Starting phenix.real_space_refine on Tue Feb 20 08:50:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bzo_7319/02_2024/6bzo_7319_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bzo_7319/02_2024/6bzo_7319.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bzo_7319/02_2024/6bzo_7319.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bzo_7319/02_2024/6bzo_7319.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bzo_7319/02_2024/6bzo_7319_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bzo_7319/02_2024/6bzo_7319_neut_trim_updated.pdb" } resolution = 3.38 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= 0.011 sd= 0.105 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: 8 Type Number sf(0) Gaussians Zn 2 6.06 5 P 55 5.49 5 Mg 1 5.21 5 S 98 5.16 5 Cl 2 4.86 5 C 16922 2.51 5 N 4841 2.21 5 O 5341 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 88": "OE1" <-> "OE2" Residue "A ARG 144": "NH1" <-> "NH2" Residue "A TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 182": "NH1" <-> "NH2" Residue "A ARG 186": "NH1" <-> "NH2" Residue "A ARG 223": "NH1" <-> "NH2" Residue "B PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 27": "OE1" <-> "OE2" Residue "B PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 158": "OE1" <-> "OE2" Residue "B TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 205": "NH1" <-> "NH2" Residue "B PHE 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 69": "NH1" <-> "NH2" Residue "C GLU 72": "OE1" <-> "OE2" Residue "C ARG 77": "NH1" <-> "NH2" Residue "C TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 228": "NH1" <-> "NH2" Residue "C PHE 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 259": "NH1" <-> "NH2" Residue "C PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 303": "OE1" <-> "OE2" Residue "C TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 313": "NH1" <-> "NH2" Residue "C TYR 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 480": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 482": "NH1" <-> "NH2" Residue "C TYR 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 554": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 596": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 652": "OE1" <-> "OE2" Residue "C TYR 657": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 855": "NH1" <-> "NH2" Residue "C PHE 906": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 925": "NH1" <-> "NH2" Residue "C ARG 1067": "NH1" <-> "NH2" Residue "C TYR 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1136": "OE1" <-> "OE2" Residue "D PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 126": "OE1" <-> "OE2" Residue "D TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 152": "OE1" <-> "OE2" Residue "D ARG 159": "NH1" <-> "NH2" Residue "D GLU 204": "OE1" <-> "OE2" Residue "D GLU 220": "OE1" <-> "OE2" Residue "D TYR 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 414": "NH1" <-> "NH2" Residue "D ARG 572": "NH1" <-> "NH2" Residue "D TYR 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 651": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 704": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 749": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 811": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 841": "NH1" <-> "NH2" Residue "D TYR 921": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 940": "NH1" <-> "NH2" Residue "D PHE 1061": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1113": "OE1" <-> "OE2" Residue "D PHE 1226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 213": "NH1" <-> "NH2" Residue "F TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 278": "NH1" <-> "NH2" Residue "F ARG 279": "NH1" <-> "NH2" Residue "F ARG 290": "NH1" <-> "NH2" Residue "F PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 384": "NH1" <-> "NH2" Residue "F ARG 418": "NH1" <-> "NH2" Residue "F PHE 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 500": "NH1" <-> "NH2" Residue "J ARG 106": "NH1" <-> "NH2" Residue "J ARG 108": "NH1" <-> "NH2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 27262 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 1724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1724 Classifications: {'peptide': 226} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 211} Chain: "B" Number of atoms: 1775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1775 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 14, 'TRANS': 220} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "C" Number of atoms: 8556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1111, 8556 Classifications: {'peptide': 1111} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'CIS': 2, 'PCIS': 2, 'PTRANS': 60, 'TRANS': 1046} Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 62 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 53 Chain: "D" Number of atoms: 9857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1263, 9857 Classifications: {'peptide': 1263} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 57, 'TRANS': 1201} Chain breaks: 2 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 26 Chain: "E" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 649 Classifications: {'peptide': 83} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 76} Chain: "F" Number of atoms: 2588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2588 Classifications: {'peptide': 326} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 316} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "J" Number of atoms: 872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 872 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 99} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "O" Number of atoms: 634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 634 Classifications: {'DNA': 31} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 30} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "P" Number of atoms: 526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 526 Classifications: {'DNA': 26} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 25} Chain: "C" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 72 Unusual residues: {'FI8': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 19086 SG CYS D 891 110.212 96.606 106.836 1.00 81.66 S ATOM 19653 SG CYS D 968 106.169 96.391 105.314 1.00 77.99 S ATOM 19695 SG CYS D 975 107.660 94.511 107.869 1.00 72.31 S ATOM 19713 SG CYS D 978 107.803 97.672 108.917 1.00 71.90 S ATOM 12528 SG CYS D 60 74.249 55.490 67.937 1.00 82.81 S ATOM 12546 SG CYS D 62 73.167 54.920 64.739 1.00 82.09 S ATOM 12655 SG CYS D 75 76.507 55.093 64.395 1.00 84.36 S ATOM 12681 SG CYS D 78 74.819 58.045 64.898 1.00 81.78 S Time building chain proxies: 14.67, per 1000 atoms: 0.54 Number of scatterers: 27262 At special positions: 0 Unit cell: (130.9, 157.3, 194.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 2 29.99 Cl 2 17.00 S 98 16.00 P 55 15.00 Mg 1 11.99 O 5341 8.00 N 4841 7.00 C 16922 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 11.67 Conformation dependent library (CDL) restraints added in 5.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1401 " pdb="ZN ZN D1401 " - pdb=" SG CYS D 978 " pdb="ZN ZN D1401 " - pdb=" SG CYS D 968 " pdb="ZN ZN D1401 " - pdb=" SG CYS D 891 " pdb="ZN ZN D1401 " - pdb=" SG CYS D 975 " pdb=" ZN D1402 " pdb="ZN ZN D1402 " - pdb=" SG CYS D 60 " pdb="ZN ZN D1402 " - pdb=" SG CYS D 78 " pdb="ZN ZN D1402 " - pdb=" SG CYS D 75 " pdb="ZN ZN D1402 " - pdb=" SG CYS D 62 " Number of angles added : 12 6670 Ramachandran restraints generated. 3335 Oldfield, 0 Emsley, 3335 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6180 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 115 helices and 31 sheets defined 34.9% alpha, 10.2% beta 26 base pairs and 44 stacking pairs defined. Time for finding SS restraints: 12.64 Creating SS restraints... Processing helix chain 'A' and resid 31 through 42 removed outlier: 3.563A pdb=" N THR A 41 " --> pdb=" O SER A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 82 removed outlier: 4.031A pdb=" N SER A 82 " --> pdb=" O LEU A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 109 No H-bonds generated for 'chain 'A' and resid 107 through 109' Processing helix chain 'A' and resid 204 through 222 removed outlier: 3.694A pdb=" N LEU A 218 " --> pdb=" O THR A 214 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N LEU A 221 " --> pdb=" O GLU A 217 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N ALA A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 44 removed outlier: 3.645A pdb=" N ASN B 36 " --> pdb=" O TYR B 32 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N SER B 37 " --> pdb=" O THR B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 80 removed outlier: 3.931A pdb=" N ILE B 77 " --> pdb=" O VAL B 73 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N LEU B 78 " --> pdb=" O THR B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 109 No H-bonds generated for 'chain 'B' and resid 107 through 109' Processing helix chain 'B' and resid 209 through 223 removed outlier: 3.866A pdb=" N LEU B 218 " --> pdb=" O THR B 214 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N LEU B 221 " --> pdb=" O GLU B 217 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ALA B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 56 removed outlier: 4.230A pdb=" N VAL C 56 " --> pdb=" O LEU C 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 53 through 56' Processing helix chain 'C' and resid 68 through 76 Processing helix chain 'C' and resid 87 through 93 removed outlier: 4.019A pdb=" N GLU C 92 " --> pdb=" O GLU C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 124 Processing helix chain 'C' and resid 226 through 228 No H-bonds generated for 'chain 'C' and resid 226 through 228' Processing helix chain 'C' and resid 234 through 241 Processing helix chain 'C' and resid 245 through 251 removed outlier: 3.817A pdb=" N VAL C 249 " --> pdb=" O SER C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 265 removed outlier: 3.846A pdb=" N THR C 261 " --> pdb=" O ILE C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 281 removed outlier: 4.418A pdb=" N ASP C 276 " --> pdb=" O GLU C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 293 No H-bonds generated for 'chain 'C' and resid 290 through 293' Processing helix chain 'C' and resid 296 through 298 No H-bonds generated for 'chain 'C' and resid 296 through 298' Processing helix chain 'C' and resid 312 through 320 removed outlier: 3.813A pdb=" N ASN C 317 " --> pdb=" O ARG C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 350 removed outlier: 3.603A pdb=" N GLU C 350 " --> pdb=" O VAL C 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 396 removed outlier: 3.762A pdb=" N ARG C 395 " --> pdb=" O VAL C 391 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 417 No H-bonds generated for 'chain 'C' and resid 414 through 417' Processing helix chain 'C' and resid 420 through 431 removed outlier: 3.754A pdb=" N PHE C 431 " --> pdb=" O LYS C 428 " (cutoff:3.500A) Processing helix chain 'C' and resid 445 through 451 Processing helix chain 'C' and resid 534 through 537 No H-bonds generated for 'chain 'C' and resid 534 through 537' Processing helix chain 'C' and resid 591 through 593 No H-bonds generated for 'chain 'C' and resid 591 through 593' Processing helix chain 'C' and resid 597 through 599 No H-bonds generated for 'chain 'C' and resid 597 through 599' Processing helix chain 'C' and resid 602 through 610 Processing helix chain 'C' and resid 632 through 635 No H-bonds generated for 'chain 'C' and resid 632 through 635' Processing helix chain 'C' and resid 739 through 743 Processing helix chain 'C' and resid 816 through 822 removed outlier: 3.561A pdb=" N LEU C 821 " --> pdb=" O GLU C 817 " (cutoff:3.500A) Processing helix chain 'C' and resid 855 through 857 No H-bonds generated for 'chain 'C' and resid 855 through 857' Processing helix chain 'C' and resid 923 through 925 No H-bonds generated for 'chain 'C' and resid 923 through 925' Processing helix chain 'C' and resid 928 through 942 removed outlier: 4.606A pdb=" N GLU C 933 " --> pdb=" O GLN C 930 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU C 936 " --> pdb=" O GLU C 933 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLY C 937 " --> pdb=" O THR C 934 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ALA C 940 " --> pdb=" O GLY C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 954 through 956 No H-bonds generated for 'chain 'C' and resid 954 through 956' Processing helix chain 'C' and resid 982 through 988 removed outlier: 4.119A pdb=" N GLN C 986 " --> pdb=" O GLU C 982 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLY C 987 " --> pdb=" O ALA C 983 " (cutoff:3.500A) Processing helix chain 'C' and resid 1037 through 1040 No H-bonds generated for 'chain 'C' and resid 1037 through 1040' Processing helix chain 'C' and resid 1071 through 1079 Processing helix chain 'C' and resid 1082 through 1090 Processing helix chain 'C' and resid 1096 through 1108 removed outlier: 3.609A pdb=" N VAL C1100 " --> pdb=" O THR C1096 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LYS C1101 " --> pdb=" O VAL C1097 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA C1105 " --> pdb=" O LYS C1101 " (cutoff:3.500A) Processing helix chain 'C' and resid 1119 through 1121 No H-bonds generated for 'chain 'C' and resid 1119 through 1121' Processing helix chain 'C' and resid 1124 through 1131 removed outlier: 4.144A pdb=" N LEU C1131 " --> pdb=" O GLU C1127 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 23 removed outlier: 3.996A pdb=" N ARG D 21 " --> pdb=" O ALA D 17 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLN D 22 " --> pdb=" O GLU D 18 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 89 removed outlier: 3.705A pdb=" N ARG D 88 " --> pdb=" O ALA D 85 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG D 89 " --> pdb=" O LYS D 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 85 through 89' Processing helix chain 'D' and resid 104 through 107 No H-bonds generated for 'chain 'D' and resid 104 through 107' Processing helix chain 'D' and resid 113 through 117 Processing helix chain 'D' and resid 122 through 129 removed outlier: 4.011A pdb=" N LYS D 127 " --> pdb=" O LYS D 123 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE D 128 " --> pdb=" O ASP D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 146 Processing helix chain 'D' and resid 148 through 184 removed outlier: 3.597A pdb=" N GLN D 165 " --> pdb=" O ALA D 161 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU D 170 " --> pdb=" O ARG D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 228 removed outlier: 3.667A pdb=" N GLU D 215 " --> pdb=" O ARG D 211 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS D 228 " --> pdb=" O SER D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 240 through 246 Processing helix chain 'D' and resid 249 through 251 No H-bonds generated for 'chain 'D' and resid 249 through 251' Processing helix chain 'D' and resid 257 through 266 Processing helix chain 'D' and resid 270 through 283 Processing helix chain 'D' and resid 290 through 304 removed outlier: 3.610A pdb=" N VAL D 298 " --> pdb=" O LYS D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 312 Processing helix chain 'D' and resid 322 through 324 No H-bonds generated for 'chain 'D' and resid 322 through 324' Processing helix chain 'D' and resid 340 through 360 removed outlier: 3.592A pdb=" N ASP D 359 " --> pdb=" O LYS D 355 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU D 360 " --> pdb=" O ARG D 356 " (cutoff:3.500A) Processing helix chain 'D' and resid 364 through 382 removed outlier: 3.596A pdb=" N ASN D 369 " --> pdb=" O ILE D 365 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 405 No H-bonds generated for 'chain 'D' and resid 403 through 405' Processing helix chain 'D' and resid 408 through 410 No H-bonds generated for 'chain 'D' and resid 408 through 410' Processing helix chain 'D' and resid 445 through 451 Processing helix chain 'D' and resid 453 through 462 removed outlier: 3.875A pdb=" N VAL D 461 " --> pdb=" O MET D 457 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASP D 462 " --> pdb=" O LYS D 458 " (cutoff:3.500A) Processing helix chain 'D' and resid 469 through 478 Processing helix chain 'D' and resid 483 through 491 removed outlier: 3.844A pdb=" N GLU D 488 " --> pdb=" O TRP D 484 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLU D 489 " --> pdb=" O ASP D 485 " (cutoff:3.500A) Processing helix chain 'D' and resid 526 through 532 removed outlier: 3.529A pdb=" N CYS D 529 " --> pdb=" O PRO D 526 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLU D 530 " --> pdb=" O LEU D 527 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA D 531 " --> pdb=" O VAL D 528 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N PHE D 532 " --> pdb=" O CYS D 529 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 526 through 532' Processing helix chain 'D' and resid 549 through 557 Processing helix chain 'D' and resid 561 through 563 No H-bonds generated for 'chain 'D' and resid 561 through 563' Processing helix chain 'D' and resid 579 through 589 removed outlier: 3.667A pdb=" N THR D 583 " --> pdb=" O LEU D 579 " (cutoff:3.500A) Processing helix chain 'D' and resid 615 through 623 Processing helix chain 'D' and resid 644 through 650 removed outlier: 3.852A pdb=" N GLU D 649 " --> pdb=" O GLU D 645 " (cutoff:3.500A) Processing helix chain 'D' and resid 668 through 674 Processing helix chain 'D' and resid 690 through 703 Processing helix chain 'D' and resid 706 through 727 removed outlier: 3.828A pdb=" N ALA D 710 " --> pdb=" O MET D 706 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N GLN D 711 " --> pdb=" O ILE D 707 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ARG D 726 " --> pdb=" O TYR D 722 " (cutoff:3.500A) Processing helix chain 'D' and resid 742 through 762 Processing helix chain 'D' and resid 767 through 792 Processing helix chain 'D' and resid 798 through 804 removed outlier: 4.557A pdb=" N VAL D 803 " --> pdb=" O ILE D 799 " (cutoff:3.500A) Processing helix chain 'D' and resid 811 through 817 Processing helix chain 'D' and resid 846 through 880 removed outlier: 4.113A pdb=" N HIS D 854 " --> pdb=" O PHE D 850 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N GLY D 855 " --> pdb=" O ILE D 851 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU D 860 " --> pdb=" O ALA D 856 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLY D 871 " --> pdb=" O THR D 867 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N TYR D 872 " --> pdb=" O ALA D 868 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU D 873 " --> pdb=" O ASP D 869 " (cutoff:3.500A) Processing helix chain 'D' and resid 946 through 955 Processing helix chain 'D' and resid 965 through 967 No H-bonds generated for 'chain 'D' and resid 965 through 967' Processing helix chain 'D' and resid 976 through 979 No H-bonds generated for 'chain 'D' and resid 976 through 979' Processing helix chain 'D' and resid 995 through 1009 removed outlier: 3.561A pdb=" N ALA D 999 " --> pdb=" O VAL D 995 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE D1003 " --> pdb=" O ALA D 999 " (cutoff:3.500A) Proline residue: D1006 - end of helix removed outlier: 5.590A pdb=" N GLN D1009 " --> pdb=" O GLU D1005 " (cutoff:3.500A) Processing helix chain 'D' and resid 1028 through 1035 Processing helix chain 'D' and resid 1118 through 1125 Processing helix chain 'D' and resid 1127 through 1145 removed outlier: 3.770A pdb=" N ILE D1132 " --> pdb=" O ARG D1128 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL D1141 " --> pdb=" O GLU D1137 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLN D1145 " --> pdb=" O VAL D1141 " (cutoff:3.500A) Processing helix chain 'D' and resid 1151 through 1160 removed outlier: 4.034A pdb=" N GLN D1160 " --> pdb=" O VAL D1156 " (cutoff:3.500A) Processing helix chain 'D' and resid 1183 through 1190 removed outlier: 3.545A pdb=" N ASN D1190 " --> pdb=" O PHE D1186 " (cutoff:3.500A) Processing helix chain 'D' and resid 1210 through 1215 Processing helix chain 'D' and resid 1220 through 1225 Processing helix chain 'D' and resid 1229 through 1236 removed outlier: 4.253A pdb=" N ASP D1235 " --> pdb=" O ARG D1231 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA D1236 " --> pdb=" O VAL D1232 " (cutoff:3.500A) Processing helix chain 'D' and resid 1250 through 1254 Processing helix chain 'D' and resid 1261 through 1263 No H-bonds generated for 'chain 'D' and resid 1261 through 1263' Processing helix chain 'D' and resid 1265 through 1268 No H-bonds generated for 'chain 'D' and resid 1265 through 1268' Processing helix chain 'D' and resid 1276 through 1281 removed outlier: 3.929A pdb=" N ALA D1281 " --> pdb=" O GLU D1277 " (cutoff:3.500A) Processing helix chain 'E' and resid 34 through 36 No H-bonds generated for 'chain 'E' and resid 34 through 36' Processing helix chain 'E' and resid 50 through 71 removed outlier: 3.740A pdb=" N LEU E 71 " --> pdb=" O TYR E 67 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 100 Processing helix chain 'F' and resid 208 through 225 removed outlier: 3.945A pdb=" N GLN F 214 " --> pdb=" O GLU F 210 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 236 Processing helix chain 'F' and resid 245 through 269 removed outlier: 3.579A pdb=" N LYS F 251 " --> pdb=" O VAL F 247 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N THR F 264 " --> pdb=" O THR F 260 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU F 265 " --> pdb=" O GLN F 261 " (cutoff:3.500A) Processing helix chain 'F' and resid 275 through 309 removed outlier: 4.122A pdb=" N MET F 281 " --> pdb=" O GLN F 277 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N ARG F 301 " --> pdb=" O GLU F 297 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N LEU F 302 " --> pdb=" O ALA F 298 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N ARG F 309 " --> pdb=" O SER F 305 " (cutoff:3.500A) Processing helix chain 'F' and resid 317 through 334 Processing helix chain 'F' and resid 343 through 361 removed outlier: 4.340A pdb=" N TRP F 349 " --> pdb=" O THR F 345 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N TRP F 350 " --> pdb=" O TYR F 346 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ILE F 355 " --> pdb=" O ILE F 351 " (cutoff:3.500A) Processing helix chain 'F' and resid 370 through 390 removed outlier: 3.527A pdb=" N VAL F 375 " --> pdb=" O HIS F 371 " (cutoff:3.500A) Processing helix chain 'F' and resid 396 through 402 Processing helix chain 'F' and resid 407 through 417 Processing helix chain 'F' and resid 447 through 466 removed outlier: 3.998A pdb=" N THR F 454 " --> pdb=" O ALA F 450 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU F 455 " --> pdb=" O VAL F 451 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N THR F 466 " --> pdb=" O SER F 462 " (cutoff:3.500A) Processing helix chain 'F' and resid 469 through 479 removed outlier: 4.328A pdb=" N GLY F 473 " --> pdb=" O GLU F 469 " (cutoff:3.500A) Processing helix chain 'F' and resid 489 through 496 removed outlier: 3.778A pdb=" N GLY F 493 " --> pdb=" O LEU F 489 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N VAL F 495 " --> pdb=" O GLU F 491 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TYR F 496 " --> pdb=" O ILE F 492 " (cutoff:3.500A) Processing helix chain 'F' and resid 500 through 514 removed outlier: 4.145A pdb=" N ILE F 506 " --> pdb=" O ARG F 502 " (cutoff:3.500A) Processing helix chain 'F' and resid 517 through 523 removed outlier: 4.377A pdb=" N VAL F 522 " --> pdb=" O SER F 518 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N LEU F 523 " --> pdb=" O ARG F 519 " (cutoff:3.500A) Processing helix chain 'J' and resid 81 through 88 removed outlier: 3.688A pdb=" N ARG J 88 " --> pdb=" O MET J 84 " (cutoff:3.500A) Processing helix chain 'J' and resid 91 through 106 Processing sheet with id= A, first strand: chain 'A' and resid 8 through 15 removed outlier: 3.776A pdb=" N GLU A 24 " --> pdb=" O THR A 8 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU A 14 " --> pdb=" O ARG A 18 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N ARG A 18 " --> pdb=" O LEU A 14 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 94 through 100 removed outlier: 3.810A pdb=" N SER A 53 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N GLU A 141 " --> pdb=" O VAL A 51 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N VAL A 51 " --> pdb=" O GLU A 141 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N GLY A 143 " --> pdb=" O ALA A 49 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N ALA A 49 " --> pdb=" O GLY A 143 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 145 through 147 Processing sheet with id= D, first strand: chain 'A' and resid 103 through 106 Processing sheet with id= E, first strand: chain 'B' and resid 8 through 10 removed outlier: 3.517A pdb=" N VAL B 22 " --> pdb=" O SER B 10 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 93 through 99 removed outlier: 4.028A pdb=" N SER B 53 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N GLU B 141 " --> pdb=" O VAL B 51 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N VAL B 51 " --> pdb=" O GLU B 141 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N GLY B 143 " --> pdb=" O ALA B 49 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N ALA B 49 " --> pdb=" O GLY B 143 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 103 through 106 removed outlier: 3.878A pdb=" N ALA B 126 " --> pdb=" O VAL B 105 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 171 through 177 removed outlier: 6.690A pdb=" N GLU B 197 " --> pdb=" O LEU B 172 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N VAL B 174 " --> pdb=" O ASP B 195 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ASP B 195 " --> pdb=" O VAL B 174 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N TYR B 176 " --> pdb=" O ILE B 193 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ILE B 193 " --> pdb=" O TYR B 176 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 166 through 168 Processing sheet with id= J, first strand: chain 'C' and resid 178 through 181 Processing sheet with id= K, first strand: chain 'C' and resid 184 through 191 Processing sheet with id= L, first strand: chain 'C' and resid 454 through 456 Processing sheet with id= M, first strand: chain 'C' and resid 528 through 531 Processing sheet with id= N, first strand: chain 'C' and resid 558 through 560 Processing sheet with id= O, first strand: chain 'C' and resid 667 through 671 removed outlier: 3.583A pdb=" N GLU C 652 " --> pdb=" O THR C 659 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N MET C 661 " --> pdb=" O ILE C 650 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N ILE C 650 " --> pdb=" O MET C 661 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 717 through 722 Processing sheet with id= Q, first strand: chain 'C' and resid 749 through 759 removed outlier: 3.710A pdb=" N GLY C 849 " --> pdb=" O TYR C 872 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ALA C 874 " --> pdb=" O VAL C 847 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N VAL C 847 " --> pdb=" O ALA C 874 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 103 through 112 removed outlier: 6.585A pdb=" N PHE C 134 " --> pdb=" O PRO C 110 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N PHE C 112 " --> pdb=" O PRO C 132 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLY C 155 " --> pdb=" O LEU C 133 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N VAL C 135 " --> pdb=" O PHE C 153 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N PHE C 153 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ALA C 137 " --> pdb=" O THR C 151 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N THR C 151 " --> pdb=" O ALA C 137 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N PHE C 139 " --> pdb=" O SER C 149 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N SER C 149 " --> pdb=" O PHE C 139 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 735 through 738 removed outlier: 7.737A pdb=" N LEU C 737 " --> pdb=" O GLY C 896 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ILE C 898 " --> pdb=" O LEU C 737 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 93 through 96 Processing sheet with id= U, first strand: chain 'D' and resid 327 through 330 Processing sheet with id= V, first strand: chain 'D' and resid 425 through 429 Processing sheet with id= W, first strand: chain 'D' and resid 430 through 432 removed outlier: 6.274A pdb=" N ILE D 522 " --> pdb=" O VAL D 431 " (cutoff:3.500A) No H-bonds generated for sheet with id= W Processing sheet with id= X, first strand: chain 'D' and resid 440 through 444 removed outlier: 6.337A pdb=" N GLU D 513 " --> pdb=" O CYS D 441 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N LEU D 443 " --> pdb=" O GLU D 513 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N MET D 515 " --> pdb=" O LEU D 443 " (cutoff:3.500A) No H-bonds generated for sheet with id= X Processing sheet with id= Y, first strand: chain 'D' and resid 632 through 637 removed outlier: 3.701A pdb=" N LEU D 637 " --> pdb=" O TRP D 662 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'D' and resid 897 through 899 removed outlier: 3.543A pdb=" N VAL D 899 " --> pdb=" O VAL D 960 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL D 960 " --> pdb=" O VAL D 899 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'D' and resid 1051 through 1056 Processing sheet with id= AB, first strand: chain 'D' and resid 1180 through 1182 removed outlier: 4.636A pdb=" N ARG D1164 " --> pdb=" O VAL D1206 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N ALA D1202 " --> pdb=" O ILE D1168 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'D' and resid 135 through 139 removed outlier: 6.616A pdb=" N THR D 253 " --> pdb=" O THR D 137 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'J' and resid 27 through 33 Processing sheet with id= AE, first strand: chain 'J' and resid 53 through 55 808 hydrogen bonds defined for protein. 2289 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 61 hydrogen bonds 122 hydrogen bond angles 0 basepair planarities 26 basepair parallelities 44 stacking parallelities Total time for adding SS restraints: 10.00 Time building geometry restraints manager: 12.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 4609 1.29 - 1.42: 6697 1.42 - 1.55: 16236 1.55 - 1.68: 116 1.68 - 1.81: 175 Bond restraints: 27833 Sorted by residual: bond pdb=" C ARG J 10 " pdb=" O ARG J 10 " ideal model delta sigma weight residual 1.234 1.161 0.073 1.07e-02 8.73e+03 4.66e+01 bond pdb=" CA ARG J 10 " pdb=" C ARG J 10 " ideal model delta sigma weight residual 1.528 1.443 0.085 1.34e-02 5.57e+03 4.01e+01 bond pdb=" C2 FI8 C1201 " pdb=" O1 FI8 C1201 " ideal model delta sigma weight residual 1.326 1.427 -0.101 2.00e-02 2.50e+03 2.56e+01 bond pdb=" C49 FI8 C1201 " pdb=" O17 FI8 C1201 " ideal model delta sigma weight residual 1.332 1.426 -0.094 2.00e-02 2.50e+03 2.21e+01 bond pdb=" CA ARG J 10 " pdb=" CB ARG J 10 " ideal model delta sigma weight residual 1.526 1.461 0.066 1.44e-02 4.82e+03 2.08e+01 ... (remaining 27828 not shown) Histogram of bond angle deviations from ideal: 100.01 - 106.80: 1217 106.80 - 113.60: 15419 113.60 - 120.40: 10602 120.40 - 127.19: 10365 127.19 - 133.99: 352 Bond angle restraints: 37955 Sorted by residual: angle pdb=" C PHE C 254 " pdb=" N SER C 255 " pdb=" CA SER C 255 " ideal model delta sigma weight residual 121.70 131.37 -9.67 1.80e+00 3.09e-01 2.89e+01 angle pdb=" C ARG J 10 " pdb=" CA ARG J 10 " pdb=" CB ARG J 10 " ideal model delta sigma weight residual 113.33 102.58 10.75 2.26e+00 1.96e-01 2.26e+01 angle pdb=" N ASP D 140 " pdb=" CA ASP D 140 " pdb=" C ASP D 140 " ideal model delta sigma weight residual 109.62 116.54 -6.92 1.50e+00 4.44e-01 2.13e+01 angle pdb=" N ARG J 10 " pdb=" CA ARG J 10 " pdb=" CB ARG J 10 " ideal model delta sigma weight residual 110.45 104.40 6.05 1.44e+00 4.82e-01 1.77e+01 angle pdb=" C LYS C 229 " pdb=" N ARG C 230 " pdb=" CA ARG C 230 " ideal model delta sigma weight residual 121.54 129.06 -7.52 1.91e+00 2.74e-01 1.55e+01 ... (remaining 37950 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.95: 16398 32.95 - 65.91: 537 65.91 - 98.86: 22 98.86 - 131.81: 0 131.81 - 164.76: 5 Dihedral angle restraints: 16962 sinusoidal: 7356 harmonic: 9606 Sorted by residual: dihedral pdb=" CA GLN D 600 " pdb=" C GLN D 600 " pdb=" N PRO D 601 " pdb=" CA PRO D 601 " ideal model delta harmonic sigma weight residual -180.00 -139.69 -40.31 0 5.00e+00 4.00e-02 6.50e+01 dihedral pdb=" CA PHE C 61 " pdb=" C PHE C 61 " pdb=" N GLU C 62 " pdb=" CA GLU C 62 " ideal model delta harmonic sigma weight residual 180.00 142.47 37.53 0 5.00e+00 4.00e-02 5.64e+01 dihedral pdb=" CA VAL D1194 " pdb=" C VAL D1194 " pdb=" N ALA D1195 " pdb=" CA ALA D1195 " ideal model delta harmonic sigma weight residual -180.00 -147.14 -32.86 0 5.00e+00 4.00e-02 4.32e+01 ... (remaining 16959 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 3806 0.060 - 0.121: 497 0.121 - 0.181: 17 0.181 - 0.241: 2 0.241 - 0.301: 2 Chirality restraints: 4324 Sorted by residual: chirality pdb=" CA PHE C 254 " pdb=" N PHE C 254 " pdb=" C PHE C 254 " pdb=" CB PHE C 254 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.27e+00 chirality pdb=" CA LEU D 910 " pdb=" N LEU D 910 " pdb=" C LEU D 910 " pdb=" CB LEU D 910 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.64e+00 chirality pdb=" CA VAL D1098 " pdb=" N VAL D1098 " pdb=" C VAL D1098 " pdb=" CB VAL D1098 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 8.75e-01 ... (remaining 4321 not shown) Planarity restraints: 4797 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 959 " -0.066 5.00e-02 4.00e+02 9.98e-02 1.59e+01 pdb=" N PRO C 960 " 0.173 5.00e-02 4.00e+02 pdb=" CA PRO C 960 " -0.052 5.00e-02 4.00e+02 pdb=" CD PRO C 960 " -0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG D1087 " 0.016 2.00e-02 2.50e+03 3.22e-02 1.04e+01 pdb=" C ARG D1087 " -0.056 2.00e-02 2.50e+03 pdb=" O ARG D1087 " 0.021 2.00e-02 2.50e+03 pdb=" N VAL D1088 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN D 600 " 0.049 5.00e-02 4.00e+02 7.44e-02 8.85e+00 pdb=" N PRO D 601 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO D 601 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO D 601 " 0.041 5.00e-02 4.00e+02 ... (remaining 4794 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.48: 215 2.48 - 3.08: 21544 3.08 - 3.69: 39811 3.69 - 4.29: 58330 4.29 - 4.90: 95986 Nonbonded interactions: 215886 Sorted by model distance: nonbonded pdb=" NH1 ARG C 633 " pdb=" OD2 ASP C 637 " model vdw 1.869 2.520 nonbonded pdb=" OE2 GLU D 323 " pdb=" O HOH D1501 " model vdw 1.934 2.440 nonbonded pdb=" OE2 GLU D 750 " pdb=" NZ LYS D 837 " model vdw 1.964 2.520 nonbonded pdb=" NZ LYS C 163 " pdb=" O GLY C 639 " model vdw 1.969 2.520 nonbonded pdb=" OG1 THR D 970 " pdb=" O GLY D 973 " model vdw 1.972 2.440 ... (remaining 215881 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 1 through 99 or (resid 100 and (name N or name CA or name \ C or name O or name CB )) or resid 101 through 129 or (resid 130 and (name N or \ name CA or name C or name O or name CB )) or resid 131 through 134 or (resid 135 \ and (name N or name CA or name C or name O or name CB )) or resid 136 through 1 \ 83 or (resid 184 and (name N or name CA or name C or name O or name CB )) or res \ id 185 or (resid 186 and (name N or name CA or name C or name O or name CB )) or \ resid 187 through 223 or (resid 224 and (name N or name CA or name C or name O \ or name CB )) or resid 225 through 226)) selection = (chain 'B' and resid 1 through 226) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 7.370 Check model and map are aligned: 0.450 Set scattering table: 0.280 Process input model: 82.270 Find NCS groups from input model: 1.110 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 95.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.101 27833 Z= 0.182 Angle : 0.548 10.745 37955 Z= 0.320 Chirality : 0.039 0.301 4324 Planarity : 0.004 0.100 4797 Dihedral : 14.705 164.764 10782 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 39.37 Ramachandran Plot: Outliers : 0.36 % Allowed : 10.13 % Favored : 89.51 % Rotamer: Outliers : 7.27 % Allowed : 9.78 % Favored : 82.95 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 5.23 % Cis-general : 0.16 % Twisted Proline : 0.58 % Twisted General : 0.13 % 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: -4.07 (0.12), residues: 3335 helix: -1.75 (0.13), residues: 1172 sheet: -2.58 (0.24), residues: 357 loop : -3.52 (0.12), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 63 HIS 0.003 0.000 HIS C 200 PHE 0.024 0.001 PHE C 254 TYR 0.007 0.001 TYR A 168 ARG 0.003 0.000 ARG D1097 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6670 Ramachandran restraints generated. 3335 Oldfield, 0 Emsley, 3335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6670 Ramachandran restraints generated. 3335 Oldfield, 0 Emsley, 3335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 2837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 203 poor density : 256 time to evaluate : 3.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 GLN cc_start: 0.7773 (mm-40) cc_final: 0.6915 (mm-40) REVERT: A 153 ARG cc_start: 0.7187 (ttp80) cc_final: 0.6825 (ptm160) REVERT: A 221 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8832 (pt) REVERT: B 27 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.8097 (pp20) REVERT: B 206 ASP cc_start: 0.7846 (m-30) cc_final: 0.7492 (t0) REVERT: C 407 GLN cc_start: 0.7123 (mm110) cc_final: 0.6787 (tt0) REVERT: C 795 GLU cc_start: 0.7644 (tp30) cc_final: 0.7363 (tp30) REVERT: C 833 ARG cc_start: 0.7962 (mtp85) cc_final: 0.7294 (ttm110) REVERT: D 1012 MET cc_start: 0.5975 (OUTLIER) cc_final: 0.5073 (mtt) REVERT: D 1080 ILE cc_start: 0.8113 (mt) cc_final: 0.7391 (mt) REVERT: D 1176 LEU cc_start: 0.8690 (mp) cc_final: 0.8315 (tp) REVERT: D 1208 MET cc_start: 0.8893 (ptt) cc_final: 0.8687 (ptm) REVERT: F 206 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.8005 (tm-30) REVERT: F 207 ASP cc_start: 0.7123 (OUTLIER) cc_final: 0.6402 (t0) REVERT: F 258 TYR cc_start: 0.8352 (t80) cc_final: 0.7790 (t80) REVERT: F 353 GLN cc_start: 0.9018 (OUTLIER) cc_final: 0.8773 (pp30) REVERT: F 418 ARG cc_start: 0.8479 (OUTLIER) cc_final: 0.7712 (mtp-110) REVERT: J 7 ARG cc_start: 0.8562 (OUTLIER) cc_final: 0.7922 (ptm-80) REVERT: J 20 ARG cc_start: 0.8827 (OUTLIER) cc_final: 0.7548 (ptp90) REVERT: J 27 ARG cc_start: 0.9017 (OUTLIER) cc_final: 0.7615 (ptp-110) REVERT: J 84 MET cc_start: 0.8580 (mtp) cc_final: 0.8373 (mtp) outliers start: 203 outliers final: 111 residues processed: 437 average time/residue: 0.4563 time to fit residues: 299.4959 Evaluate side-chains 276 residues out of total 2837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 155 time to evaluate : 3.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 27 GLU Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 141 GLU Chi-restraints excluded: chain B residue 153 ARG Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain C residue 79 ASP Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 192 ASP Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain C residue 196 ASP Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 203 LYS Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 232 GLN Chi-restraints excluded: chain C residue 266 ASN Chi-restraints excluded: chain C residue 343 GLU Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 397 GLU Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 500 LEU Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 571 VAL Chi-restraints excluded: chain C residue 577 ASP Chi-restraints excluded: chain C residue 589 VAL Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 709 ASP Chi-restraints excluded: chain C residue 797 ARG Chi-restraints excluded: chain C residue 814 LEU Chi-restraints excluded: chain C residue 835 THR Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 899 LEU Chi-restraints excluded: chain C residue 936 LEU Chi-restraints excluded: chain C residue 950 LYS Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 963 LEU Chi-restraints excluded: chain C residue 965 GLU Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1057 LEU Chi-restraints excluded: chain C residue 1076 MET Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 67 ARG Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 86 LYS Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 152 GLU Chi-restraints excluded: chain D residue 164 ASP Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 263 LYS Chi-restraints excluded: chain D residue 414 ARG Chi-restraints excluded: chain D residue 463 LEU Chi-restraints excluded: chain D residue 469 ILE Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 499 ASN Chi-restraints excluded: chain D residue 506 ARG Chi-restraints excluded: chain D residue 517 VAL Chi-restraints excluded: chain D residue 639 GLN Chi-restraints excluded: chain D residue 677 LEU Chi-restraints excluded: chain D residue 741 ARG Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 862 ASP Chi-restraints excluded: chain D residue 883 ASP Chi-restraints excluded: chain D residue 911 ILE Chi-restraints excluded: chain D residue 957 ILE Chi-restraints excluded: chain D residue 1012 MET Chi-restraints excluded: chain D residue 1057 ASP Chi-restraints excluded: chain D residue 1061 PHE Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1096 GLU Chi-restraints excluded: chain D residue 1097 ARG Chi-restraints excluded: chain D residue 1098 VAL Chi-restraints excluded: chain D residue 1099 LEU Chi-restraints excluded: chain D residue 1121 VAL Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain F residue 206 GLU Chi-restraints excluded: chain F residue 207 ASP Chi-restraints excluded: chain F residue 240 LEU Chi-restraints excluded: chain F residue 246 GLU Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 282 MET Chi-restraints excluded: chain F residue 286 ARG Chi-restraints excluded: chain F residue 332 VAL Chi-restraints excluded: chain F residue 353 GLN Chi-restraints excluded: chain F residue 375 VAL Chi-restraints excluded: chain F residue 397 GLU Chi-restraints excluded: chain F residue 398 GLU Chi-restraints excluded: chain F residue 418 ARG Chi-restraints excluded: chain F residue 423 LEU Chi-restraints excluded: chain F residue 460 LEU Chi-restraints excluded: chain F residue 461 GLN Chi-restraints excluded: chain F residue 492 ILE Chi-restraints excluded: chain F residue 527 LEU Chi-restraints excluded: chain J residue 4 ARG Chi-restraints excluded: chain J residue 7 ARG Chi-restraints excluded: chain J residue 20 ARG Chi-restraints excluded: chain J residue 27 ARG Chi-restraints excluded: chain J residue 76 LYS Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain J residue 98 LEU Chi-restraints excluded: chain J residue 99 LYS Chi-restraints excluded: chain J residue 103 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 284 optimal weight: 0.4980 chunk 255 optimal weight: 3.9990 chunk 141 optimal weight: 6.9990 chunk 87 optimal weight: 6.9990 chunk 172 optimal weight: 20.0000 chunk 136 optimal weight: 3.9990 chunk 264 optimal weight: 9.9990 chunk 102 optimal weight: 6.9990 chunk 160 optimal weight: 0.9980 chunk 196 optimal weight: 4.9990 chunk 306 optimal weight: 6.9990 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 HIS B 5 GLN B 79 ASN B 151 GLN C 57 GLN C 317 ASN C 349 HIS C 388 GLN C 442 GLN C 476 HIS C 479 HIS ** C 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 612 GLN ** C 920 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 986 GLN C1066 GLN D 175 GLN ** D 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 439 HIS D 499 ASN D 505 HIS D 540 GLN D 639 GLN D 687 GLN D1084 GLN D1139 GLN D1145 GLN D1251 ASN ** E 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 106 HIS F 293 ASN ** F 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 325 ASN F 353 GLN F 388 GLN F 457 GLN ** F 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 36 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 27833 Z= 0.344 Angle : 0.695 12.332 37955 Z= 0.351 Chirality : 0.045 0.197 4324 Planarity : 0.005 0.113 4797 Dihedral : 15.919 164.725 4685 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.04 % Favored : 91.69 % Rotamer: Outliers : 5.73 % Allowed : 13.01 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.23 % Cis-general : 0.16 % Twisted Proline : 1.16 % Twisted General : 0.13 % 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: -2.60 (0.13), residues: 3335 helix: -0.48 (0.15), residues: 1206 sheet: -1.87 (0.24), residues: 375 loop : -2.68 (0.13), residues: 1754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 955 HIS 0.004 0.001 HIS D 854 PHE 0.016 0.002 PHE C 61 TYR 0.016 0.001 TYR A 168 ARG 0.008 0.001 ARG D 211 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6670 Ramachandran restraints generated. 3335 Oldfield, 0 Emsley, 3335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6670 Ramachandran restraints generated. 3335 Oldfield, 0 Emsley, 3335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 2837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 169 time to evaluate : 3.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 GLN cc_start: 0.7813 (mm-40) cc_final: 0.7297 (tp-100) REVERT: A 223 ARG cc_start: 0.8537 (OUTLIER) cc_final: 0.8244 (ttp80) REVERT: B 123 MET cc_start: 0.8156 (ttm) cc_final: 0.7818 (ttm) REVERT: B 191 LYS cc_start: 0.8979 (tttt) cc_final: 0.8778 (ttpp) REVERT: B 206 ASP cc_start: 0.8060 (m-30) cc_final: 0.7732 (t0) REVERT: C 407 GLN cc_start: 0.7481 (mm110) cc_final: 0.7218 (tt0) REVERT: C 439 PHE cc_start: 0.7874 (m-80) cc_final: 0.7658 (m-80) REVERT: C 455 LEU cc_start: 0.9325 (OUTLIER) cc_final: 0.8898 (mt) REVERT: C 607 MET cc_start: 0.8472 (mtt) cc_final: 0.8116 (mtt) REVERT: C 795 GLU cc_start: 0.7574 (tp30) cc_final: 0.7300 (tp30) REVERT: C 926 MET cc_start: 0.8968 (mmm) cc_final: 0.8764 (mmm) REVERT: C 1076 MET cc_start: 0.8605 (OUTLIER) cc_final: 0.8381 (mmt) REVERT: D 207 GLN cc_start: 0.7440 (OUTLIER) cc_final: 0.7100 (tm-30) REVERT: D 506 ARG cc_start: 0.9366 (OUTLIER) cc_final: 0.8452 (ptt-90) REVERT: D 653 HIS cc_start: 0.6205 (p90) cc_final: 0.5920 (p90) REVERT: D 672 MET cc_start: 0.9109 (mtp) cc_final: 0.8906 (mtp) REVERT: D 733 MET cc_start: 0.8359 (ppp) cc_final: 0.8048 (ttp) REVERT: D 741 ARG cc_start: 0.7553 (OUTLIER) cc_final: 0.6201 (ppp80) REVERT: D 1012 MET cc_start: 0.7375 (OUTLIER) cc_final: 0.7044 (mpp) REVERT: F 202 PHE cc_start: 0.6735 (t80) cc_final: 0.6529 (t80) REVERT: F 258 TYR cc_start: 0.8507 (t80) cc_final: 0.8183 (t80) REVERT: J 7 ARG cc_start: 0.8700 (OUTLIER) cc_final: 0.8097 (ptm-80) REVERT: J 84 MET cc_start: 0.8610 (mtp) cc_final: 0.8398 (mtp) outliers start: 160 outliers final: 98 residues processed: 315 average time/residue: 0.3993 time to fit residues: 200.1450 Evaluate side-chains 251 residues out of total 2837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 145 time to evaluate : 3.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 223 ARG Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 153 ARG Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain C residue 196 ASP Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 203 LYS Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 232 GLN Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 266 ASN Chi-restraints excluded: chain C residue 343 GLU Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 397 GLU Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 440 MET Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 571 VAL Chi-restraints excluded: chain C residue 577 ASP Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 649 VAL Chi-restraints excluded: chain C residue 686 GLN Chi-restraints excluded: chain C residue 718 ASN Chi-restraints excluded: chain C residue 797 ARG Chi-restraints excluded: chain C residue 835 THR Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 936 LEU Chi-restraints excluded: chain C residue 950 LYS Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1057 LEU Chi-restraints excluded: chain C residue 1076 MET Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 67 ARG Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 86 LYS Chi-restraints excluded: chain D residue 152 GLU Chi-restraints excluded: chain D residue 207 GLN Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 261 ILE Chi-restraints excluded: chain D residue 337 THR Chi-restraints excluded: chain D residue 414 ARG Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain D residue 463 LEU Chi-restraints excluded: chain D residue 469 ILE Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 505 HIS Chi-restraints excluded: chain D residue 506 ARG Chi-restraints excluded: chain D residue 517 VAL Chi-restraints excluded: chain D residue 677 LEU Chi-restraints excluded: chain D residue 741 ARG Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 862 ASP Chi-restraints excluded: chain D residue 957 ILE Chi-restraints excluded: chain D residue 1012 MET Chi-restraints excluded: chain D residue 1025 THR Chi-restraints excluded: chain D residue 1033 GLU Chi-restraints excluded: chain D residue 1057 ASP Chi-restraints excluded: chain D residue 1061 PHE Chi-restraints excluded: chain D residue 1098 VAL Chi-restraints excluded: chain D residue 1121 VAL Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain F residue 205 ASP Chi-restraints excluded: chain F residue 240 LEU Chi-restraints excluded: chain F residue 246 GLU Chi-restraints excluded: chain F residue 282 MET Chi-restraints excluded: chain F residue 375 VAL Chi-restraints excluded: chain F residue 418 ARG Chi-restraints excluded: chain F residue 423 LEU Chi-restraints excluded: chain F residue 460 LEU Chi-restraints excluded: chain F residue 461 GLN Chi-restraints excluded: chain F residue 492 ILE Chi-restraints excluded: chain F residue 503 ILE Chi-restraints excluded: chain J residue 7 ARG Chi-restraints excluded: chain J residue 9 SER Chi-restraints excluded: chain J residue 15 SER Chi-restraints excluded: chain J residue 76 LYS Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain J residue 98 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 170 optimal weight: 9.9990 chunk 94 optimal weight: 0.9980 chunk 254 optimal weight: 6.9990 chunk 208 optimal weight: 0.5980 chunk 84 optimal weight: 1.9990 chunk 306 optimal weight: 3.9990 chunk 331 optimal weight: 10.0000 chunk 273 optimal weight: 0.0970 chunk 304 optimal weight: 9.9990 chunk 104 optimal weight: 0.9980 chunk 245 optimal weight: 0.6980 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 266 ASN ** C 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 920 HIS D 329 GLN ** D 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 369 ASN D 505 HIS ** D 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 69 ASN F 322 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 27833 Z= 0.159 Angle : 0.593 12.107 37955 Z= 0.300 Chirality : 0.042 0.164 4324 Planarity : 0.005 0.109 4797 Dihedral : 14.944 165.692 4579 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.91 % Favored : 93.85 % Rotamer: Outliers : 4.98 % Allowed : 13.97 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.23 % Cis-general : 0.16 % Twisted Proline : 1.16 % Twisted General : 0.13 % 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: -1.69 (0.14), residues: 3335 helix: 0.35 (0.15), residues: 1201 sheet: -1.25 (0.26), residues: 373 loop : -2.23 (0.14), residues: 1761 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 63 HIS 0.016 0.001 HIS D 505 PHE 0.012 0.001 PHE C 214 TYR 0.018 0.001 TYR C 278 ARG 0.008 0.000 ARG D 211 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6670 Ramachandran restraints generated. 3335 Oldfield, 0 Emsley, 3335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6670 Ramachandran restraints generated. 3335 Oldfield, 0 Emsley, 3335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 180 time to evaluate : 3.455 Fit side-chains revert: symmetry clash REVERT: A 133 LYS cc_start: 0.8293 (tmtt) cc_final: 0.8026 (tptp) REVERT: A 151 GLN cc_start: 0.7844 (mm-40) cc_final: 0.6737 (tp-100) REVERT: A 223 ARG cc_start: 0.8447 (OUTLIER) cc_final: 0.8166 (ttp80) REVERT: B 206 ASP cc_start: 0.8064 (m-30) cc_final: 0.7727 (t0) REVERT: C 238 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8553 (tt) REVERT: C 281 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.8022 (tt) REVERT: C 407 GLN cc_start: 0.7730 (mm110) cc_final: 0.7473 (tt0) REVERT: C 429 GLU cc_start: 0.7251 (OUTLIER) cc_final: 0.7042 (mp0) REVERT: C 441 ASP cc_start: 0.7492 (t70) cc_final: 0.7256 (p0) REVERT: C 455 LEU cc_start: 0.9264 (OUTLIER) cc_final: 0.8898 (mt) REVERT: C 465 ARG cc_start: 0.7867 (ttm-80) cc_final: 0.7638 (ttm-80) REVERT: D 67 ARG cc_start: 0.7458 (OUTLIER) cc_final: 0.6818 (mmp80) REVERT: D 86 LYS cc_start: 0.9537 (OUTLIER) cc_final: 0.9336 (pttm) REVERT: D 154 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7839 (mp0) REVERT: D 207 GLN cc_start: 0.7508 (OUTLIER) cc_final: 0.7164 (tm-30) REVERT: D 357 LEU cc_start: 0.9207 (OUTLIER) cc_final: 0.8825 (tt) REVERT: D 663 MET cc_start: 0.8474 (mmm) cc_final: 0.8158 (mmm) REVERT: D 741 ARG cc_start: 0.7479 (OUTLIER) cc_final: 0.6546 (ppp80) REVERT: F 204 TRP cc_start: 0.8473 (p-90) cc_final: 0.8151 (p-90) REVERT: F 246 GLU cc_start: 0.8707 (OUTLIER) cc_final: 0.8176 (pm20) REVERT: F 258 TYR cc_start: 0.8409 (t80) cc_final: 0.8095 (t80) REVERT: F 359 MET cc_start: 0.8633 (tpp) cc_final: 0.8332 (ttt) REVERT: J 7 ARG cc_start: 0.8643 (OUTLIER) cc_final: 0.8098 (ptm-80) outliers start: 139 outliers final: 73 residues processed: 307 average time/residue: 0.3910 time to fit residues: 192.7699 Evaluate side-chains 233 residues out of total 2837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 147 time to evaluate : 3.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 223 ARG Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 153 ARG Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 79 ASP Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 203 LYS Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 343 GLU Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 397 GLU Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 429 GLU Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 532 THR Chi-restraints excluded: chain C residue 571 VAL Chi-restraints excluded: chain C residue 577 ASP Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 686 GLN Chi-restraints excluded: chain C residue 797 ARG Chi-restraints excluded: chain C residue 835 THR Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 950 LYS Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1057 LEU Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain D residue 67 ARG Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 86 LYS Chi-restraints excluded: chain D residue 154 GLU Chi-restraints excluded: chain D residue 207 GLN Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 414 ARG Chi-restraints excluded: chain D residue 463 LEU Chi-restraints excluded: chain D residue 469 ILE Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 506 ARG Chi-restraints excluded: chain D residue 517 VAL Chi-restraints excluded: chain D residue 676 LEU Chi-restraints excluded: chain D residue 677 LEU Chi-restraints excluded: chain D residue 741 ARG Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 862 ASP Chi-restraints excluded: chain D residue 957 ILE Chi-restraints excluded: chain D residue 1025 THR Chi-restraints excluded: chain D residue 1061 PHE Chi-restraints excluded: chain D residue 1080 ILE Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1098 VAL Chi-restraints excluded: chain E residue 45 ASP Chi-restraints excluded: chain E residue 69 ASN Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain F residue 205 ASP Chi-restraints excluded: chain F residue 240 LEU Chi-restraints excluded: chain F residue 246 GLU Chi-restraints excluded: chain F residue 281 MET Chi-restraints excluded: chain F residue 423 LEU Chi-restraints excluded: chain F residue 460 LEU Chi-restraints excluded: chain F residue 461 GLN Chi-restraints excluded: chain F residue 492 ILE Chi-restraints excluded: chain J residue 7 ARG Chi-restraints excluded: chain J residue 9 SER Chi-restraints excluded: chain J residue 76 LYS Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain J residue 98 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 302 optimal weight: 6.9990 chunk 230 optimal weight: 8.9990 chunk 159 optimal weight: 4.9990 chunk 33 optimal weight: 10.0000 chunk 146 optimal weight: 9.9990 chunk 205 optimal weight: 2.9990 chunk 307 optimal weight: 8.9990 chunk 325 optimal weight: 0.0030 chunk 160 optimal weight: 0.4980 chunk 291 optimal weight: 8.9990 chunk 87 optimal weight: 6.9990 overall best weight: 3.0996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 27833 Z= 0.359 Angle : 0.653 14.257 37955 Z= 0.333 Chirality : 0.044 0.162 4324 Planarity : 0.005 0.115 4797 Dihedral : 14.823 164.132 4537 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.86 % Favored : 91.93 % Rotamer: Outliers : 4.98 % Allowed : 15.12 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.23 % Cis-general : 0.16 % Twisted Proline : 1.16 % Twisted General : 0.16 % 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: -1.51 (0.14), residues: 3335 helix: 0.39 (0.15), residues: 1207 sheet: -1.05 (0.26), residues: 371 loop : -2.07 (0.14), residues: 1757 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 223 HIS 0.005 0.001 HIS D 854 PHE 0.019 0.002 PHE C 906 TYR 0.020 0.001 TYR C 278 ARG 0.005 0.000 ARG D 211 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6670 Ramachandran restraints generated. 3335 Oldfield, 0 Emsley, 3335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6670 Ramachandran restraints generated. 3335 Oldfield, 0 Emsley, 3335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 150 time to evaluate : 3.512 Fit side-chains revert: symmetry clash REVERT: A 223 ARG cc_start: 0.8503 (OUTLIER) cc_final: 0.8183 (ttp80) REVERT: B 123 MET cc_start: 0.8176 (ttm) cc_final: 0.7812 (ttm) REVERT: B 206 ASP cc_start: 0.8109 (m-30) cc_final: 0.7880 (t0) REVERT: C 281 LEU cc_start: 0.8336 (OUTLIER) cc_final: 0.8017 (tt) REVERT: C 429 GLU cc_start: 0.7459 (OUTLIER) cc_final: 0.7243 (mp0) REVERT: C 441 ASP cc_start: 0.7620 (t70) cc_final: 0.7354 (p0) REVERT: C 467 ARG cc_start: 0.7900 (OUTLIER) cc_final: 0.7457 (ppt170) REVERT: D 154 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7791 (mp0) REVERT: D 207 GLN cc_start: 0.7489 (OUTLIER) cc_final: 0.7185 (tm-30) REVERT: D 219 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8307 (mm) REVERT: D 357 LEU cc_start: 0.9246 (OUTLIER) cc_final: 0.8876 (tt) REVERT: D 506 ARG cc_start: 0.9443 (OUTLIER) cc_final: 0.8467 (ptt-90) REVERT: D 741 ARG cc_start: 0.7688 (OUTLIER) cc_final: 0.6802 (ppp80) REVERT: D 1012 MET cc_start: 0.6922 (mpp) cc_final: 0.6622 (mpp) REVERT: D 1080 ILE cc_start: 0.7431 (OUTLIER) cc_final: 0.6630 (tp) REVERT: F 202 PHE cc_start: 0.6842 (t80) cc_final: 0.6379 (t80) REVERT: F 418 ARG cc_start: 0.8726 (OUTLIER) cc_final: 0.7298 (mtm-85) REVERT: F 423 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8605 (tp) REVERT: J 7 ARG cc_start: 0.8686 (OUTLIER) cc_final: 0.8113 (ptm-80) outliers start: 139 outliers final: 99 residues processed: 282 average time/residue: 0.3850 time to fit residues: 174.0703 Evaluate side-chains 254 residues out of total 2837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 141 time to evaluate : 3.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 LEU Chi-restraints excluded: chain A residue 5 GLN Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 223 ARG Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 79 ASP Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 196 ASP Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 203 LYS Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 266 ASN Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 343 GLU Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 397 GLU Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 429 GLU Chi-restraints excluded: chain C residue 440 MET Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain C residue 467 ARG Chi-restraints excluded: chain C residue 532 THR Chi-restraints excluded: chain C residue 571 VAL Chi-restraints excluded: chain C residue 577 ASP Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 649 VAL Chi-restraints excluded: chain C residue 686 GLN Chi-restraints excluded: chain C residue 773 ILE Chi-restraints excluded: chain C residue 797 ARG Chi-restraints excluded: chain C residue 835 THR Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 933 GLU Chi-restraints excluded: chain C residue 950 LYS Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 991 CYS Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1057 LEU Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain D residue 44 ASP Chi-restraints excluded: chain D residue 67 ARG Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 86 LYS Chi-restraints excluded: chain D residue 154 GLU Chi-restraints excluded: chain D residue 207 GLN Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 414 ARG Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain D residue 463 LEU Chi-restraints excluded: chain D residue 469 ILE Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 506 ARG Chi-restraints excluded: chain D residue 517 VAL Chi-restraints excluded: chain D residue 660 ASP Chi-restraints excluded: chain D residue 676 LEU Chi-restraints excluded: chain D residue 677 LEU Chi-restraints excluded: chain D residue 741 ARG Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 825 THR Chi-restraints excluded: chain D residue 862 ASP Chi-restraints excluded: chain D residue 883 ASP Chi-restraints excluded: chain D residue 957 ILE Chi-restraints excluded: chain D residue 1025 THR Chi-restraints excluded: chain D residue 1033 GLU Chi-restraints excluded: chain D residue 1061 PHE Chi-restraints excluded: chain D residue 1080 ILE Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1098 VAL Chi-restraints excluded: chain D residue 1111 LEU Chi-restraints excluded: chain D residue 1238 ILE Chi-restraints excluded: chain E residue 45 ASP Chi-restraints excluded: chain E residue 69 ASN Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain F residue 205 ASP Chi-restraints excluded: chain F residue 240 LEU Chi-restraints excluded: chain F residue 246 GLU Chi-restraints excluded: chain F residue 310 TYR Chi-restraints excluded: chain F residue 382 ILE Chi-restraints excluded: chain F residue 418 ARG Chi-restraints excluded: chain F residue 423 LEU Chi-restraints excluded: chain F residue 460 LEU Chi-restraints excluded: chain F residue 461 GLN Chi-restraints excluded: chain F residue 492 ILE Chi-restraints excluded: chain F residue 503 ILE Chi-restraints excluded: chain J residue 7 ARG Chi-restraints excluded: chain J residue 9 SER Chi-restraints excluded: chain J residue 15 SER Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 76 LYS Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain J residue 98 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 271 optimal weight: 0.0870 chunk 184 optimal weight: 9.9990 chunk 4 optimal weight: 1.9990 chunk 242 optimal weight: 10.0000 chunk 134 optimal weight: 0.9980 chunk 277 optimal weight: 5.9990 chunk 225 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 166 optimal weight: 0.4980 chunk 292 optimal weight: 9.9990 chunk 82 optimal weight: 10.0000 overall best weight: 1.1162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 468 ASN E 69 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 27833 Z= 0.179 Angle : 0.582 14.433 37955 Z= 0.295 Chirality : 0.041 0.197 4324 Planarity : 0.004 0.121 4797 Dihedral : 14.455 164.855 4531 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.21 % Favored : 93.58 % Rotamer: Outliers : 4.77 % Allowed : 15.59 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.23 % Cis-general : 0.16 % Twisted Proline : 1.16 % Twisted General : 0.13 % 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: -1.13 (0.14), residues: 3335 helix: 0.73 (0.16), residues: 1199 sheet: -0.99 (0.26), residues: 379 loop : -1.81 (0.14), residues: 1757 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 63 HIS 0.004 0.001 HIS E 106 PHE 0.008 0.001 PHE C 153 TYR 0.019 0.001 TYR C 278 ARG 0.003 0.000 ARG C 279 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6670 Ramachandran restraints generated. 3335 Oldfield, 0 Emsley, 3335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6670 Ramachandran restraints generated. 3335 Oldfield, 0 Emsley, 3335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 153 time to evaluate : 3.617 Fit side-chains revert: symmetry clash REVERT: A 223 ARG cc_start: 0.8441 (OUTLIER) cc_final: 0.8156 (ttp80) REVERT: B 123 MET cc_start: 0.8180 (ttm) cc_final: 0.7819 (ttm) REVERT: B 206 ASP cc_start: 0.8088 (m-30) cc_final: 0.7886 (t0) REVERT: C 281 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.8032 (tt) REVERT: C 429 GLU cc_start: 0.7307 (OUTLIER) cc_final: 0.7105 (mp0) REVERT: C 455 LEU cc_start: 0.9262 (OUTLIER) cc_final: 0.8941 (mt) REVERT: C 467 ARG cc_start: 0.7838 (OUTLIER) cc_final: 0.7431 (ppt170) REVERT: C 559 VAL cc_start: 0.8620 (t) cc_final: 0.8212 (m) REVERT: D 86 LYS cc_start: 0.9485 (OUTLIER) cc_final: 0.9257 (pttm) REVERT: D 154 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7878 (mp0) REVERT: D 357 LEU cc_start: 0.9245 (OUTLIER) cc_final: 0.8854 (tt) REVERT: D 506 ARG cc_start: 0.9446 (OUTLIER) cc_final: 0.8302 (ptt-90) REVERT: D 741 ARG cc_start: 0.7565 (OUTLIER) cc_final: 0.6466 (ppp80) REVERT: D 978 CYS cc_start: 0.8935 (OUTLIER) cc_final: 0.8624 (m) REVERT: D 1012 MET cc_start: 0.6794 (mpp) cc_final: 0.6492 (mpp) REVERT: E 73 GLU cc_start: 0.7767 (pp20) cc_final: 0.7565 (pp20) REVERT: F 204 TRP cc_start: 0.8277 (p-90) cc_final: 0.7960 (p-90) REVERT: F 246 GLU cc_start: 0.8682 (OUTLIER) cc_final: 0.8191 (pm20) REVERT: F 418 ARG cc_start: 0.8721 (OUTLIER) cc_final: 0.7443 (mtm-85) REVERT: J 7 ARG cc_start: 0.8644 (OUTLIER) cc_final: 0.8134 (ptm-80) REVERT: J 99 LYS cc_start: 0.8963 (tppt) cc_final: 0.8575 (tptp) outliers start: 133 outliers final: 91 residues processed: 275 average time/residue: 0.4189 time to fit residues: 185.1049 Evaluate side-chains 249 residues out of total 2837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 144 time to evaluate : 3.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 LEU Chi-restraints excluded: chain A residue 5 GLN Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 223 ARG Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 196 ASP Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 203 LYS Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 266 ASN Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 343 GLU Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 397 GLU Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 429 GLU Chi-restraints excluded: chain C residue 440 MET Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 467 ARG Chi-restraints excluded: chain C residue 532 THR Chi-restraints excluded: chain C residue 571 VAL Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 686 GLN Chi-restraints excluded: chain C residue 773 ILE Chi-restraints excluded: chain C residue 835 THR Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 950 LYS Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1057 LEU Chi-restraints excluded: chain C residue 1131 LEU Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain D residue 67 ARG Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 86 LYS Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 154 GLU Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 414 ARG Chi-restraints excluded: chain D residue 463 LEU Chi-restraints excluded: chain D residue 469 ILE Chi-restraints excluded: chain D residue 506 ARG Chi-restraints excluded: chain D residue 517 VAL Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 660 ASP Chi-restraints excluded: chain D residue 676 LEU Chi-restraints excluded: chain D residue 677 LEU Chi-restraints excluded: chain D residue 741 ARG Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 862 ASP Chi-restraints excluded: chain D residue 957 ILE Chi-restraints excluded: chain D residue 978 CYS Chi-restraints excluded: chain D residue 1025 THR Chi-restraints excluded: chain D residue 1033 GLU Chi-restraints excluded: chain D residue 1061 PHE Chi-restraints excluded: chain D residue 1078 ASP Chi-restraints excluded: chain D residue 1080 ILE Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1098 VAL Chi-restraints excluded: chain D residue 1238 ILE Chi-restraints excluded: chain E residue 45 ASP Chi-restraints excluded: chain E residue 69 ASN Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain F residue 205 ASP Chi-restraints excluded: chain F residue 240 LEU Chi-restraints excluded: chain F residue 246 GLU Chi-restraints excluded: chain F residue 310 TYR Chi-restraints excluded: chain F residue 328 LEU Chi-restraints excluded: chain F residue 375 VAL Chi-restraints excluded: chain F residue 418 ARG Chi-restraints excluded: chain F residue 423 LEU Chi-restraints excluded: chain F residue 435 LEU Chi-restraints excluded: chain F residue 460 LEU Chi-restraints excluded: chain F residue 461 GLN Chi-restraints excluded: chain F residue 492 ILE Chi-restraints excluded: chain F residue 503 ILE Chi-restraints excluded: chain J residue 7 ARG Chi-restraints excluded: chain J residue 9 SER Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 76 LYS Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain J residue 98 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 109 optimal weight: 3.9990 chunk 293 optimal weight: 0.0050 chunk 64 optimal weight: 10.0000 chunk 191 optimal weight: 7.9990 chunk 80 optimal weight: 6.9990 chunk 326 optimal weight: 20.0000 chunk 270 optimal weight: 7.9990 chunk 150 optimal weight: 6.9990 chunk 27 optimal weight: 10.0000 chunk 107 optimal weight: 2.9990 chunk 171 optimal weight: 30.0000 overall best weight: 4.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 341 ASN ** D1084 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 69 ASN E 70 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.080 27833 Z= 0.459 Angle : 0.693 14.584 37955 Z= 0.354 Chirality : 0.046 0.176 4324 Planarity : 0.005 0.127 4797 Dihedral : 14.801 163.835 4520 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.49 % Favored : 91.30 % Rotamer: Outliers : 5.63 % Allowed : 15.59 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.23 % Cis-general : 0.16 % Twisted Proline : 1.16 % Twisted General : 0.16 % 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: -1.37 (0.14), residues: 3335 helix: 0.51 (0.15), residues: 1197 sheet: -1.06 (0.26), residues: 388 loop : -1.96 (0.14), residues: 1750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 955 HIS 0.005 0.001 HIS F 371 PHE 0.022 0.002 PHE C 906 TYR 0.023 0.002 TYR E 56 ARG 0.008 0.001 ARG D 211 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6670 Ramachandran restraints generated. 3335 Oldfield, 0 Emsley, 3335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6670 Ramachandran restraints generated. 3335 Oldfield, 0 Emsley, 3335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 141 time to evaluate : 3.420 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 223 ARG cc_start: 0.8534 (OUTLIER) cc_final: 0.8244 (ttp80) REVERT: B 123 MET cc_start: 0.8210 (ttm) cc_final: 0.7813 (ttm) REVERT: C 281 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.8048 (tt) REVERT: C 455 LEU cc_start: 0.9305 (OUTLIER) cc_final: 0.8987 (mt) REVERT: C 467 ARG cc_start: 0.7853 (OUTLIER) cc_final: 0.7386 (ppt170) REVERT: C 559 VAL cc_start: 0.8659 (t) cc_final: 0.8259 (m) REVERT: C 797 ARG cc_start: 0.8098 (OUTLIER) cc_final: 0.7338 (ppt-90) REVERT: C 881 ASP cc_start: 0.8874 (OUTLIER) cc_final: 0.8207 (p0) REVERT: C 1127 GLU cc_start: 0.8445 (mm-30) cc_final: 0.8209 (tp30) REVERT: D 154 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.7661 (mp0) REVERT: D 207 GLN cc_start: 0.7523 (OUTLIER) cc_final: 0.7282 (tm-30) REVERT: D 357 LEU cc_start: 0.9295 (OUTLIER) cc_final: 0.8885 (tt) REVERT: D 506 ARG cc_start: 0.9436 (OUTLIER) cc_final: 0.8371 (ptt-90) REVERT: D 639 GLN cc_start: 0.8923 (OUTLIER) cc_final: 0.8380 (mp10) REVERT: D 741 ARG cc_start: 0.7707 (OUTLIER) cc_final: 0.6669 (ppp80) REVERT: D 978 CYS cc_start: 0.9088 (OUTLIER) cc_final: 0.8794 (m) REVERT: D 1012 MET cc_start: 0.7163 (mpp) cc_final: 0.6793 (mpp) REVERT: D 1080 ILE cc_start: 0.7564 (OUTLIER) cc_final: 0.6642 (tp) REVERT: D 1273 GLN cc_start: 0.8786 (OUTLIER) cc_final: 0.7633 (pp30) REVERT: F 418 ARG cc_start: 0.8790 (OUTLIER) cc_final: 0.7505 (mtm-85) REVERT: F 423 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8723 (tp) REVERT: J 7 ARG cc_start: 0.8696 (OUTLIER) cc_final: 0.8115 (ptm-80) outliers start: 157 outliers final: 113 residues processed: 289 average time/residue: 0.3901 time to fit residues: 182.8560 Evaluate side-chains 267 residues out of total 2837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 136 time to evaluate : 3.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 LEU Chi-restraints excluded: chain A residue 5 GLN Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 223 ARG Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 79 ASN Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain C residue 79 ASP Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 196 ASP Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 203 LYS Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 266 ASN Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 323 HIS Chi-restraints excluded: chain C residue 343 GLU Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 397 GLU Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 440 MET Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 467 ARG Chi-restraints excluded: chain C residue 532 THR Chi-restraints excluded: chain C residue 571 VAL Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 632 LEU Chi-restraints excluded: chain C residue 649 VAL Chi-restraints excluded: chain C residue 686 GLN Chi-restraints excluded: chain C residue 773 ILE Chi-restraints excluded: chain C residue 797 ARG Chi-restraints excluded: chain C residue 835 THR Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 881 ASP Chi-restraints excluded: chain C residue 933 GLU Chi-restraints excluded: chain C residue 950 LYS Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 963 LEU Chi-restraints excluded: chain C residue 991 CYS Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1057 LEU Chi-restraints excluded: chain C residue 1131 LEU Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain D residue 29 LYS Chi-restraints excluded: chain D residue 44 ASP Chi-restraints excluded: chain D residue 67 ARG Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 86 LYS Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 154 GLU Chi-restraints excluded: chain D residue 207 GLN Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 414 ARG Chi-restraints excluded: chain D residue 463 LEU Chi-restraints excluded: chain D residue 469 ILE Chi-restraints excluded: chain D residue 506 ARG Chi-restraints excluded: chain D residue 517 VAL Chi-restraints excluded: chain D residue 576 MET Chi-restraints excluded: chain D residue 639 GLN Chi-restraints excluded: chain D residue 660 ASP Chi-restraints excluded: chain D residue 676 LEU Chi-restraints excluded: chain D residue 677 LEU Chi-restraints excluded: chain D residue 741 ARG Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 825 THR Chi-restraints excluded: chain D residue 862 ASP Chi-restraints excluded: chain D residue 883 ASP Chi-restraints excluded: chain D residue 936 VAL Chi-restraints excluded: chain D residue 957 ILE Chi-restraints excluded: chain D residue 978 CYS Chi-restraints excluded: chain D residue 1025 THR Chi-restraints excluded: chain D residue 1033 GLU Chi-restraints excluded: chain D residue 1057 ASP Chi-restraints excluded: chain D residue 1061 PHE Chi-restraints excluded: chain D residue 1078 ASP Chi-restraints excluded: chain D residue 1080 ILE Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1097 ARG Chi-restraints excluded: chain D residue 1098 VAL Chi-restraints excluded: chain D residue 1238 ILE Chi-restraints excluded: chain D residue 1273 GLN Chi-restraints excluded: chain E residue 45 ASP Chi-restraints excluded: chain E residue 69 ASN Chi-restraints excluded: chain E residue 70 GLN Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain F residue 205 ASP Chi-restraints excluded: chain F residue 240 LEU Chi-restraints excluded: chain F residue 246 GLU Chi-restraints excluded: chain F residue 281 MET Chi-restraints excluded: chain F residue 310 TYR Chi-restraints excluded: chain F residue 375 VAL Chi-restraints excluded: chain F residue 382 ILE Chi-restraints excluded: chain F residue 418 ARG Chi-restraints excluded: chain F residue 423 LEU Chi-restraints excluded: chain F residue 460 LEU Chi-restraints excluded: chain F residue 461 GLN Chi-restraints excluded: chain F residue 463 VAL Chi-restraints excluded: chain F residue 492 ILE Chi-restraints excluded: chain J residue 7 ARG Chi-restraints excluded: chain J residue 9 SER Chi-restraints excluded: chain J residue 15 SER Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 76 LYS Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain J residue 98 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 314 optimal weight: 7.9990 chunk 36 optimal weight: 5.9990 chunk 185 optimal weight: 5.9990 chunk 238 optimal weight: 3.9990 chunk 184 optimal weight: 7.9990 chunk 274 optimal weight: 8.9990 chunk 182 optimal weight: 4.9990 chunk 324 optimal weight: 8.9990 chunk 203 optimal weight: 0.8980 chunk 198 optimal weight: 3.9990 chunk 149 optimal weight: 0.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1084 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 69 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 27833 Z= 0.341 Angle : 0.646 14.653 37955 Z= 0.329 Chirality : 0.044 0.176 4324 Planarity : 0.005 0.125 4797 Dihedral : 14.705 164.481 4520 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.50 % Favored : 92.29 % Rotamer: Outliers : 5.63 % Allowed : 15.94 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.23 % Cis-general : 0.16 % Twisted Proline : 1.16 % Twisted General : 0.16 % 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: -1.28 (0.14), residues: 3335 helix: 0.57 (0.15), residues: 1193 sheet: -0.99 (0.26), residues: 385 loop : -1.88 (0.14), residues: 1757 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 204 HIS 0.005 0.001 HIS E 106 PHE 0.017 0.001 PHE C 906 TYR 0.026 0.001 TYR E 56 ARG 0.006 0.000 ARG C 279 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6670 Ramachandran restraints generated. 3335 Oldfield, 0 Emsley, 3335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6670 Ramachandran restraints generated. 3335 Oldfield, 0 Emsley, 3335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 139 time to evaluate : 3.475 Fit side-chains revert: symmetry clash REVERT: A 223 ARG cc_start: 0.8520 (OUTLIER) cc_final: 0.8262 (ttp80) REVERT: B 123 MET cc_start: 0.8191 (ttm) cc_final: 0.7776 (ttm) REVERT: C 281 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.8042 (tt) REVERT: C 429 GLU cc_start: 0.7356 (mp0) cc_final: 0.7036 (mp0) REVERT: C 455 LEU cc_start: 0.9301 (OUTLIER) cc_final: 0.8969 (mt) REVERT: C 467 ARG cc_start: 0.7844 (OUTLIER) cc_final: 0.7372 (ppt170) REVERT: C 559 VAL cc_start: 0.8648 (t) cc_final: 0.8251 (m) REVERT: C 797 ARG cc_start: 0.8048 (OUTLIER) cc_final: 0.7276 (ppt-90) REVERT: D 86 LYS cc_start: 0.9456 (OUTLIER) cc_final: 0.9218 (pttm) REVERT: D 154 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7651 (mp0) REVERT: D 207 GLN cc_start: 0.7541 (OUTLIER) cc_final: 0.7306 (tm-30) REVERT: D 357 LEU cc_start: 0.9299 (OUTLIER) cc_final: 0.8899 (tt) REVERT: D 427 ARG cc_start: 0.8508 (OUTLIER) cc_final: 0.8266 (ptp90) REVERT: D 506 ARG cc_start: 0.9439 (OUTLIER) cc_final: 0.8375 (ptt-90) REVERT: D 639 GLN cc_start: 0.8940 (OUTLIER) cc_final: 0.8370 (mp10) REVERT: D 741 ARG cc_start: 0.7660 (OUTLIER) cc_final: 0.6484 (ppp80) REVERT: D 978 CYS cc_start: 0.9062 (OUTLIER) cc_final: 0.8754 (m) REVERT: D 1012 MET cc_start: 0.7260 (mpp) cc_final: 0.6840 (mpp) REVERT: D 1273 GLN cc_start: 0.8777 (OUTLIER) cc_final: 0.7627 (pp30) REVERT: E 79 VAL cc_start: 0.9248 (OUTLIER) cc_final: 0.8952 (m) REVERT: F 204 TRP cc_start: 0.8195 (p-90) cc_final: 0.7793 (p-90) REVERT: F 418 ARG cc_start: 0.8760 (OUTLIER) cc_final: 0.7459 (mtm-85) REVERT: F 423 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8716 (tp) REVERT: J 7 ARG cc_start: 0.8705 (OUTLIER) cc_final: 0.8120 (ptm-80) REVERT: J 99 LYS cc_start: 0.9008 (tppt) cc_final: 0.8597 (tptp) outliers start: 157 outliers final: 119 residues processed: 287 average time/residue: 0.4029 time to fit residues: 184.9642 Evaluate side-chains 271 residues out of total 2837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 133 time to evaluate : 3.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 LEU Chi-restraints excluded: chain A residue 5 GLN Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 223 ARG Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 79 ASN Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 153 ARG Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain C residue 79 ASP Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 192 ASP Chi-restraints excluded: chain C residue 196 ASP Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 203 LYS Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 266 ASN Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 323 HIS Chi-restraints excluded: chain C residue 343 GLU Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 397 GLU Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 440 MET Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 467 ARG Chi-restraints excluded: chain C residue 532 THR Chi-restraints excluded: chain C residue 571 VAL Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 649 VAL Chi-restraints excluded: chain C residue 686 GLN Chi-restraints excluded: chain C residue 773 ILE Chi-restraints excluded: chain C residue 797 ARG Chi-restraints excluded: chain C residue 835 THR Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 933 GLU Chi-restraints excluded: chain C residue 950 LYS Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 991 CYS Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1057 LEU Chi-restraints excluded: chain C residue 1131 LEU Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain D residue 44 ASP Chi-restraints excluded: chain D residue 67 ARG Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 86 LYS Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 154 GLU Chi-restraints excluded: chain D residue 207 GLN Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 414 ARG Chi-restraints excluded: chain D residue 427 ARG Chi-restraints excluded: chain D residue 441 CYS Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain D residue 463 LEU Chi-restraints excluded: chain D residue 469 ILE Chi-restraints excluded: chain D residue 506 ARG Chi-restraints excluded: chain D residue 517 VAL Chi-restraints excluded: chain D residue 576 MET Chi-restraints excluded: chain D residue 639 GLN Chi-restraints excluded: chain D residue 660 ASP Chi-restraints excluded: chain D residue 667 THR Chi-restraints excluded: chain D residue 676 LEU Chi-restraints excluded: chain D residue 677 LEU Chi-restraints excluded: chain D residue 741 ARG Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 825 THR Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 862 ASP Chi-restraints excluded: chain D residue 883 ASP Chi-restraints excluded: chain D residue 936 VAL Chi-restraints excluded: chain D residue 957 ILE Chi-restraints excluded: chain D residue 978 CYS Chi-restraints excluded: chain D residue 1025 THR Chi-restraints excluded: chain D residue 1033 GLU Chi-restraints excluded: chain D residue 1057 ASP Chi-restraints excluded: chain D residue 1061 PHE Chi-restraints excluded: chain D residue 1078 ASP Chi-restraints excluded: chain D residue 1080 ILE Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1097 ARG Chi-restraints excluded: chain D residue 1098 VAL Chi-restraints excluded: chain D residue 1238 ILE Chi-restraints excluded: chain D residue 1273 GLN Chi-restraints excluded: chain E residue 45 ASP Chi-restraints excluded: chain E residue 69 ASN Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain F residue 205 ASP Chi-restraints excluded: chain F residue 240 LEU Chi-restraints excluded: chain F residue 246 GLU Chi-restraints excluded: chain F residue 281 MET Chi-restraints excluded: chain F residue 310 TYR Chi-restraints excluded: chain F residue 375 VAL Chi-restraints excluded: chain F residue 382 ILE Chi-restraints excluded: chain F residue 418 ARG Chi-restraints excluded: chain F residue 423 LEU Chi-restraints excluded: chain F residue 460 LEU Chi-restraints excluded: chain F residue 461 GLN Chi-restraints excluded: chain F residue 463 VAL Chi-restraints excluded: chain F residue 492 ILE Chi-restraints excluded: chain F residue 503 ILE Chi-restraints excluded: chain J residue 7 ARG Chi-restraints excluded: chain J residue 9 SER Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 76 LYS Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain J residue 98 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 200 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 193 optimal weight: 0.7980 chunk 97 optimal weight: 6.9990 chunk 63 optimal weight: 8.9990 chunk 62 optimal weight: 1.9990 chunk 206 optimal weight: 2.9990 chunk 221 optimal weight: 3.9990 chunk 160 optimal weight: 4.9990 chunk 30 optimal weight: 7.9990 chunk 255 optimal weight: 0.9980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 293 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.2876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 27833 Z= 0.211 Angle : 0.597 14.382 37955 Z= 0.303 Chirality : 0.042 0.201 4324 Planarity : 0.005 0.123 4797 Dihedral : 14.452 164.776 4520 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.02 % Favored : 92.83 % Rotamer: Outliers : 5.02 % Allowed : 16.23 % Favored : 78.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.23 % Cis-general : 0.16 % Twisted Proline : 1.16 % Twisted General : 0.16 % 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: -1.01 (0.14), residues: 3335 helix: 0.81 (0.16), residues: 1196 sheet: -0.94 (0.26), residues: 381 loop : -1.72 (0.14), residues: 1758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 63 HIS 0.006 0.001 HIS E 106 PHE 0.010 0.001 PHE C 906 TYR 0.022 0.001 TYR C 278 ARG 0.012 0.000 ARG C 279 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6670 Ramachandran restraints generated. 3335 Oldfield, 0 Emsley, 3335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6670 Ramachandran restraints generated. 3335 Oldfield, 0 Emsley, 3335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 147 time to evaluate : 3.428 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 223 ARG cc_start: 0.8464 (OUTLIER) cc_final: 0.8219 (ttp80) REVERT: B 123 MET cc_start: 0.8151 (ttm) cc_final: 0.7793 (ttm) REVERT: C 281 LEU cc_start: 0.8326 (OUTLIER) cc_final: 0.8031 (tt) REVERT: C 455 LEU cc_start: 0.9283 (OUTLIER) cc_final: 0.8938 (mt) REVERT: C 467 ARG cc_start: 0.7890 (OUTLIER) cc_final: 0.7410 (ppt170) REVERT: C 559 VAL cc_start: 0.8604 (t) cc_final: 0.8227 (m) REVERT: C 797 ARG cc_start: 0.8022 (OUTLIER) cc_final: 0.7310 (ppt-90) REVERT: C 833 ARG cc_start: 0.7742 (mtp85) cc_final: 0.7212 (ttm110) REVERT: C 881 ASP cc_start: 0.8827 (OUTLIER) cc_final: 0.8318 (p0) REVERT: D 86 LYS cc_start: 0.9449 (OUTLIER) cc_final: 0.9225 (pttm) REVERT: D 143 MET cc_start: 0.7771 (mmp) cc_final: 0.7170 (mtm) REVERT: D 154 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7733 (mp0) REVERT: D 207 GLN cc_start: 0.7555 (OUTLIER) cc_final: 0.7308 (tm-30) REVERT: D 357 LEU cc_start: 0.9280 (OUTLIER) cc_final: 0.8875 (tt) REVERT: D 427 ARG cc_start: 0.8490 (OUTLIER) cc_final: 0.8277 (ptp90) REVERT: D 506 ARG cc_start: 0.9440 (OUTLIER) cc_final: 0.8299 (ptt-90) REVERT: D 639 GLN cc_start: 0.8924 (OUTLIER) cc_final: 0.8548 (mm-40) REVERT: D 741 ARG cc_start: 0.7515 (OUTLIER) cc_final: 0.6246 (ppp80) REVERT: D 978 CYS cc_start: 0.8955 (OUTLIER) cc_final: 0.8651 (m) REVERT: F 204 TRP cc_start: 0.8111 (p-90) cc_final: 0.7635 (p-90) REVERT: F 418 ARG cc_start: 0.8716 (OUTLIER) cc_final: 0.7255 (mtm-85) REVERT: F 423 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8670 (tp) REVERT: J 7 ARG cc_start: 0.8626 (OUTLIER) cc_final: 0.8147 (ptm-80) REVERT: J 99 LYS cc_start: 0.8926 (tppt) cc_final: 0.8496 (tptp) outliers start: 140 outliers final: 101 residues processed: 277 average time/residue: 0.4054 time to fit residues: 180.5894 Evaluate side-chains 259 residues out of total 2837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 140 time to evaluate : 3.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 LEU Chi-restraints excluded: chain A residue 5 GLN Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 223 ARG Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 79 ASN Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 196 ASP Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 203 LYS Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 266 ASN Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 323 HIS Chi-restraints excluded: chain C residue 343 GLU Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 397 GLU Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 440 MET Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 467 ARG Chi-restraints excluded: chain C residue 532 THR Chi-restraints excluded: chain C residue 571 VAL Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 686 GLN Chi-restraints excluded: chain C residue 797 ARG Chi-restraints excluded: chain C residue 835 THR Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 881 ASP Chi-restraints excluded: chain C residue 933 GLU Chi-restraints excluded: chain C residue 950 LYS Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 991 CYS Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1057 LEU Chi-restraints excluded: chain C residue 1131 LEU Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain D residue 44 ASP Chi-restraints excluded: chain D residue 67 ARG Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 86 LYS Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 154 GLU Chi-restraints excluded: chain D residue 207 GLN Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 414 ARG Chi-restraints excluded: chain D residue 427 ARG Chi-restraints excluded: chain D residue 463 LEU Chi-restraints excluded: chain D residue 469 ILE Chi-restraints excluded: chain D residue 506 ARG Chi-restraints excluded: chain D residue 517 VAL Chi-restraints excluded: chain D residue 639 GLN Chi-restraints excluded: chain D residue 660 ASP Chi-restraints excluded: chain D residue 667 THR Chi-restraints excluded: chain D residue 676 LEU Chi-restraints excluded: chain D residue 677 LEU Chi-restraints excluded: chain D residue 741 ARG Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 825 THR Chi-restraints excluded: chain D residue 862 ASP Chi-restraints excluded: chain D residue 883 ASP Chi-restraints excluded: chain D residue 936 VAL Chi-restraints excluded: chain D residue 957 ILE Chi-restraints excluded: chain D residue 978 CYS Chi-restraints excluded: chain D residue 1025 THR Chi-restraints excluded: chain D residue 1033 GLU Chi-restraints excluded: chain D residue 1061 PHE Chi-restraints excluded: chain D residue 1080 ILE Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1097 ARG Chi-restraints excluded: chain D residue 1098 VAL Chi-restraints excluded: chain D residue 1238 ILE Chi-restraints excluded: chain E residue 45 ASP Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain F residue 205 ASP Chi-restraints excluded: chain F residue 240 LEU Chi-restraints excluded: chain F residue 246 GLU Chi-restraints excluded: chain F residue 281 MET Chi-restraints excluded: chain F residue 310 TYR Chi-restraints excluded: chain F residue 375 VAL Chi-restraints excluded: chain F residue 382 ILE Chi-restraints excluded: chain F residue 418 ARG Chi-restraints excluded: chain F residue 423 LEU Chi-restraints excluded: chain F residue 460 LEU Chi-restraints excluded: chain F residue 461 GLN Chi-restraints excluded: chain F residue 492 ILE Chi-restraints excluded: chain F residue 503 ILE Chi-restraints excluded: chain J residue 7 ARG Chi-restraints excluded: chain J residue 9 SER Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 76 LYS Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain J residue 98 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 295 optimal weight: 9.9990 chunk 311 optimal weight: 0.9990 chunk 283 optimal weight: 7.9990 chunk 302 optimal weight: 4.9990 chunk 182 optimal weight: 7.9990 chunk 131 optimal weight: 4.9990 chunk 237 optimal weight: 3.9990 chunk 92 optimal weight: 5.9990 chunk 273 optimal weight: 0.0470 chunk 286 optimal weight: 0.0870 chunk 301 optimal weight: 5.9990 overall best weight: 2.0262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 293 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.2916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 27833 Z= 0.252 Angle : 0.608 14.691 37955 Z= 0.308 Chirality : 0.042 0.192 4324 Planarity : 0.005 0.124 4797 Dihedral : 14.457 164.288 4519 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.32 % Favored : 92.53 % Rotamer: Outliers : 4.77 % Allowed : 16.66 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.23 % Cis-general : 0.16 % Twisted Proline : 1.16 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.15), residues: 3335 helix: 0.89 (0.16), residues: 1194 sheet: -0.94 (0.26), residues: 383 loop : -1.66 (0.14), residues: 1758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 63 HIS 0.006 0.001 HIS E 106 PHE 0.013 0.001 PHE C 906 TYR 0.026 0.001 TYR E 56 ARG 0.008 0.000 ARG C 279 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6670 Ramachandran restraints generated. 3335 Oldfield, 0 Emsley, 3335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6670 Ramachandran restraints generated. 3335 Oldfield, 0 Emsley, 3335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 143 time to evaluate : 3.407 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 223 ARG cc_start: 0.8491 (OUTLIER) cc_final: 0.8242 (ttp80) REVERT: B 123 MET cc_start: 0.8154 (ttm) cc_final: 0.7778 (ttm) REVERT: B 141 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7636 (pm20) REVERT: C 281 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.8025 (tt) REVERT: C 455 LEU cc_start: 0.9290 (OUTLIER) cc_final: 0.8934 (mt) REVERT: C 467 ARG cc_start: 0.7857 (OUTLIER) cc_final: 0.7389 (ppt170) REVERT: C 559 VAL cc_start: 0.8616 (t) cc_final: 0.8249 (m) REVERT: C 797 ARG cc_start: 0.8027 (OUTLIER) cc_final: 0.7347 (ppt-90) REVERT: C 833 ARG cc_start: 0.7739 (mtp85) cc_final: 0.7217 (ttm110) REVERT: C 881 ASP cc_start: 0.8850 (OUTLIER) cc_final: 0.8332 (p0) REVERT: D 86 LYS cc_start: 0.9446 (OUTLIER) cc_final: 0.9219 (pttm) REVERT: D 154 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7694 (mp0) REVERT: D 207 GLN cc_start: 0.7555 (OUTLIER) cc_final: 0.7318 (tm-30) REVERT: D 357 LEU cc_start: 0.9286 (OUTLIER) cc_final: 0.8870 (tt) REVERT: D 506 ARG cc_start: 0.9442 (OUTLIER) cc_final: 0.8297 (ptt-90) REVERT: D 639 GLN cc_start: 0.8927 (OUTLIER) cc_final: 0.8549 (mm-40) REVERT: D 741 ARG cc_start: 0.7512 (OUTLIER) cc_final: 0.6264 (ppp80) REVERT: D 978 CYS cc_start: 0.8963 (OUTLIER) cc_final: 0.8669 (m) REVERT: D 1080 ILE cc_start: 0.7390 (OUTLIER) cc_final: 0.6772 (tp) REVERT: D 1273 GLN cc_start: 0.8717 (OUTLIER) cc_final: 0.7620 (pp30) REVERT: F 204 TRP cc_start: 0.8066 (p-90) cc_final: 0.7654 (p-90) REVERT: F 418 ARG cc_start: 0.8724 (OUTLIER) cc_final: 0.7321 (mtm-85) REVERT: J 7 ARG cc_start: 0.8615 (OUTLIER) cc_final: 0.8194 (ptm-80) REVERT: J 99 LYS cc_start: 0.8886 (tppt) cc_final: 0.8454 (tptp) outliers start: 133 outliers final: 107 residues processed: 265 average time/residue: 0.3942 time to fit residues: 168.4624 Evaluate side-chains 267 residues out of total 2837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 141 time to evaluate : 3.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 LEU Chi-restraints excluded: chain A residue 5 GLN Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 223 ARG Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 24 GLU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 79 ASN Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 141 GLU Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 196 ASP Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 203 LYS Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 266 ASN Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 323 HIS Chi-restraints excluded: chain C residue 343 GLU Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 397 GLU Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 440 MET Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 467 ARG Chi-restraints excluded: chain C residue 532 THR Chi-restraints excluded: chain C residue 571 VAL Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 632 LEU Chi-restraints excluded: chain C residue 649 VAL Chi-restraints excluded: chain C residue 686 GLN Chi-restraints excluded: chain C residue 797 ARG Chi-restraints excluded: chain C residue 835 THR Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 881 ASP Chi-restraints excluded: chain C residue 933 GLU Chi-restraints excluded: chain C residue 950 LYS Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 991 CYS Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1057 LEU Chi-restraints excluded: chain C residue 1131 LEU Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain D residue 44 ASP Chi-restraints excluded: chain D residue 67 ARG Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 86 LYS Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 154 GLU Chi-restraints excluded: chain D residue 207 GLN Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 414 ARG Chi-restraints excluded: chain D residue 441 CYS Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain D residue 463 LEU Chi-restraints excluded: chain D residue 469 ILE Chi-restraints excluded: chain D residue 506 ARG Chi-restraints excluded: chain D residue 517 VAL Chi-restraints excluded: chain D residue 639 GLN Chi-restraints excluded: chain D residue 660 ASP Chi-restraints excluded: chain D residue 667 THR Chi-restraints excluded: chain D residue 676 LEU Chi-restraints excluded: chain D residue 677 LEU Chi-restraints excluded: chain D residue 741 ARG Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 825 THR Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 862 ASP Chi-restraints excluded: chain D residue 883 ASP Chi-restraints excluded: chain D residue 936 VAL Chi-restraints excluded: chain D residue 957 ILE Chi-restraints excluded: chain D residue 978 CYS Chi-restraints excluded: chain D residue 1025 THR Chi-restraints excluded: chain D residue 1033 GLU Chi-restraints excluded: chain D residue 1057 ASP Chi-restraints excluded: chain D residue 1061 PHE Chi-restraints excluded: chain D residue 1080 ILE Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1097 ARG Chi-restraints excluded: chain D residue 1098 VAL Chi-restraints excluded: chain D residue 1238 ILE Chi-restraints excluded: chain D residue 1273 GLN Chi-restraints excluded: chain E residue 45 ASP Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain F residue 205 ASP Chi-restraints excluded: chain F residue 240 LEU Chi-restraints excluded: chain F residue 246 GLU Chi-restraints excluded: chain F residue 310 TYR Chi-restraints excluded: chain F residue 375 VAL Chi-restraints excluded: chain F residue 382 ILE Chi-restraints excluded: chain F residue 418 ARG Chi-restraints excluded: chain F residue 460 LEU Chi-restraints excluded: chain F residue 461 GLN Chi-restraints excluded: chain F residue 492 ILE Chi-restraints excluded: chain F residue 503 ILE Chi-restraints excluded: chain J residue 7 ARG Chi-restraints excluded: chain J residue 9 SER Chi-restraints excluded: chain J residue 15 SER Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 76 LYS Chi-restraints excluded: chain J residue 98 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 198 optimal weight: 4.9990 chunk 320 optimal weight: 9.9990 chunk 195 optimal weight: 0.7980 chunk 151 optimal weight: 6.9990 chunk 222 optimal weight: 1.9990 chunk 335 optimal weight: 7.9990 chunk 309 optimal weight: 4.9990 chunk 267 optimal weight: 2.9990 chunk 27 optimal weight: 9.9990 chunk 206 optimal weight: 4.9990 chunk 163 optimal weight: 6.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 293 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 27833 Z= 0.357 Angle : 0.649 14.208 37955 Z= 0.330 Chirality : 0.044 0.184 4324 Planarity : 0.005 0.126 4797 Dihedral : 14.592 163.923 4515 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.92 % Favored : 91.90 % Rotamer: Outliers : 4.77 % Allowed : 16.73 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.23 % Cis-general : 0.16 % Twisted Proline : 1.16 % Twisted General : 0.13 % 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: -1.02 (0.14), residues: 3335 helix: 0.78 (0.15), residues: 1194 sheet: -0.91 (0.26), residues: 384 loop : -1.71 (0.14), residues: 1757 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 723 HIS 0.006 0.001 HIS E 106 PHE 0.017 0.001 PHE C 906 TYR 0.034 0.001 TYR E 56 ARG 0.015 0.000 ARG C 279 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6670 Ramachandran restraints generated. 3335 Oldfield, 0 Emsley, 3335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6670 Ramachandran restraints generated. 3335 Oldfield, 0 Emsley, 3335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 135 time to evaluate : 3.324 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 223 ARG cc_start: 0.8537 (OUTLIER) cc_final: 0.8291 (ttp80) REVERT: B 123 MET cc_start: 0.8174 (ttm) cc_final: 0.7823 (ttm) REVERT: B 141 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7701 (pm20) REVERT: C 281 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.8051 (tt) REVERT: C 455 LEU cc_start: 0.9307 (OUTLIER) cc_final: 0.8955 (mt) REVERT: C 467 ARG cc_start: 0.7893 (OUTLIER) cc_final: 0.7382 (ppt170) REVERT: C 559 VAL cc_start: 0.8664 (t) cc_final: 0.8297 (m) REVERT: C 797 ARG cc_start: 0.8049 (OUTLIER) cc_final: 0.7390 (ppt-90) REVERT: C 833 ARG cc_start: 0.7773 (mtp85) cc_final: 0.7248 (ttm110) REVERT: C 881 ASP cc_start: 0.8868 (OUTLIER) cc_final: 0.8219 (p0) REVERT: D 86 LYS cc_start: 0.9479 (OUTLIER) cc_final: 0.9229 (pttm) REVERT: D 143 MET cc_start: 0.7799 (mmp) cc_final: 0.7154 (mtm) REVERT: D 154 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7699 (mp0) REVERT: D 207 GLN cc_start: 0.7590 (OUTLIER) cc_final: 0.7360 (tm-30) REVERT: D 357 LEU cc_start: 0.9293 (OUTLIER) cc_final: 0.8874 (tt) REVERT: D 506 ARG cc_start: 0.9454 (OUTLIER) cc_final: 0.8401 (ptt-90) REVERT: D 639 GLN cc_start: 0.8936 (OUTLIER) cc_final: 0.8540 (mm-40) REVERT: D 741 ARG cc_start: 0.7537 (OUTLIER) cc_final: 0.6306 (ppp80) REVERT: D 978 CYS cc_start: 0.9036 (OUTLIER) cc_final: 0.8741 (m) REVERT: D 1080 ILE cc_start: 0.7488 (OUTLIER) cc_final: 0.6839 (tp) REVERT: D 1273 GLN cc_start: 0.8757 (OUTLIER) cc_final: 0.7641 (pp30) REVERT: F 204 TRP cc_start: 0.8047 (p-90) cc_final: 0.7590 (p-90) REVERT: F 246 GLU cc_start: 0.8699 (OUTLIER) cc_final: 0.8192 (pm20) REVERT: F 418 ARG cc_start: 0.8770 (OUTLIER) cc_final: 0.7467 (mtm-85) REVERT: J 7 ARG cc_start: 0.8611 (OUTLIER) cc_final: 0.8123 (ptm-80) outliers start: 133 outliers final: 108 residues processed: 261 average time/residue: 0.4121 time to fit residues: 173.4741 Evaluate side-chains 262 residues out of total 2837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 134 time to evaluate : 3.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 LEU Chi-restraints excluded: chain A residue 5 GLN Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 223 ARG Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 24 GLU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 79 ASN Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 141 GLU Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 196 ASP Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 203 LYS Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 266 ASN Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 323 HIS Chi-restraints excluded: chain C residue 343 GLU Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 397 GLU Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 440 MET Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 467 ARG Chi-restraints excluded: chain C residue 532 THR Chi-restraints excluded: chain C residue 571 VAL Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 632 LEU Chi-restraints excluded: chain C residue 649 VAL Chi-restraints excluded: chain C residue 686 GLN Chi-restraints excluded: chain C residue 797 ARG Chi-restraints excluded: chain C residue 835 THR Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 881 ASP Chi-restraints excluded: chain C residue 933 GLU Chi-restraints excluded: chain C residue 950 LYS Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 991 CYS Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1057 LEU Chi-restraints excluded: chain C residue 1131 LEU Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain D residue 44 ASP Chi-restraints excluded: chain D residue 67 ARG Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 86 LYS Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 154 GLU Chi-restraints excluded: chain D residue 207 GLN Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 414 ARG Chi-restraints excluded: chain D residue 441 CYS Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain D residue 463 LEU Chi-restraints excluded: chain D residue 469 ILE Chi-restraints excluded: chain D residue 506 ARG Chi-restraints excluded: chain D residue 517 VAL Chi-restraints excluded: chain D residue 639 GLN Chi-restraints excluded: chain D residue 660 ASP Chi-restraints excluded: chain D residue 667 THR Chi-restraints excluded: chain D residue 676 LEU Chi-restraints excluded: chain D residue 677 LEU Chi-restraints excluded: chain D residue 741 ARG Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 825 THR Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 862 ASP Chi-restraints excluded: chain D residue 883 ASP Chi-restraints excluded: chain D residue 936 VAL Chi-restraints excluded: chain D residue 957 ILE Chi-restraints excluded: chain D residue 978 CYS Chi-restraints excluded: chain D residue 1025 THR Chi-restraints excluded: chain D residue 1033 GLU Chi-restraints excluded: chain D residue 1057 ASP Chi-restraints excluded: chain D residue 1061 PHE Chi-restraints excluded: chain D residue 1080 ILE Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1097 ARG Chi-restraints excluded: chain D residue 1098 VAL Chi-restraints excluded: chain D residue 1210 ILE Chi-restraints excluded: chain D residue 1238 ILE Chi-restraints excluded: chain D residue 1273 GLN Chi-restraints excluded: chain E residue 45 ASP Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain F residue 205 ASP Chi-restraints excluded: chain F residue 240 LEU Chi-restraints excluded: chain F residue 246 GLU Chi-restraints excluded: chain F residue 310 TYR Chi-restraints excluded: chain F residue 375 VAL Chi-restraints excluded: chain F residue 382 ILE Chi-restraints excluded: chain F residue 418 ARG Chi-restraints excluded: chain F residue 460 LEU Chi-restraints excluded: chain F residue 461 GLN Chi-restraints excluded: chain F residue 492 ILE Chi-restraints excluded: chain F residue 503 ILE Chi-restraints excluded: chain J residue 7 ARG Chi-restraints excluded: chain J residue 9 SER Chi-restraints excluded: chain J residue 15 SER Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 76 LYS Chi-restraints excluded: chain J residue 98 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 212 optimal weight: 3.9990 chunk 284 optimal weight: 0.6980 chunk 81 optimal weight: 3.9990 chunk 246 optimal weight: 10.0000 chunk 39 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 267 optimal weight: 0.9980 chunk 112 optimal weight: 0.7980 chunk 274 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 chunk 49 optimal weight: 3.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 775 ASN E 69 ASN F 293 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.092466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.065661 restraints weight = 66696.932| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 2.83 r_work: 0.2838 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.3004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 27833 Z= 0.238 Angle : 0.601 14.602 37955 Z= 0.305 Chirality : 0.042 0.179 4324 Planarity : 0.005 0.124 4797 Dihedral : 14.426 164.374 4515 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.05 % Favored : 92.80 % Rotamer: Outliers : 4.73 % Allowed : 16.80 % Favored : 78.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.23 % Cis-general : 0.16 % Twisted Proline : 1.16 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.15), residues: 3335 helix: 0.94 (0.16), residues: 1193 sheet: -0.80 (0.26), residues: 373 loop : -1.62 (0.14), residues: 1769 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 63 HIS 0.007 0.001 HIS E 106 PHE 0.012 0.001 PHE C 906 TYR 0.029 0.001 TYR E 56 ARG 0.003 0.000 ARG C 563 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5584.63 seconds wall clock time: 102 minutes 29.05 seconds (6149.05 seconds total)