (mm) cc_final: 0.8727 (mt) REVERT: A 1047 TYR cc_start: 0.8962 (m-80) cc_final: 0.8627 (m-80) REVERT: C 67 ASP cc_start: 0.4458 (OUTLIER) cc_final: 0.4215 (p0) REVERT: C 119 ILE cc_start: -0.2432 (tp) cc_final: -0.2727 (tt) REVERT: C 123 MET cc_start: 0.1317 (OUTLIER) cc_final: 0.1057 (ppp) REVERT: C 455 MET cc_start: -0.1624 (tmm) cc_final: -0.2296 (tmm) REVERT: C 536 GLU cc_start: 0.6301 (OUTLIER) cc_final: 0.5414 (pt0) REVERT: B 856 ASN cc_start: 0.7669 (OUTLIER) cc_final: 0.7331 (t0) REVERT: B 900 MET cc_start: 0.8238 (OUTLIER) cc_final: 0.7327 (mtm) REVERT: B 904 TYR cc_start: 0.7430 (t80) cc_final: 0.6934 (t80) REVERT: D 563 GLN cc_start: 0.4279 (OUTLIER) cc_final: 0.3093 (mt0) outliers start: 93 outliers final: 74 residues processed: 360 average time/residue: 0.3697 time to fit residues: 222.6876 Evaluate side-chains 353 residues out of total 3343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 272 time to evaluate : 3.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 941 THR Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 123 MET Chi-restraints excluded: chain C residue 438 PHE Chi-restraints excluded: chain C residue 515 TYR Chi-restraints excluded: chain C residue 536 GLU Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain B residue 737 ASP Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 764 ASN Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 874 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain D residue 104 TRP Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 301 CYS Chi-restraints excluded: chain D residue 318 PHE Chi-restraints excluded: chain D residue 517 LEU Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 563 GLN Chi-restraints excluded: chain D residue 572 THR Chi-restraints excluded: chain D residue 658 ASN Chi-restraints excluded: chain D residue 729 VAL Chi-restraints excluded: chain D residue 732 THR Chi-restraints excluded: chain D residue 874 THR Chi-restraints excluded: chain D residue 881 THR Chi-restraints excluded: chain D residue 929 SER Chi-restraints excluded: chain D residue 959 LEU Chi-restraints excluded: chain D residue 969 ASN Chi-restraints excluded: chain D residue 976 VAL Chi-restraints excluded: chain D residue 996 LEU Chi-restraints excluded: chain D residue 1040 VAL Chi-restraints excluded: chain D residue 1074 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 331 optimal weight: 5.9990 chunk 349 optimal weight: 0.0070 chunk 318 optimal weight: 8.9990 chunk 339 optimal weight: 0.7980 chunk 348 optimal weight: 3.9990 chunk 204 optimal weight: 0.6980 chunk 147 optimal weight: 0.0010 chunk 266 optimal weight: 0.9990 chunk 104 optimal weight: 0.8980 chunk 306 optimal weight: 0.9990 chunk 321 optimal weight: 0.8980 overall best weight: 0.4804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN ** D 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1002 GLN D1054 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5912 moved from start: 0.8000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.065 30804 Z= 0.142 Angle : 0.548 13.560 41889 Z= 0.272 Chirality : 0.043 0.201 4671 Planarity : 0.004 0.047 5431 Dihedral : 4.051 20.719 4087 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.86 % Favored : 97.11 % Rotamer: Outliers : 1.85 % Allowed : 15.97 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.13), residues: 3774 helix: 1.26 (0.16), residues: 1034 sheet: -0.27 (0.18), residues: 714 loop : -0.88 (0.13), residues: 2026 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP B 104 HIS 0.007 0.001 HIS A 242 PHE 0.026 0.001 PHE A 565 TYR 0.020 0.001 TYR D 495 ARG 0.008 0.000 ARG A 765 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 3343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 305 time to evaluate : 3.668 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 205 SER cc_start: 0.7110 (t) cc_final: 0.6909 (p) REVERT: A 918 GLU cc_start: 0.7216 (OUTLIER) cc_final: 0.6419 (mp0) REVERT: A 979 ASP cc_start: 0.8029 (m-30) cc_final: 0.7741 (m-30) REVERT: A 1034 LEU cc_start: 0.9045 (mm) cc_final: 0.8762 (mt) REVERT: A 1047 TYR cc_start: 0.8916 (m-80) cc_final: 0.8591 (m-80) REVERT: C 119 ILE cc_start: -0.2856 (tp) cc_final: -0.3074 (tt) REVERT: C 123 MET cc_start: 0.0831 (OUTLIER) cc_final: 0.0621 (ppp) REVERT: C 366 MET cc_start: 0.1845 (tpp) cc_final: -0.0585 (ttm) REVERT: C 455 MET cc_start: -0.1744 (tmm) cc_final: -0.2528 (tmm) REVERT: C 536 GLU cc_start: 0.6208 (OUTLIER) cc_final: 0.4559 (pm20) REVERT: B 365 TYR cc_start: 0.4246 (m-80) cc_final: 0.1781 (t80) REVERT: B 764 ASN cc_start: 0.8401 (OUTLIER) cc_final: 0.8019 (m-40) REVERT: B 904 TYR cc_start: 0.7185 (t80) cc_final: 0.6663 (t80) outliers start: 62 outliers final: 46 residues processed: 348 average time/residue: 0.3863 time to fit residues: 226.9613 Evaluate side-chains 334 residues out of total 3343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 284 time to evaluate : 3.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 941 THR Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 123 MET Chi-restraints excluded: chain C residue 438 PHE Chi-restraints excluded: chain C residue 536 GLU Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 764 ASN Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain D residue 104 TRP Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 301 CYS Chi-restraints excluded: chain D residue 517 LEU Chi-restraints excluded: chain D residue 572 THR Chi-restraints excluded: chain D residue 959 LEU Chi-restraints excluded: chain D residue 996 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 338 optimal weight: 1.9990 chunk 222 optimal weight: 6.9990 chunk 359 optimal weight: 4.9990 chunk 219 optimal weight: 0.7980 chunk 170 optimal weight: 3.9990 chunk 249 optimal weight: 2.9990 chunk 376 optimal weight: 6.9990 chunk 346 optimal weight: 0.8980 chunk 299 optimal weight: 0.0060 chunk 31 optimal weight: 0.6980 chunk 231 optimal weight: 3.9990 overall best weight: 0.8798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 ASN B 856 ASN ** B 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5928 moved from start: 0.8092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 30804 Z= 0.149 Angle : 0.537 12.865 41889 Z= 0.269 Chirality : 0.043 0.174 4671 Planarity : 0.004 0.047 5431 Dihedral : 3.974 27.005 4087 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.31 % Favored : 96.66 % Rotamer: Outliers : 1.53 % Allowed : 16.36 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.13), residues: 3774 helix: 1.33 (0.16), residues: 1047 sheet: -0.21 (0.18), residues: 692 loop : -0.83 (0.13), residues: 2035 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP B 104 HIS 0.005 0.001 HIS A 242 PHE 0.043 0.001 PHE B 275 TYR 0.018 0.001 TYR D 170 ARG 0.007 0.000 ARG A 765 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 3343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 294 time to evaluate : 3.461 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 205 SER cc_start: 0.7073 (t) cc_final: 0.6871 (p) REVERT: A 918 GLU cc_start: 0.7174 (OUTLIER) cc_final: 0.6359 (mp0) REVERT: A 979 ASP cc_start: 0.8006 (m-30) cc_final: 0.7719 (m-30) REVERT: A 1034 LEU cc_start: 0.9040 (mm) cc_final: 0.8752 (mt) REVERT: A 1047 TYR cc_start: 0.8895 (m-80) cc_final: 0.8652 (m-80) REVERT: C 119 ILE cc_start: -0.2932 (tp) cc_final: -0.3170 (tt) REVERT: C 123 MET cc_start: 0.0894 (OUTLIER) cc_final: 0.0681 (ppp) REVERT: C 366 MET cc_start: 0.2039 (tpp) cc_final: -0.0341 (ttt) REVERT: C 455 MET cc_start: -0.1775 (tmm) cc_final: -0.2511 (tmm) REVERT: C 536 GLU cc_start: 0.6191 (OUTLIER) cc_final: 0.4536 (pm20) REVERT: C 606 TRP cc_start: 0.0905 (p90) cc_final: -0.0468 (p90) REVERT: B 365 TYR cc_start: 0.4317 (m-80) cc_final: 0.1973 (t80) REVERT: B 745 ASP cc_start: 0.5986 (OUTLIER) cc_final: 0.5762 (m-30) REVERT: B 764 ASN cc_start: 0.8398 (OUTLIER) cc_final: 0.8032 (m-40) REVERT: B 856 ASN cc_start: 0.7547 (OUTLIER) cc_final: 0.7305 (t0) REVERT: B 904 TYR cc_start: 0.7145 (t80) cc_final: 0.6636 (t80) outliers start: 51 outliers final: 43 residues processed: 330 average time/residue: 0.3831 time to fit residues: 215.1814 Evaluate side-chains 329 residues out of total 3343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 280 time to evaluate : 3.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 941 THR Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 123 MET Chi-restraints excluded: chain C residue 536 GLU Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 764 ASN Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain D residue 104 TRP Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 301 CYS Chi-restraints excluded: chain D residue 517 LEU Chi-restraints excluded: chain D residue 572 THR Chi-restraints excluded: chain D residue 959 LEU Chi-restraints excluded: chain D residue 996 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 183 optimal weight: 7.9990 chunk 238 optimal weight: 0.8980 chunk 319 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 276 optimal weight: 7.9990 chunk 44 optimal weight: 0.7980 chunk 83 optimal weight: 4.9990 chunk 300 optimal weight: 7.9990 chunk 125 optimal weight: 9.9990 chunk 308 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.152263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.118812 restraints weight = 95268.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.121044 restraints weight = 46204.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.122370 restraints weight = 28705.452| |-----------------------------------------------------------------------------| r_work (final): 0.3910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6922 moved from start: 0.8334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 30804 Z= 0.217 Angle : 0.569 12.871 41889 Z= 0.287 Chirality : 0.044 0.294 4671 Planarity : 0.004 0.046 5431 Dihedral : 4.096 26.393 4087 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.95 % Favored : 96.03 % Rotamer: Outliers : 1.71 % Allowed : 16.51 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.13), residues: 3774 helix: 1.22 (0.16), residues: 1044 sheet: -0.31 (0.18), residues: 718 loop : -0.85 (0.13), residues: 2012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP B 104 HIS 0.005 0.001 HIS A 242 PHE 0.041 0.002 PHE B 275 TYR 0.016 0.001 TYR D1138 ARG 0.007 0.000 ARG A 765 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6484.58 seconds wall clock time: 117 minutes 49.44 seconds (7069.44 seconds total)