Starting phenix.real_space_refine on Fri Dec 15 01:21:33 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wro_37784/12_2023/8wro_37784.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wro_37784/12_2023/8wro_37784.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wro_37784/12_2023/8wro_37784.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wro_37784/12_2023/8wro_37784.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wro_37784/12_2023/8wro_37784.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wro_37784/12_2023/8wro_37784.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.045 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 146 5.16 5 C 19060 2.51 5 N 4969 2.21 5 O 5632 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 77": "OD1" <-> "OD2" Residue "A TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 982": "OD1" <-> "OD2" Residue "B PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 924": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1064": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1089": "OE1" <-> "OE2" Residue "B TYR 1135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 348": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 450": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 633": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 777": "OE1" <-> "OE2" Residue "C GLU 985": "OE1" <-> "OE2" Residue "C ASP 1136": "OD1" <-> "OD2" Residue "D GLU 430": "OE1" <-> "OE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 29807 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 8364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1067, 8364 Classifications: {'peptide': 1067} Link IDs: {'PTRANS': 57, 'TRANS': 1009} Chain breaks: 5 Chain: "B" Number of atoms: 8295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1059, 8295 Classifications: {'peptide': 1059} Link IDs: {'PTRANS': 57, 'TRANS': 1001} Chain breaks: 5 Chain: "C" Number of atoms: 8303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1060, 8303 Classifications: {'peptide': 1060} Link IDs: {'PTRANS': 57, 'TRANS': 1002} Chain breaks: 5 Chain: "D" Number of atoms: 4845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 594, 4845 Classifications: {'peptide': 594} Link IDs: {'PTRANS': 27, 'TRANS': 566} Time building chain proxies: 14.69, per 1000 atoms: 0.49 Number of scatterers: 29807 At special positions: 0 Unit cell: (151.84, 164.32, 236.08, 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 146 16.00 O 5632 8.00 N 4969 7.00 C 19060 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 133 " distance=2.03 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 163 " distance=2.03 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 298 " distance=2.03 Simple disulfide: pdb=" SG CYS A 333 " - pdb=" SG CYS A 358 " distance=2.03 Simple disulfide: pdb=" SG CYS A 388 " - pdb=" SG CYS A 522 " distance=2.03 Simple disulfide: pdb=" SG CYS A 535 " - pdb=" SG CYS A 587 " distance=2.03 Simple disulfide: pdb=" SG CYS A 614 " - pdb=" SG CYS A 646 " distance=2.03 Simple disulfide: pdb=" SG CYS A 659 " - pdb=" SG CYS A 668 " distance=2.03 Simple disulfide: pdb=" SG CYS A 735 " - pdb=" SG CYS A 757 " distance=2.03 Simple disulfide: pdb=" SG CYS A 740 " - pdb=" SG CYS A 746 " distance=2.03 Simple disulfide: pdb=" SG CYS A1029 " - pdb=" SG CYS A1040 " distance=2.03 Simple disulfide: pdb=" SG CYS A1079 " - pdb=" SG CYS A1123 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 133 " distance=2.03 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 163 " distance=2.03 Simple disulfide: pdb=" SG CYS B 288 " - pdb=" SG CYS B 298 " distance=2.03 Simple disulfide: pdb=" SG CYS B 333 " - pdb=" SG CYS B 358 " distance=2.03 Simple disulfide: pdb=" SG CYS B 388 " - pdb=" SG CYS B 522 " distance=2.03 Simple disulfide: pdb=" SG CYS B 477 " - pdb=" SG CYS B 485 " distance=2.03 Simple disulfide: pdb=" SG CYS B 535 " - pdb=" SG CYS B 587 " distance=2.03 Simple disulfide: pdb=" SG CYS B 614 " - pdb=" SG CYS B 646 " distance=2.03 Simple disulfide: pdb=" SG CYS B 659 " - pdb=" SG CYS B 668 " distance=2.03 Simple disulfide: pdb=" SG CYS B 735 " - pdb=" SG CYS B 757 " distance=2.03 Simple disulfide: pdb=" SG CYS B 740 " - pdb=" SG CYS B 746 " distance=2.03 Simple disulfide: pdb=" SG CYS B1029 " - pdb=" SG CYS B1040 " distance=2.03 Simple disulfide: pdb=" SG CYS B1079 " - pdb=" SG CYS B1123 " distance=2.04 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 133 " distance=2.03 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 163 " distance=2.02 Simple disulfide: pdb=" SG CYS C 288 " - pdb=" SG CYS C 298 " distance=2.03 Simple disulfide: pdb=" SG CYS C 333 " - pdb=" SG CYS C 358 " distance=2.03 Simple disulfide: pdb=" SG CYS C 388 " - pdb=" SG CYS C 522 " distance=2.04 Simple disulfide: pdb=" SG CYS C 535 " - pdb=" SG CYS C 587 " distance=2.03 Simple disulfide: pdb=" SG CYS C 614 " - pdb=" SG CYS C 646 " distance=2.03 Simple disulfide: pdb=" SG CYS C 659 " - pdb=" SG CYS C 668 " distance=2.03 Simple disulfide: pdb=" SG CYS C 735 " - pdb=" SG CYS C 757 " distance=2.04 Simple disulfide: pdb=" SG CYS C 740 " - pdb=" SG CYS C 746 " distance=2.03 Simple disulfide: pdb=" SG CYS C1029 " - pdb=" SG CYS C1040 " distance=2.03 Simple disulfide: pdb=" SG CYS C1079 " - pdb=" SG CYS C1123 " distance=2.03 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " 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: 11.73 Conformation dependent library (CDL) restraints added in 5.3 seconds 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7100 Finding SS restraints... Secondary structure from input PDB file: 81 helices and 48 sheets defined 28.1% alpha, 17.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.30 Creating SS restraints... Processing helix chain 'A' and resid 291 through 300 Processing helix chain 'A' and resid 334 through 340 Processing helix chain 'A' and resid 361 through 368 removed outlier: 3.785A pdb=" N ASN A 367 " --> pdb=" O VAL A 364 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N PHE A 368 " --> pdb=" O ILE A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 405 Processing helix chain 'A' and resid 734 through 740 Processing helix chain 'A' and resid 743 through 751 removed outlier: 3.541A pdb=" N SER A 747 " --> pdb=" O SER A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 752 through 754 No H-bonds generated for 'chain 'A' and resid 752 through 754' Processing helix chain 'A' and resid 756 through 775 removed outlier: 4.312A pdb=" N THR A 775 " --> pdb=" O GLN A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 776 through 778 No H-bonds generated for 'chain 'A' and resid 776 through 778' Processing helix chain 'A' and resid 813 through 823 Processing helix chain 'A' and resid 847 through 852 Processing helix chain 'A' and resid 863 through 881 Processing helix chain 'A' and resid 883 through 887 Processing helix chain 'A' and resid 894 through 905 Processing helix chain 'A' and resid 912 through 915 Processing helix chain 'A' and resid 916 through 938 removed outlier: 4.075A pdb=" N GLN A 932 " --> pdb=" O ILE A 928 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ASP A 933 " --> pdb=" O GLY A 929 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N THR A 938 " --> pdb=" O SER A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 964 removed outlier: 3.548A pdb=" N GLN A 946 " --> pdb=" O LEU A 942 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ASN A 952 " --> pdb=" O VAL A 948 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N SER A 964 " --> pdb=" O VAL A 960 " (cutoff:3.500A) Processing helix chain 'A' and resid 973 through 981 removed outlier: 3.934A pdb=" N ILE A 977 " --> pdb=" O VAL A 973 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 987 removed outlier: 3.650A pdb=" N GLU A 987 " --> pdb=" O PRO A 983 " (cutoff:3.500A) Processing helix chain 'A' and resid 991 through 1030 removed outlier: 3.601A pdb=" N GLU A1014 " --> pdb=" O ILE A1010 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 301 Processing helix chain 'B' and resid 334 through 340 removed outlier: 3.521A pdb=" N VAL B 338 " --> pdb=" O PRO B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 384 Processing helix chain 'B' and resid 403 through 407 removed outlier: 3.952A pdb=" N ILE B 407 " --> pdb=" O VAL B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 419 Processing helix chain 'B' and resid 735 through 740 Processing helix chain 'B' and resid 743 through 751 removed outlier: 3.536A pdb=" N SER B 747 " --> pdb=" O SER B 743 " (cutoff:3.500A) Processing helix chain 'B' and resid 756 through 774 removed outlier: 3.694A pdb=" N LEU B 760 " --> pdb=" O PHE B 756 " (cutoff:3.500A) Processing helix chain 'B' and resid 775 through 780 Processing helix chain 'B' and resid 813 through 823 Processing helix chain 'B' and resid 849 through 853 removed outlier: 3.781A pdb=" N ASN B 853 " --> pdb=" O GLN B 850 " (cutoff:3.500A) Processing helix chain 'B' and resid 863 through 881 Processing helix chain 'B' and resid 883 through 887 removed outlier: 3.564A pdb=" N GLY B 886 " --> pdb=" O TRP B 883 " (cutoff:3.500A) Processing helix chain 'B' and resid 894 through 905 removed outlier: 3.598A pdb=" N GLY B 905 " --> pdb=" O TYR B 901 " (cutoff:3.500A) Processing helix chain 'B' and resid 910 through 916 removed outlier: 3.907A pdb=" N TYR B 914 " --> pdb=" O GLN B 910 " (cutoff:3.500A) Processing helix chain 'B' and resid 916 through 938 removed outlier: 3.685A pdb=" N ILE B 931 " --> pdb=" O ALA B 927 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N GLN B 932 " --> pdb=" O ILE B 928 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ASP B 933 " --> pdb=" O GLY B 929 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N THR B 938 " --> pdb=" O SER B 934 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 961 removed outlier: 5.074A pdb=" N VAL B 948 " --> pdb=" O LYS B 944 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ASN B 952 " --> pdb=" O VAL B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 973 through 980 removed outlier: 3.958A pdb=" N ILE B 977 " --> pdb=" O VAL B 973 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU B 978 " --> pdb=" O LEU B 974 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N SER B 979 " --> pdb=" O ASN B 975 " (cutoff:3.500A) Processing helix chain 'B' and resid 982 through 1030 removed outlier: 4.061A pdb=" N GLU B 987 " --> pdb=" O PRO B 983 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N VAL B 988 " --> pdb=" O PRO B 984 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N GLN B 989 " --> pdb=" O GLU B 985 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASP B 991 " --> pdb=" O GLU B 987 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N ARG B 992 " --> pdb=" O VAL B 988 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU B 993 " --> pdb=" O GLN B 989 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLU B1014 " --> pdb=" O ILE B1010 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 301 Processing helix chain 'C' and resid 404 through 408 removed outlier: 3.738A pdb=" N ILE C 407 " --> pdb=" O VAL C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 502 Processing helix chain 'C' and resid 734 through 739 Processing helix chain 'C' and resid 743 through 751 removed outlier: 3.666A pdb=" N SER C 747 " --> pdb=" O SER C 743 " (cutoff:3.500A) Processing helix chain 'C' and resid 757 through 780 removed outlier: 3.508A pdb=" N LYS C 761 " --> pdb=" O CYS C 757 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N THR C 775 " --> pdb=" O GLN C 771 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N GLN C 776 " --> pdb=" O ASP C 772 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLU C 777 " --> pdb=" O LYS C 773 " (cutoff:3.500A) Processing helix chain 'C' and resid 813 through 823 removed outlier: 3.638A pdb=" N VAL C 823 " --> pdb=" O LEU C 819 " (cutoff:3.500A) Processing helix chain 'C' and resid 865 through 881 Processing helix chain 'C' and resid 883 through 888 removed outlier: 3.704A pdb=" N ALA C 887 " --> pdb=" O TRP C 883 " (cutoff:3.500A) Processing helix chain 'C' and resid 894 through 905 Processing helix chain 'C' and resid 910 through 916 removed outlier: 3.939A pdb=" N TYR C 914 " --> pdb=" O GLN C 910 " (cutoff:3.500A) Processing helix chain 'C' and resid 916 through 938 removed outlier: 3.734A pdb=" N ILE C 931 " --> pdb=" O ALA C 927 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N GLN C 932 " --> pdb=" O ILE C 928 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ASP C 933 " --> pdb=" O GLY C 929 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N THR C 938 " --> pdb=" O SER C 934 " (cutoff:3.500A) Processing helix chain 'C' and resid 939 through 941 No H-bonds generated for 'chain 'C' and resid 939 through 941' Processing helix chain 'C' and resid 942 through 961 removed outlier: 4.621A pdb=" N VAL C 948 " --> pdb=" O LYS C 944 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N HIS C 951 " --> pdb=" O ASP C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 962 through 965 Processing helix chain 'C' and resid 973 through 980 removed outlier: 3.809A pdb=" N ILE C 977 " --> pdb=" O VAL C 973 " (cutoff:3.500A) Processing helix chain 'C' and resid 982 through 985 Processing helix chain 'C' and resid 986 through 1030 removed outlier: 4.078A pdb=" N ARG C 992 " --> pdb=" O VAL C 988 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU C 993 " --> pdb=" O GLN C 989 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 53 removed outlier: 3.670A pdb=" N GLN D 24 " --> pdb=" O THR D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 81 Processing helix chain 'D' and resid 90 through 101 Processing helix chain 'D' and resid 109 through 129 removed outlier: 3.615A pdb=" N TYR D 127 " --> pdb=" O MET D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 154 removed outlier: 3.607A pdb=" N ILE D 151 " --> pdb=" O GLY D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 194 removed outlier: 3.779A pdb=" N GLU D 171 " --> pdb=" O SER D 167 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL D 172 " --> pdb=" O TRP D 168 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N LYS D 174 " --> pdb=" O SER D 170 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N GLN D 175 " --> pdb=" O GLU D 171 " (cutoff:3.500A) Proline residue: D 178 - end of helix Processing helix chain 'D' and resid 198 through 204 Processing helix chain 'D' and resid 218 through 252 removed outlier: 3.597A pdb=" N LEU D 222 " --> pdb=" O SER D 218 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ILE D 223 " --> pdb=" O ARG D 219 " (cutoff:3.500A) Proline residue: D 235 - end of helix removed outlier: 3.781A pdb=" N ASN D 250 " --> pdb=" O ALA D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 268 removed outlier: 3.988A pdb=" N GLY D 268 " --> pdb=" O HIS D 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 265 through 268' Processing helix chain 'D' and resid 293 through 301 Processing helix chain 'D' and resid 303 through 319 Processing helix chain 'D' and resid 325 through 331 removed outlier: 4.517A pdb=" N GLU D 329 " --> pdb=" O GLN D 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 385 removed outlier: 3.513A pdb=" N PHE D 369 " --> pdb=" O THR D 365 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N TYR D 385 " --> pdb=" O TYR D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 397 through 412 removed outlier: 4.252A pdb=" N HIS D 401 " --> pdb=" O ASN D 397 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLU D 402 " --> pdb=" O GLU D 398 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA D 412 " --> pdb=" O MET D 408 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 421 Processing helix chain 'D' and resid 431 through 446 Processing helix chain 'D' and resid 448 through 465 removed outlier: 4.487A pdb=" N PHE D 452 " --> pdb=" O GLY D 448 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 484 Processing helix chain 'D' and resid 498 through 502 Processing helix chain 'D' and resid 503 through 508 Processing helix chain 'D' and resid 512 through 533 Processing helix chain 'D' and resid 547 through 559 removed outlier: 3.933A pdb=" N GLY D 551 " --> pdb=" O SER D 547 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 575 removed outlier: 3.564A pdb=" N VAL D 573 " --> pdb=" O ALA D 569 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 597 Proline residue: D 590 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 44 through 52 removed outlier: 3.887A pdb=" N ASP A 50 " --> pdb=" O ARG A 270 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG A 270 " --> pdb=" O ASP A 50 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ASP A 284 " --> pdb=" O LYS A 275 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 60 through 62 removed outlier: 3.988A pdb=" N THR A 60 " --> pdb=" O VAL A 264 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL A 264 " --> pdb=" O THR A 60 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N TYR A 262 " --> pdb=" O PHE A 62 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE A 200 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N VAL A 224 " --> pdb=" O ILE A 200 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N SER A 202 " --> pdb=" O PRO A 222 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 123 through 128 removed outlier: 3.938A pdb=" N TRP A 101 " --> pdb=" O ILE A 116 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 308 through 311 removed outlier: 3.745A pdb=" N GLY A 308 " --> pdb=" O THR A 596 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N THR A 596 " --> pdb=" O GLY A 308 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 321 through 325 removed outlier: 3.717A pdb=" N VAL A 536 " --> pdb=" O GLY A 547 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY A 547 " --> pdb=" O VAL A 536 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU A 543 " --> pdb=" O PHE A 540 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N ASP A 571 " --> pdb=" O ILE A 584 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ALA A 572 " --> pdb=" O GLY A 563 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 353 through 356 removed outlier: 3.864A pdb=" N SER A 511 " --> pdb=" O TYR A 393 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N THR A 427 " --> pdb=" O PHE A 512 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 353 through 356 removed outlier: 3.864A pdb=" N SER A 511 " --> pdb=" O TYR A 393 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N THR A 427 " --> pdb=" O PHE A 512 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ILE A 431 " --> pdb=" O VAL A 508 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N TRP A 433 " --> pdb=" O ARG A 506 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 449 through 451 Processing sheet with id=AA9, first strand: chain 'A' and resid 661 through 664 removed outlier: 6.238A pdb=" N ALA A 669 " --> pdb=" O PRO A 662 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 699 through 700 Processing sheet with id=AB2, first strand: chain 'A' and resid 708 through 725 removed outlier: 6.851A pdb=" N SER A 708 " --> pdb=" O THR A1073 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N THR A1073 " --> pdb=" O SER A 708 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ALA A 710 " --> pdb=" O ASN A1071 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ASN A1071 " --> pdb=" O ALA A 710 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N GLU A1069 " --> pdb=" O PRO A 712 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ASN A 714 " --> pdb=" O ALA A1067 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N SER A 718 " --> pdb=" O THR A1063 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N TYR A1064 " --> pdb=" O HIS A1045 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N HIS A1045 " --> pdb=" O TYR A1064 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 708 through 725 removed outlier: 6.851A pdb=" N SER A 708 " --> pdb=" O THR A1073 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N THR A1073 " --> pdb=" O SER A 708 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ALA A 710 " --> pdb=" O ASN A1071 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ASN A1071 " --> pdb=" O ALA A 710 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N GLU A1069 " --> pdb=" O PRO A 712 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ASN A 714 " --> pdb=" O ALA A1067 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N SER A 718 " --> pdb=" O THR A1063 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR A1073 " --> pdb=" O SER A1094 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 730 through 732 removed outlier: 4.794A pdb=" N LYS A 730 " --> pdb=" O LEU A 858 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1117 through 1120 Processing sheet with id=AB6, first strand: chain 'B' and resid 26 through 27 Processing sheet with id=AB7, first strand: chain 'B' and resid 49 through 52 Processing sheet with id=AB8, first strand: chain 'B' and resid 81 through 82 removed outlier: 4.207A pdb=" N LEU B 81 " --> pdb=" O PHE B 235 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ARG B 234 " --> pdb=" O PHE B 103 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N PHE B 103 " --> pdb=" O ARG B 234 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N GLN B 236 " --> pdb=" O TRP B 101 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N TRP B 101 " --> pdb=" O GLN B 236 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N LEU B 238 " --> pdb=" O ARG B 99 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL B 123 " --> pdb=" O SER B 169 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N SER B 169 " --> pdb=" O VAL B 123 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE B 125 " --> pdb=" O TYR B 167 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 221 through 227 removed outlier: 6.455A pdb=" N SER B 202 " --> pdb=" O PRO B 222 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 274 through 276 removed outlier: 6.966A pdb=" N LYS B 275 " --> pdb=" O THR B 283 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 322 through 324 removed outlier: 7.012A pdb=" N ILE B 323 " --> pdb=" O ASN B 539 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL B 536 " --> pdb=" O GLY B 547 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N ASP B 571 " --> pdb=" O ILE B 584 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N GLY B 563 " --> pdb=" O ASP B 571 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 353 through 355 removed outlier: 3.609A pdb=" N GLY B 428 " --> pdb=" O TYR B 377 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 358 through 359 removed outlier: 6.652A pdb=" N CYS B 358 " --> pdb=" O CYS B 522 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'B' and resid 449 through 451 Processing sheet with id=AC6, first strand: chain 'B' and resid 592 through 595 Processing sheet with id=AC7, first strand: chain 'B' and resid 651 through 652 removed outlier: 5.706A pdb=" N GLU B 651 " --> pdb=" O ALA B 691 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N THR B 693 " --> pdb=" O GLU B 651 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ALA B 669 " --> pdb=" O PRO B 662 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 708 through 712 removed outlier: 3.773A pdb=" N THR B1073 " --> pdb=" O SER B1094 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N GLN B1103 " --> pdb=" O GLU B1108 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N GLU B1108 " --> pdb=" O GLN B1103 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 715 through 716 removed outlier: 3.647A pdb=" N GLU B 722 " --> pdb=" O PHE B1059 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 715 through 716 removed outlier: 3.703A pdb=" N ALA B1053 " --> pdb=" O GLY B1056 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N TYR B1064 " --> pdb=" O HIS B1045 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N HIS B1045 " --> pdb=" O TYR B1064 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 731 through 733 Processing sheet with id=AD3, first strand: chain 'B' and resid 1117 through 1122 removed outlier: 4.437A pdb=" N ALA B1084 " --> pdb=" O SER B1120 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 26 through 27 removed outlier: 4.019A pdb=" N THR C 26 " --> pdb=" O VAL C 59 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL C 59 " --> pdb=" O THR C 26 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'C' and resid 46 through 52 removed outlier: 3.803A pdb=" N HIS C 46 " --> pdb=" O LEU C 274 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU C 274 " --> pdb=" O HIS C 46 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR C 48 " --> pdb=" O PHE C 272 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ASP C 284 " --> pdb=" O LYS C 275 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 81 through 82 removed outlier: 3.960A pdb=" N LEU C 81 " --> pdb=" O PHE C 235 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N GLN C 236 " --> pdb=" O TRP C 101 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N TRP C 101 " --> pdb=" O GLN C 236 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N LEU C 238 " --> pdb=" O ARG C 99 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 221 through 227 removed outlier: 6.998A pdb=" N SER C 202 " --> pdb=" O PRO C 222 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL C 224 " --> pdb=" O ILE C 200 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 308 through 309 removed outlier: 3.515A pdb=" N GLY C 308 " --> pdb=" O THR C 596 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N THR C 596 " --> pdb=" O GLY C 308 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY C 591 " --> pdb=" O GLN C 610 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LEU C 647 " --> pdb=" O PHE C 640 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 322 through 323 Processing sheet with id=AE1, first strand: chain 'C' and resid 395 through 400 removed outlier: 4.122A pdb=" N ILE C 399 " --> pdb=" O TYR C 505 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 449 through 451 Processing sheet with id=AE3, first strand: chain 'C' and resid 548 through 551 Processing sheet with id=AE4, first strand: chain 'C' and resid 661 through 662 removed outlier: 3.760A pdb=" N ILE C 661 " --> pdb=" O ALA C 669 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 708 through 712 Processing sheet with id=AE6, first strand: chain 'C' and resid 715 through 716 removed outlier: 3.500A pdb=" N THR C 720 " --> pdb=" O HIS C1061 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 715 through 716 removed outlier: 6.058A pdb=" N TYR C1064 " --> pdb=" O HIS C1045 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N HIS C1045 " --> pdb=" O TYR C1064 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 1117 through 1122 removed outlier: 4.481A pdb=" N ALA C1084 " --> pdb=" O SER C1120 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE C1078 " --> pdb=" O HIS C1085 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1091 through 1094 Processing sheet with id=AF1, first strand: chain 'D' and resid 131 through 132 removed outlier: 3.647A pdb=" N VAL D 132 " --> pdb=" O LEU D 142 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU D 142 " --> pdb=" O VAL D 132 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'D' and resid 262 through 263 removed outlier: 5.452A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'D' and resid 347 through 352 removed outlier: 6.494A pdb=" N ASP D 355 " --> pdb=" O LEU D 351 " (cutoff:3.500A) 1041 hydrogen bonds defined for protein. 2931 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.40 Time building geometry restraints manager: 12.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8551 1.33 - 1.46: 8066 1.46 - 1.59: 13729 1.59 - 1.71: 1 1.71 - 1.84: 197 Bond restraints: 30544 Sorted by residual: bond pdb=" C PRO C 983 " pdb=" O PRO C 983 " ideal model delta sigma weight residual 1.240 1.208 0.032 1.12e-02 7.97e+03 8.17e+00 bond pdb=" N GLU C 985 " pdb=" CA GLU C 985 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.29e-02 6.01e+03 5.43e+00 bond pdb=" CB PRO C 334 " pdb=" CG PRO C 334 " ideal model delta sigma weight residual 1.492 1.602 -0.110 5.00e-02 4.00e+02 4.88e+00 bond pdb=" N ARG C 980 " pdb=" CA ARG C 980 " ideal model delta sigma weight residual 1.457 1.485 -0.028 1.29e-02 6.01e+03 4.70e+00 bond pdb=" N ASP C 982 " pdb=" CA ASP C 982 " ideal model delta sigma weight residual 1.451 1.487 -0.037 1.78e-02 3.16e+03 4.23e+00 ... (remaining 30539 not shown) Histogram of bond angle deviations from ideal: 95.07 - 102.92: 141 102.92 - 110.78: 9731 110.78 - 118.63: 14113 118.63 - 126.48: 17128 126.48 - 134.34: 447 Bond angle restraints: 41560 Sorted by residual: angle pdb=" CG1 ILE B 19 " pdb=" CB ILE B 19 " pdb=" CG2 ILE B 19 " ideal model delta sigma weight residual 110.70 95.07 15.63 3.00e+00 1.11e-01 2.72e+01 angle pdb=" C GLU D 479 " pdb=" N MET D 480 " pdb=" CA MET D 480 " ideal model delta sigma weight residual 122.06 112.47 9.59 1.86e+00 2.89e-01 2.66e+01 angle pdb=" CB MET B 694 " pdb=" CG MET B 694 " pdb=" SD MET B 694 " ideal model delta sigma weight residual 112.70 127.22 -14.52 3.00e+00 1.11e-01 2.34e+01 angle pdb=" CA MET A 150 " pdb=" CB MET A 150 " pdb=" CG MET A 150 " ideal model delta sigma weight residual 114.10 123.65 -9.55 2.00e+00 2.50e-01 2.28e+01 angle pdb=" CA PRO C 334 " pdb=" N PRO C 334 " pdb=" CD PRO C 334 " ideal model delta sigma weight residual 112.00 105.41 6.59 1.40e+00 5.10e-01 2.21e+01 ... (remaining 41555 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 15311 18.00 - 36.00: 2114 36.00 - 53.99: 592 53.99 - 71.99: 123 71.99 - 89.99: 59 Dihedral angle restraints: 18199 sinusoidal: 7166 harmonic: 11033 Sorted by residual: dihedral pdb=" CB CYS C 735 " pdb=" SG CYS C 735 " pdb=" SG CYS C 757 " pdb=" CB CYS C 757 " ideal model delta sinusoidal sigma weight residual -86.00 0.25 -86.25 1 1.00e+01 1.00e-02 8.97e+01 dihedral pdb=" CB CYS C 15 " pdb=" SG CYS C 15 " pdb=" SG CYS C 133 " pdb=" CB CYS C 133 " ideal model delta sinusoidal sigma weight residual 93.00 171.74 -78.74 1 1.00e+01 1.00e-02 7.73e+01 dihedral pdb=" CB CYS C 288 " pdb=" SG CYS C 288 " pdb=" SG CYS C 298 " pdb=" CB CYS C 298 " ideal model delta sinusoidal sigma weight residual -86.00 -162.86 76.86 1 1.00e+01 1.00e-02 7.42e+01 ... (remaining 18196 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 4139 0.081 - 0.163: 475 0.163 - 0.244: 16 0.244 - 0.325: 2 0.325 - 0.407: 1 Chirality restraints: 4633 Sorted by residual: chirality pdb=" CB ILE B 19 " pdb=" CA ILE B 19 " pdb=" CG1 ILE B 19 " pdb=" CG2 ILE B 19 " both_signs ideal model delta sigma weight residual False 2.64 3.05 -0.41 2.00e-01 2.50e+01 4.13e+00 chirality pdb=" CB ILE A 98 " pdb=" CA ILE A 98 " pdb=" CG1 ILE A 98 " pdb=" CG2 ILE A 98 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" CG LEU C 81 " pdb=" CB LEU C 81 " pdb=" CD1 LEU C 81 " pdb=" CD2 LEU C 81 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.04e+00 ... (remaining 4630 not shown) Planarity restraints: 5380 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 980 " 0.415 9.50e-02 1.11e+02 1.86e-01 2.12e+01 pdb=" NE ARG C 980 " -0.026 2.00e-02 2.50e+03 pdb=" CZ ARG C 980 " 0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG C 980 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG C 980 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 461 " 0.024 2.00e-02 2.50e+03 1.95e-02 9.47e+00 pdb=" CG TRP D 461 " -0.051 2.00e-02 2.50e+03 pdb=" CD1 TRP D 461 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP D 461 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP D 461 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP D 461 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP D 461 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 461 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 461 " 0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP D 461 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 982 " -0.049 5.00e-02 4.00e+02 7.41e-02 8.79e+00 pdb=" N PRO A 983 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO A 983 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 983 " -0.040 5.00e-02 4.00e+02 ... (remaining 5377 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 5778 2.77 - 3.30: 28495 3.30 - 3.83: 51396 3.83 - 4.37: 54580 4.37 - 4.90: 93629 Nonbonded interactions: 233878 Sorted by model distance: nonbonded pdb=" O ASP A 933 " pdb=" OG SER A 937 " model vdw 2.237 2.440 nonbonded pdb=" O TYR C 310 " pdb=" OG SER C 593 " model vdw 2.243 2.440 nonbonded pdb=" O ASN A 436 " pdb=" OG SER A 440 " model vdw 2.258 2.440 nonbonded pdb=" O SER A 964 " pdb=" OG SER A 964 " model vdw 2.269 2.440 nonbonded pdb=" O SER A 24 " pdb=" OG1 THR A 60 " model vdw 2.277 2.440 ... (remaining 233873 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 140 or resid 149 through 824 or resid 847 throu \ gh 1137)) selection = chain 'B' selection = (chain 'C' and (resid 14 through 824 or resid 847 through 1137)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 11.560 Check model and map are aligned: 0.400 Set scattering table: 0.240 Process input model: 75.630 Find NCS groups from input model: 2.040 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 96.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6930 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.110 30544 Z= 0.263 Angle : 0.791 15.632 41560 Z= 0.413 Chirality : 0.049 0.407 4633 Planarity : 0.006 0.186 5380 Dihedral : 18.348 89.988 10979 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.44 % Favored : 91.45 % Rotamer: Outliers : 0.33 % Allowed : 34.33 % Favored : 65.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.06 (0.13), residues: 3742 helix: 0.45 (0.16), residues: 956 sheet: -1.36 (0.20), residues: 616 loop : -2.33 (0.12), residues: 2170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP D 461 HIS 0.009 0.001 HIS C 336 PHE 0.036 0.002 PHE C 397 TYR 0.024 0.001 TYR C 362 ARG 0.006 0.000 ARG C1104 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 3315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 464 time to evaluate : 3.395 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 outliers start: 11 outliers final: 3 residues processed: 472 average time/residue: 0.3927 time to fit residues: 302.0792 Evaluate side-chains 248 residues out of total 3315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 245 time to evaluate : 3.415 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2518 time to fit residues: 6.2353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 317 optimal weight: 0.7980 chunk 284 optimal weight: 0.0020 chunk 158 optimal weight: 0.6980 chunk 97 optimal weight: 0.5980 chunk 192 optimal weight: 0.2980 chunk 152 optimal weight: 0.6980 chunk 294 optimal weight: 3.9990 chunk 114 optimal weight: 0.2980 chunk 179 optimal weight: 3.9990 chunk 219 optimal weight: 8.9990 chunk 341 optimal weight: 50.0000 overall best weight: 0.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 131 GLN ** B 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 502 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 748 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 892 GLN B 910 GLN B 946 GLN ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1103 GLN D 64 ASN D 188 ASN D 250 ASN D 429 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7032 moved from start: 0.1595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 30544 Z= 0.165 Angle : 0.598 9.876 41560 Z= 0.305 Chirality : 0.043 0.189 4633 Planarity : 0.005 0.068 5380 Dihedral : 4.654 25.139 4059 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.84 % Favored : 93.05 % Rotamer: Outliers : 3.14 % Allowed : 34.33 % Favored : 62.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.13), residues: 3742 helix: 1.05 (0.17), residues: 977 sheet: -1.36 (0.20), residues: 627 loop : -2.18 (0.13), residues: 2138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 461 HIS 0.014 0.001 HIS A1080 PHE 0.028 0.001 PHE B 189 TYR 0.022 0.001 TYR C 262 ARG 0.009 0.000 ARG C 75 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 3315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 266 time to evaluate : 3.541 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 outliers start: 104 outliers final: 35 residues processed: 360 average time/residue: 0.3919 time to fit residues: 235.1511 Evaluate side-chains 261 residues out of total 3315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 226 time to evaluate : 3.312 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 0 residues processed: 35 average time/residue: 0.2972 time to fit residues: 23.1871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 189 optimal weight: 3.9990 chunk 105 optimal weight: 8.9990 chunk 284 optimal weight: 0.6980 chunk 232 optimal weight: 20.0000 chunk 94 optimal weight: 4.9990 chunk 342 optimal weight: 30.0000 chunk 369 optimal weight: 50.0000 chunk 304 optimal weight: 3.9990 chunk 339 optimal weight: 50.0000 chunk 116 optimal weight: 20.0000 chunk 274 optimal weight: 9.9990 overall best weight: 4.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 ASN A 204 HIS A 242 HIS A 279 ASN ** A 687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 748 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 898 GLN ** A 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1105 ASN ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 ASN ** B 502 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 748 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 759 GLN B 784 GLN B 853 ASN B 917 GLN ** B 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 952 ASN ** B1045 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1061 HIS ** B1085 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 46 HIS ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS ** C 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 904 ASN ** C1045 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 330 ASN ** D 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.5469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.100 30544 Z= 0.494 Angle : 0.874 14.211 41560 Z= 0.456 Chirality : 0.050 0.311 4633 Planarity : 0.007 0.073 5380 Dihedral : 5.717 35.278 4059 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 24.81 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.54 % Favored : 90.38 % Rotamer: Outliers : 7.12 % Allowed : 31.86 % Favored : 61.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.14 (0.13), residues: 3742 helix: 0.36 (0.16), residues: 1005 sheet: -1.29 (0.21), residues: 548 loop : -2.45 (0.12), residues: 2189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP C 630 HIS 0.011 0.002 HIS C 46 PHE 0.042 0.003 PHE C1118 TYR 0.039 0.003 TYR B 362 ARG 0.016 0.001 ARG B 75 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 3315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 236 poor density : 206 time to evaluate : 3.729 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 outliers start: 236 outliers final: 107 residues processed: 429 average time/residue: 0.3935 time to fit residues: 281.9994 Evaluate side-chains 264 residues out of total 3315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 157 time to evaluate : 3.418 Switching outliers to nearest non-outliers outliers start: 107 outliers final: 0 residues processed: 107 average time/residue: 0.3362 time to fit residues: 72.7461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 337 optimal weight: 4.9990 chunk 257 optimal weight: 8.9990 chunk 177 optimal weight: 0.9980 chunk 37 optimal weight: 6.9990 chunk 163 optimal weight: 4.9990 chunk 229 optimal weight: 3.9990 chunk 343 optimal weight: 8.9990 chunk 363 optimal weight: 8.9990 chunk 179 optimal weight: 6.9990 chunk 325 optimal weight: 5.9990 chunk 97 optimal weight: 1.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 748 ASN ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 917 GLN A 923 GLN A1033 GLN B 231 ASN ** B 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 478 ASN B 502 HIS B 706 ASN ** B 748 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 853 ASN ** B 898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1045 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1055 HIS D 61 ASN D 388 GLN ** D 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.6418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.099 30544 Z= 0.340 Angle : 0.686 15.304 41560 Z= 0.354 Chirality : 0.045 0.272 4633 Planarity : 0.005 0.063 5380 Dihedral : 5.224 28.020 4059 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 18.64 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.62 % Favored : 92.28 % Rotamer: Outliers : 4.25 % Allowed : 32.22 % Favored : 63.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.13), residues: 3742 helix: 0.95 (0.17), residues: 982 sheet: -1.54 (0.21), residues: 560 loop : -2.40 (0.12), residues: 2200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP D 461 HIS 0.009 0.001 HIS D 228 PHE 0.030 0.002 PHE B 397 TYR 0.030 0.002 TYR B 348 ARG 0.009 0.001 ARG B 75 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 3315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 168 time to evaluate : 3.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 141 outliers final: 61 residues processed: 296 average time/residue: 0.4127 time to fit residues: 204.4747 Evaluate side-chains 207 residues out of total 3315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 146 time to evaluate : 3.379 Switching outliers to nearest non-outliers outliers start: 61 outliers final: 0 residues processed: 61 average time/residue: 0.3068 time to fit residues: 39.2269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 302 optimal weight: 4.9990 chunk 206 optimal weight: 0.6980 chunk 5 optimal weight: 10.0000 chunk 270 optimal weight: 9.9990 chunk 149 optimal weight: 0.8980 chunk 310 optimal weight: 0.0970 chunk 251 optimal weight: 20.0000 chunk 0 optimal weight: 9.9990 chunk 185 optimal weight: 0.5980 chunk 326 optimal weight: 7.9990 chunk 91 optimal weight: 0.0670 overall best weight: 0.4716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 917 GLN A 954 GLN ** B 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 ASN ** B 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 484 ASN ** B 748 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 853 ASN ** B1007 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1045 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 898 GLN C 951 HIS ** D 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.6522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.075 30544 Z= 0.159 Angle : 0.590 10.054 41560 Z= 0.298 Chirality : 0.043 0.169 4633 Planarity : 0.004 0.061 5380 Dihedral : 4.736 30.391 4059 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 14.78 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.24 % Favored : 92.68 % Rotamer: Outliers : 1.87 % Allowed : 33.03 % Favored : 65.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.13), residues: 3742 helix: 1.19 (0.17), residues: 984 sheet: -1.43 (0.21), residues: 552 loop : -2.21 (0.12), residues: 2206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 203 HIS 0.011 0.001 HIS D 239 PHE 0.020 0.001 PHE B 397 TYR 0.036 0.001 TYR C 262 ARG 0.018 0.000 ARG D 518 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 3315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 169 time to evaluate : 3.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 62 outliers final: 26 residues processed: 224 average time/residue: 0.3930 time to fit residues: 147.2161 Evaluate side-chains 170 residues out of total 3315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 144 time to evaluate : 3.344 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.2670 time to fit residues: 17.9361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 122 optimal weight: 0.8980 chunk 327 optimal weight: 7.9990 chunk 71 optimal weight: 4.9990 chunk 213 optimal weight: 7.9990 chunk 89 optimal weight: 9.9990 chunk 363 optimal weight: 0.8980 chunk 301 optimal weight: 7.9990 chunk 168 optimal weight: 0.8980 chunk 30 optimal weight: 9.9990 chunk 120 optimal weight: 2.9990 chunk 190 optimal weight: 2.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 748 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 853 ASN ** B 898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 951 HIS ** B1007 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1045 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 204 HIS ** C 898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1051 GLN ** D 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 556 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.6968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 30544 Z= 0.222 Angle : 0.598 11.328 41560 Z= 0.302 Chirality : 0.042 0.155 4633 Planarity : 0.004 0.060 5380 Dihedral : 4.649 32.556 4059 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 16.47 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.72 % Favored : 92.20 % Rotamer: Outliers : 1.90 % Allowed : 33.03 % Favored : 65.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.14), residues: 3742 helix: 1.28 (0.17), residues: 989 sheet: -1.45 (0.21), residues: 571 loop : -2.13 (0.13), residues: 2182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP D 203 HIS 0.009 0.001 HIS C 336 PHE 0.034 0.001 PHE B 198 TYR 0.031 0.001 TYR B 201 ARG 0.006 0.000 ARG B 454 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 3315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 149 time to evaluate : 3.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 63 outliers final: 20 residues processed: 206 average time/residue: 0.3942 time to fit residues: 135.9491 Evaluate side-chains 159 residues out of total 3315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 139 time to evaluate : 3.298 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.2697 time to fit residues: 14.7101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 350 optimal weight: 20.0000 chunk 41 optimal weight: 20.0000 chunk 207 optimal weight: 6.9990 chunk 265 optimal weight: 5.9990 chunk 205 optimal weight: 2.9990 chunk 306 optimal weight: 4.9990 chunk 203 optimal weight: 0.7980 chunk 362 optimal weight: 10.0000 chunk 226 optimal weight: 9.9990 chunk 220 optimal weight: 10.0000 chunk 167 optimal weight: 5.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 610 GLN ** B 748 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 853 ASN ** B 898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1045 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1045 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 556 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.8159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 30544 Z= 0.430 Angle : 0.747 16.418 41560 Z= 0.381 Chirality : 0.046 0.263 4633 Planarity : 0.005 0.064 5380 Dihedral : 5.245 31.548 4059 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 23.21 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.91 % Favored : 89.98 % Rotamer: Outliers : 2.23 % Allowed : 33.18 % Favored : 64.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.13), residues: 3742 helix: 1.05 (0.17), residues: 973 sheet: -1.63 (0.21), residues: 566 loop : -2.32 (0.12), residues: 2203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 203 HIS 0.009 0.002 HIS C 336 PHE 0.048 0.002 PHE B 198 TYR 0.052 0.002 TYR A 492 ARG 0.015 0.001 ARG B 187 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 3315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 147 time to evaluate : 3.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 74 outliers final: 40 residues processed: 212 average time/residue: 0.4072 time to fit residues: 144.9679 Evaluate side-chains 171 residues out of total 3315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 131 time to evaluate : 3.258 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 0 residues processed: 40 average time/residue: 0.2721 time to fit residues: 24.9123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 224 optimal weight: 8.9990 chunk 144 optimal weight: 10.0000 chunk 216 optimal weight: 10.0000 chunk 109 optimal weight: 10.0000 chunk 71 optimal weight: 0.6980 chunk 70 optimal weight: 2.9990 chunk 230 optimal weight: 0.0980 chunk 246 optimal weight: 0.9980 chunk 179 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 284 optimal weight: 4.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 748 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 759 GLN B 853 ASN ** B1045 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 131 GLN C 414 ASN ** C 898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 962 GLN ** D 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 378 HIS ** D 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.8253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 30544 Z= 0.189 Angle : 0.623 12.781 41560 Z= 0.312 Chirality : 0.043 0.155 4633 Planarity : 0.004 0.060 5380 Dihedral : 4.818 27.992 4059 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 16.58 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.22 % Favored : 92.70 % Rotamer: Outliers : 0.72 % Allowed : 34.21 % Favored : 65.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.14), residues: 3742 helix: 1.19 (0.17), residues: 982 sheet: -1.55 (0.21), residues: 565 loop : -2.16 (0.13), residues: 2195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 203 HIS 0.009 0.001 HIS C 336 PHE 0.022 0.001 PHE B 191 TYR 0.026 0.001 TYR B 201 ARG 0.005 0.000 ARG B 354 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 3315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 151 time to evaluate : 3.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 10 residues processed: 170 average time/residue: 0.4082 time to fit residues: 117.1521 Evaluate side-chains 144 residues out of total 3315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 134 time to evaluate : 3.725 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.2788 time to fit residues: 9.8850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 329 optimal weight: 9.9990 chunk 347 optimal weight: 9.9990 chunk 316 optimal weight: 0.2980 chunk 337 optimal weight: 9.9990 chunk 203 optimal weight: 0.9990 chunk 147 optimal weight: 5.9990 chunk 265 optimal weight: 0.9990 chunk 103 optimal weight: 0.9990 chunk 305 optimal weight: 4.9990 chunk 319 optimal weight: 20.0000 chunk 336 optimal weight: 3.9990 overall best weight: 1.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 748 ASN B 853 ASN B 951 HIS ** B1045 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1105 ASN ** C 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.8414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 30544 Z= 0.205 Angle : 0.625 11.833 41560 Z= 0.312 Chirality : 0.043 0.186 4633 Planarity : 0.004 0.061 5380 Dihedral : 4.703 26.378 4059 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 17.25 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.91 % Favored : 92.01 % Rotamer: Outliers : 0.42 % Allowed : 34.51 % Favored : 65.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.14), residues: 3742 helix: 1.26 (0.17), residues: 978 sheet: -1.56 (0.21), residues: 559 loop : -2.14 (0.13), residues: 2205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 203 HIS 0.018 0.001 HIS D 374 PHE 0.025 0.001 PHE A 426 TYR 0.025 0.001 TYR B 201 ARG 0.018 0.001 ARG D 115 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 3315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 142 time to evaluate : 3.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 2 residues processed: 154 average time/residue: 0.4232 time to fit residues: 107.9207 Evaluate side-chains 138 residues out of total 3315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 136 time to evaluate : 3.322 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2609 time to fit residues: 5.6033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 221 optimal weight: 6.9990 chunk 357 optimal weight: 20.0000 chunk 217 optimal weight: 2.9990 chunk 169 optimal weight: 0.6980 chunk 248 optimal weight: 2.9990 chunk 374 optimal weight: 20.0000 chunk 344 optimal weight: 1.9990 chunk 298 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 230 optimal weight: 5.9990 chunk 182 optimal weight: 2.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 484 ASN ** A 687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 853 ASN ** B 898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1045 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 752 GLN ** C 898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1033 GLN ** D 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.8737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 30544 Z= 0.242 Angle : 0.630 12.467 41560 Z= 0.315 Chirality : 0.043 0.196 4633 Planarity : 0.004 0.058 5380 Dihedral : 4.711 26.276 4059 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 18.22 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.07 % Favored : 91.85 % Rotamer: Outliers : 0.36 % Allowed : 34.60 % Favored : 65.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.14), residues: 3742 helix: 1.29 (0.17), residues: 978 sheet: -1.60 (0.21), residues: 575 loop : -2.11 (0.13), residues: 2189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 203 HIS 0.023 0.001 HIS D 374 PHE 0.022 0.001 PHE B 191 TYR 0.025 0.001 TYR B 201 ARG 0.013 0.001 ARG D 115 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 3315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 140 time to evaluate : 3.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 7 residues processed: 149 average time/residue: 0.4310 time to fit residues: 107.8752 Evaluate side-chains 141 residues out of total 3315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 134 time to evaluate : 3.661 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.3059 time to fit residues: 8.6152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 236 optimal weight: 5.9990 chunk 317 optimal weight: 20.0000 chunk 91 optimal weight: 10.0000 chunk 275 optimal weight: 0.4980 chunk 44 optimal weight: 8.9990 chunk 82 optimal weight: 0.6980 chunk 298 optimal weight: 0.9990 chunk 125 optimal weight: 7.9990 chunk 306 optimal weight: 4.9990 chunk 37 optimal weight: 40.0000 chunk 55 optimal weight: 8.9990 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 687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1095 ASN ** B 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 853 ASN ** B 898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1045 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1116 ASN ** C 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 531 GLN ** D 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.098700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.068062 restraints weight = 147686.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.067820 restraints weight = 91771.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.068563 restraints weight = 64575.826| |-----------------------------------------------------------------------------| r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.9207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 30544 Z= 0.286 Angle : 0.668 14.137 41560 Z= 0.335 Chirality : 0.043 0.162 4633 Planarity : 0.005 0.118 5380 Dihedral : 4.848 26.367 4059 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 19.18 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.58 % Favored : 91.31 % Rotamer: Outliers : 0.63 % Allowed : 34.42 % Favored : 64.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.14), residues: 3742 helix: 1.27 (0.17), residues: 973 sheet: -1.72 (0.21), residues: 582 loop : -2.11 (0.13), residues: 2187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 461 HIS 0.019 0.001 HIS D 374 PHE 0.021 0.002 PHE B 191 TYR 0.037 0.002 TYR C 450 ARG 0.010 0.001 ARG C 400 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5606.51 seconds wall clock time: 104 minutes 9.44 seconds (6249.44 seconds total)