Starting phenix.real_space_refine on Tue Feb 20 13:22:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c04_7320/02_2024/6c04_7320_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c04_7320/02_2024/6c04_7320.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c04_7320/02_2024/6c04_7320.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c04_7320/02_2024/6c04_7320.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c04_7320/02_2024/6c04_7320_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c04_7320/02_2024/6c04_7320_neut.pdb" } resolution = 3.27 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= 0.121 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 94 5.49 5 Mg 1 5.21 5 S 99 5.16 5 C 17249 2.51 5 N 4986 2.21 5 O 5551 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped 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 TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 158": "OE1" <-> "OE2" Residue "B ARG 205": "NH1" <-> "NH2" Residue "C ARG 45": "NH1" <-> "NH2" Residue "C ARG 69": "NH1" <-> "NH2" Residue "C GLU 72": "OE1" <-> "OE2" Residue "C GLU 76": "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 ASP 192": "OD1" <-> "OD2" Residue "C ARG 228": "NH1" <-> "NH2" Residue "C PHE 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 256": "OE1" <-> "OE2" Residue "C ARG 259": "NH1" <-> "NH2" Residue "C PHE 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 313": "NH1" <-> "NH2" Residue "C GLU 343": "OE1" <-> "OE2" Residue "C TYR 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 471": "OE1" <-> "OE2" Residue "C ARG 482": "NH1" <-> "NH2" Residue "C TYR 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 811": "OE1" <-> "OE2" Residue "C ARG 855": "NH1" <-> "NH2" Residue "C ARG 925": "NH1" <-> "NH2" Residue "C ASP 947": "OD1" <-> "OD2" Residue "C GLU 962": "OE1" <-> "OE2" Residue "C PHE 1063": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1067": "NH1" <-> "NH2" Residue "C TYR 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 3": "OD1" <-> "OD2" Residue "D PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 159": "NH1" <-> "NH2" Residue "D GLU 220": "OE1" <-> "OE2" Residue "D TYR 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 530": "OE1" <-> "OE2" Residue "D ARG 572": "NH1" <-> "NH2" Residue "D TYR 704": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 796": "OD1" <-> "OD2" 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 ARG 1052": "NH1" <-> "NH2" Residue "D PHE 1061": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 1103": "OD1" <-> "OD2" Residue "D GLU 1113": "OE1" <-> "OE2" Residue "D ASP 1117": "OD1" <-> "OD2" Residue "D ASP 1182": "OD1" <-> "OD2" Residue "D GLU 1199": "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 GLU 254": "OE1" <-> "OE2" 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 TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 384": "NH1" <-> "NH2" Residue "F ARG 418": "NH1" <-> "NH2" Residue "F ASP 432": "OD1" <-> "OD2" Residue "F ASP 449": "OD1" <-> "OD2" Residue "F PHE 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 500": "NH1" <-> "NH2" Residue "F GLU 501": "OE1" <-> "OE2" Residue "F ARG 524": "NH1" <-> "NH2" Residue "J GLU 95": "OE1" <-> "OE2" Residue "J ARG 109": "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: 27982 Number of models: 1 Model: "" Number of chains: 12 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: 8585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1111, 8585 Classifications: {'peptide': 1111} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 60, 'TRANS': 1047} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 35 Chain: "D" Number of atoms: 9881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1267, 9881 Classifications: {'peptide': 1267} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 57, 'TRANS': 1205} 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: 2508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2508 Classifications: {'peptide': 319} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 8, 'TRANS': 310} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 28 Chain: "J" Number of atoms: 881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 881 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 100} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 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: "G" Number of atoms: 362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 362 Classifications: {'DNA': 18} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 17} Chain: "H" Number of atoms: 454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 454 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 19148 SG CYS D 891 110.170 98.088 101.242 1.00 65.59 S ATOM 19715 SG CYS D 968 106.556 98.505 100.222 1.00 61.83 S ATOM 19757 SG CYS D 975 107.695 95.793 103.719 1.00 58.39 S ATOM 19775 SG CYS D 978 107.754 99.698 103.398 1.00 56.44 S ATOM 12590 SG CYS D 60 72.528 58.187 61.442 1.00 81.27 S ATOM 12608 SG CYS D 62 70.655 57.237 58.467 1.00 83.22 S ATOM 12717 SG CYS D 75 74.308 58.015 58.106 1.00 79.56 S ATOM 12743 SG CYS D 78 73.059 61.297 58.990 1.00 78.56 S Time building chain proxies: 14.34, per 1000 atoms: 0.51 Number of scatterers: 27982 At special positions: 0 Unit cell: (129.8, 162.8, 189.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 99 16.00 P 94 15.00 Mg 1 11.99 O 5551 8.00 N 4986 7.00 C 17249 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: 11.37 Conformation dependent library (CDL) restraints added in 4.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D2000 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 978 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 968 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 975 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 891 " pdb=" ZN D2001 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 78 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 60 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 75 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 62 " Number of angles added : 12 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6172 Finding SS restraints... Secondary structure from input PDB file: 113 helices and 41 sheets defined 39.2% alpha, 13.9% beta 39 base pairs and 78 stacking pairs defined. Time for finding SS restraints: 9.17 Creating SS restraints... Processing helix chain 'A' and resid 30 through 43 removed outlier: 3.510A pdb=" N LEU A 34 " --> pdb=" O PHE A 30 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N THR A 41 " --> pdb=" O SER A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 81 Processing helix chain 'A' and resid 108 through 110 No H-bonds generated for 'chain 'A' and resid 108 through 110' Processing helix chain 'A' and resid 203 through 220 removed outlier: 3.899A pdb=" N SER A 210 " --> pdb=" O ASP A 206 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA A 211 " --> pdb=" O ALA A 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 45 removed outlier: 3.708A pdb=" N LEU B 34 " --> pdb=" O PHE B 30 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ASN B 36 " --> pdb=" O TYR B 32 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N SER B 37 " --> pdb=" O THR B 33 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N SER B 45 " --> pdb=" O THR B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 77 Processing helix chain 'B' and resid 108 through 110 No H-bonds generated for 'chain 'B' and resid 108 through 110' Processing helix chain 'B' and resid 205 through 217 removed outlier: 3.605A pdb=" N ALA B 209 " --> pdb=" O ARG B 205 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER B 210 " --> pdb=" O ASP B 206 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ALA B 211 " --> pdb=" O ALA B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 224 Processing helix chain 'C' and resid 54 through 66 removed outlier: 4.171A pdb=" N SER C 60 " --> pdb=" O VAL C 56 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU C 64 " --> pdb=" O SER C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 76 removed outlier: 3.950A pdb=" N ALA C 75 " --> pdb=" O ARG C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 94 removed outlier: 3.789A pdb=" N VAL C 89 " --> pdb=" O GLY C 85 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU C 92 " --> pdb=" O GLU C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 125 Processing helix chain 'C' and resid 233 through 241 removed outlier: 3.697A pdb=" N LEU C 237 " --> pdb=" O PRO C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 252 Processing helix chain 'C' and resid 257 through 264 Processing helix chain 'C' and resid 270 through 282 removed outlier: 3.711A pdb=" N ASP C 276 " --> pdb=" O GLU C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 294 removed outlier: 3.991A pdb=" N GLN C 293 " --> pdb=" O LYS C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 299 removed outlier: 3.710A pdb=" N LEU C 299 " --> pdb=" O LEU C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 311 through 321 Processing helix chain 'C' and resid 334 through 347 removed outlier: 3.925A pdb=" N VAL C 338 " --> pdb=" O THR C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 401 removed outlier: 3.560A pdb=" N LEU C 384 " --> pdb=" O THR C 380 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ARG C 395 " --> pdb=" O VAL C 391 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG C 398 " --> pdb=" O SER C 394 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N VAL C 399 " --> pdb=" O ARG C 395 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL C 400 " --> pdb=" O MET C 396 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG C 401 " --> pdb=" O GLU C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 418 removed outlier: 3.815A pdb=" N LEU C 417 " --> pdb=" O THR C 413 " (cutoff:3.500A) Processing helix chain 'C' and resid 420 through 432 Processing helix chain 'C' and resid 444 through 452 removed outlier: 3.806A pdb=" N LYS C 452 " --> pdb=" O GLY C 448 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 480 removed outlier: 3.967A pdb=" N TYR C 480 " --> pdb=" O PRO C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 537 removed outlier: 4.273A pdb=" N ASP C 537 " --> pdb=" O ALA C 533 " (cutoff:3.500A) Processing helix chain 'C' and resid 590 through 594 removed outlier: 3.510A pdb=" N MET C 593 " --> pdb=" O ALA C 590 " (cutoff:3.500A) Processing helix chain 'C' and resid 596 through 600 removed outlier: 3.743A pdb=" N HIS C 599 " --> pdb=" O PHE C 596 " (cutoff:3.500A) Processing helix chain 'C' and resid 601 through 611 Processing helix chain 'C' and resid 632 through 637 removed outlier: 3.793A pdb=" N ILE C 636 " --> pdb=" O LEU C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 739 through 744 Processing helix chain 'C' and resid 815 through 826 removed outlier: 3.604A pdb=" N PHE C 825 " --> pdb=" O LEU C 821 " (cutoff:3.500A) Processing helix chain 'C' and resid 928 through 943 removed outlier: 3.770A pdb=" N THR C 934 " --> pdb=" O GLN C 930 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TRP C 938 " --> pdb=" O THR C 934 " (cutoff:3.500A) Processing helix chain 'C' and resid 954 through 958 removed outlier: 3.601A pdb=" N ALA C 957 " --> pdb=" O ASP C 954 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ARG C 958 " --> pdb=" O TRP C 955 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 954 through 958' Processing helix chain 'C' and resid 981 through 989 removed outlier: 3.868A pdb=" N GLN C 986 " --> pdb=" O GLU C 982 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLY C 987 " --> pdb=" O ALA C 983 " (cutoff:3.500A) Processing helix chain 'C' and resid 1036 through 1040 removed outlier: 3.600A pdb=" N ASP C1039 " --> pdb=" O LEU C1036 " (cutoff:3.500A) Processing helix chain 'C' and resid 1069 through 1080 removed outlier: 3.758A pdb=" N CYS C1073 " --> pdb=" O GLY C1069 " (cutoff:3.500A) Processing helix chain 'C' and resid 1081 through 1090 removed outlier: 3.748A pdb=" N LEU C1085 " --> pdb=" O ALA C1081 " (cutoff:3.500A) Processing helix chain 'C' and resid 1095 through 1109 removed outlier: 4.261A pdb=" N VAL C1100 " --> pdb=" O THR C1096 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS C1101 " --> pdb=" O VAL C1097 " (cutoff:3.500A) Processing helix chain 'C' and resid 1120 through 1130 removed outlier: 3.795A pdb=" N LEU C1124 " --> pdb=" O SER C1120 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS C1126 " --> pdb=" O LYS C1122 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 24 removed outlier: 3.675A pdb=" N GLN D 22 " --> pdb=" O GLU D 18 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 53 Processing helix chain 'D' and resid 104 through 107 Processing helix chain 'D' and resid 112 through 119 Processing helix chain 'D' and resid 121 through 130 removed outlier: 3.703A pdb=" N LYS D 127 " --> pdb=" O LYS D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 147 Processing helix chain 'D' and resid 147 through 184 Processing helix chain 'D' and resid 190 through 228 removed outlier: 3.827A pdb=" N ARG D 194 " --> pdb=" O LYS D 190 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N TRP D 223 " --> pdb=" O LEU D 219 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS D 228 " --> pdb=" O SER D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 239 through 247 Processing helix chain 'D' and resid 257 through 267 Processing helix chain 'D' and resid 269 through 284 removed outlier: 3.584A pdb=" N GLU D 273 " --> pdb=" O ASP D 269 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE D 281 " --> pdb=" O LEU D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 305 removed outlier: 4.323A pdb=" N LYS D 294 " --> pdb=" O LEU D 290 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N VAL D 298 " --> pdb=" O LYS D 294 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N SER D 305 " --> pdb=" O ALA D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 311 removed outlier: 3.659A pdb=" N GLY D 311 " --> pdb=" O SER D 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 308 through 311' Processing helix chain 'D' and resid 340 through 361 removed outlier: 3.659A pdb=" N ASP D 359 " --> pdb=" O LYS D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 383 removed outlier: 3.555A pdb=" N VAL D 367 " --> pdb=" O PRO D 363 " (cutoff:3.500A) Processing helix chain 'D' and resid 402 through 406 Processing helix chain 'D' and resid 407 through 410 removed outlier: 4.019A pdb=" N GLN D 410 " --> pdb=" O LYS D 407 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 407 through 410' Processing helix chain 'D' and resid 411 through 416 Processing helix chain 'D' and resid 445 through 452 Processing helix chain 'D' and resid 452 through 463 removed outlier: 4.205A pdb=" N VAL D 461 " --> pdb=" O MET D 457 " (cutoff:3.500A) Processing helix chain 'D' and resid 468 through 478 Processing helix chain 'D' and resid 482 through 492 removed outlier: 3.779A pdb=" N VAL D 486 " --> pdb=" O GLN D 482 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU D 488 " --> pdb=" O TRP D 484 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLU D 489 " --> pdb=" O ASP D 485 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA D 492 " --> pdb=" O GLU D 488 " (cutoff:3.500A) Processing helix chain 'D' and resid 505 through 507 No H-bonds generated for 'chain 'D' and resid 505 through 507' Processing helix chain 'D' and resid 528 through 533 Processing helix chain 'D' and resid 548 through 558 Processing helix chain 'D' and resid 578 through 589 removed outlier: 3.984A pdb=" N THR D 583 " --> pdb=" O LEU D 579 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 624 removed outlier: 3.578A pdb=" N ARG D 624 " --> pdb=" O MET D 620 " (cutoff:3.500A) Processing helix chain 'D' and resid 643 through 651 removed outlier: 3.798A pdb=" N GLU D 649 " --> pdb=" O GLU D 645 " (cutoff:3.500A) Processing helix chain 'D' and resid 668 through 675 Processing helix chain 'D' and resid 689 through 704 removed outlier: 3.837A pdb=" N GLN D 693 " --> pdb=" O HIS D 689 " (cutoff:3.500A) Processing helix chain 'D' and resid 705 through 725 removed outlier: 3.569A pdb=" N VAL D 709 " --> pdb=" O PRO D 705 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ALA D 710 " --> pdb=" O MET D 706 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLN D 711 " --> pdb=" O ILE D 707 " (cutoff:3.500A) Processing helix chain 'D' and resid 741 through 763 removed outlier: 3.722A pdb=" N ILE D 745 " --> pdb=" O ARG D 741 " (cutoff:3.500A) Processing helix chain 'D' and resid 766 through 793 Processing helix chain 'D' and resid 797 through 805 removed outlier: 3.908A pdb=" N ILE D 802 " --> pdb=" O PRO D 798 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N VAL D 803 " --> pdb=" O ILE D 799 " (cutoff:3.500A) Processing helix chain 'D' and resid 810 through 818 removed outlier: 4.132A pdb=" N THR D 814 " --> pdb=" O ASN D 810 " (cutoff:3.500A) Processing helix chain 'D' and resid 845 through 881 removed outlier: 4.200A pdb=" N HIS D 854 " --> pdb=" O PHE D 850 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N GLY D 855 " --> pdb=" O ILE D 851 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LEU D 860 " --> pdb=" O ALA D 856 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLY D 871 " --> pdb=" O THR D 867 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N TYR D 872 " --> pdb=" O ALA D 868 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU D 873 " --> pdb=" O ASP D 869 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER D 881 " --> pdb=" O LEU D 877 " (cutoff:3.500A) Processing helix chain 'D' and resid 945 through 955 Processing helix chain 'D' and resid 976 through 980 Processing helix chain 'D' and resid 994 through 1005 removed outlier: 3.618A pdb=" N ILE D1003 " --> pdb=" O ALA D 999 " (cutoff:3.500A) Processing helix chain 'D' and resid 1006 through 1010 removed outlier: 3.622A pdb=" N LEU D1010 " --> pdb=" O GLY D1007 " (cutoff:3.500A) Processing helix chain 'D' and resid 1027 through 1036 removed outlier: 3.523A pdb=" N VAL D1031 " --> pdb=" O GLY D1027 " (cutoff:3.500A) Processing helix chain 'D' and resid 1117 through 1126 removed outlier: 3.624A pdb=" N VAL D1121 " --> pdb=" O ASP D1117 " (cutoff:3.500A) Processing helix chain 'D' and resid 1126 through 1144 removed outlier: 3.914A pdb=" N ILE D1132 " --> pdb=" O ARG D1128 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N VAL D1141 " --> pdb=" O GLU D1137 " (cutoff:3.500A) Processing helix chain 'D' and resid 1150 through 1160 removed outlier: 4.144A pdb=" N ILE D1154 " --> pdb=" O HIS D1150 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLN D1160 " --> pdb=" O VAL D1156 " (cutoff:3.500A) Processing helix chain 'D' and resid 1183 through 1192 Processing helix chain 'D' and resid 1193 through 1195 No H-bonds generated for 'chain 'D' and resid 1193 through 1195' Processing helix chain 'D' and resid 1209 through 1216 Processing helix chain 'D' and resid 1220 through 1225 removed outlier: 3.755A pdb=" N SER D1225 " --> pdb=" O LEU D1221 " (cutoff:3.500A) Processing helix chain 'D' and resid 1228 through 1237 removed outlier: 3.897A pdb=" N ASP D1235 " --> pdb=" O ARG D1231 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA D1237 " --> pdb=" O LEU D1233 " (cutoff:3.500A) Processing helix chain 'D' and resid 1249 through 1255 Processing helix chain 'D' and resid 1264 through 1269 Processing helix chain 'D' and resid 1275 through 1281 Processing helix chain 'E' and resid 33 through 37 removed outlier: 3.895A pdb=" N THR E 36 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ASN E 37 " --> pdb=" O GLY E 34 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 33 through 37' Processing helix chain 'E' and resid 49 through 70 removed outlier: 3.649A pdb=" N LEU E 53 " --> pdb=" O SER E 49 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL E 54 " --> pdb=" O LYS E 50 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ASN E 69 " --> pdb=" O ASN E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 101 Processing helix chain 'F' and resid 226 through 236 Processing helix chain 'F' and resid 244 through 266 removed outlier: 3.857A pdb=" N GLU F 248 " --> pdb=" O GLU F 244 " (cutoff:3.500A) Processing helix chain 'F' and resid 274 through 308 removed outlier: 3.518A pdb=" N ARG F 290 " --> pdb=" O ARG F 286 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA F 291 " --> pdb=" O ASP F 287 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LYS F 292 " --> pdb=" O GLY F 288 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ASN F 293 " --> pdb=" O ASP F 289 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LEU F 296 " --> pdb=" O LYS F 292 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N ARG F 301 " --> pdb=" O GLU F 297 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N LEU F 302 " --> pdb=" O ALA F 298 " (cutoff:3.500A) Processing helix chain 'F' and resid 316 through 334 Processing helix chain 'F' and resid 336 through 340 removed outlier: 3.833A pdb=" N LYS F 339 " --> pdb=" O ASP F 336 " (cutoff:3.500A) Processing helix chain 'F' and resid 342 through 362 removed outlier: 3.926A pdb=" N TYR F 346 " --> pdb=" O LYS F 342 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N TRP F 349 " --> pdb=" O THR F 345 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N TRP F 350 " --> pdb=" O TYR F 346 " (cutoff:3.500A) Processing helix chain 'F' and resid 369 through 391 Processing helix chain 'F' and resid 395 through 404 removed outlier: 3.632A pdb=" N LYS F 401 " --> pdb=" O GLU F 397 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLU F 402 " --> pdb=" O GLU F 398 " (cutoff:3.500A) Processing helix chain 'F' and resid 406 through 415 removed outlier: 3.530A pdb=" N VAL F 410 " --> pdb=" O THR F 406 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU F 411 " --> pdb=" O PRO F 407 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLU F 412 " --> pdb=" O GLU F 408 " (cutoff:3.500A) Processing helix chain 'F' and resid 434 through 438 removed outlier: 3.726A pdb=" N ASP F 437 " --> pdb=" O GLN F 434 " (cutoff:3.500A) Processing helix chain 'F' and resid 449 through 465 removed outlier: 3.554A pdb=" N THR F 454 " --> pdb=" O ALA F 450 " (cutoff:3.500A) Processing helix chain 'F' and resid 468 through 479 removed outlier: 3.760A pdb=" N ALA F 472 " --> pdb=" O SER F 468 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLY F 473 " --> pdb=" O GLU F 469 " (cutoff:3.500A) Processing helix chain 'F' and resid 488 through 497 removed outlier: 3.650A pdb=" N VAL F 495 " --> pdb=" O GLU F 491 " (cutoff:3.500A) Processing helix chain 'F' and resid 499 through 515 removed outlier: 3.580A pdb=" N SER F 512 " --> pdb=" O SER F 508 " (cutoff:3.500A) Processing helix chain 'F' and resid 516 through 525 removed outlier: 5.082A pdb=" N VAL F 522 " --> pdb=" O SER F 518 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N LEU F 523 " --> pdb=" O ARG F 519 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ASP F 525 " --> pdb=" O GLN F 521 " (cutoff:3.500A) Processing helix chain 'J' and resid 81 through 87 Processing helix chain 'J' and resid 90 through 111 removed outlier: 3.501A pdb=" N LYS J 99 " --> pdb=" O GLU J 95 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N GLU J 100 " --> pdb=" O GLU J 96 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG J 109 " --> pdb=" O ILE J 105 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ARG J 110 " --> pdb=" O ARG J 106 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 13 removed outlier: 5.916A pdb=" N ASP A 190 " --> pdb=" O PRO A 25 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N LYS A 191 " --> pdb=" O VAL A 178 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N VAL A 178 " --> pdb=" O LYS A 191 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ILE A 193 " --> pdb=" O TYR A 176 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N TYR A 176 " --> pdb=" O ILE A 193 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ASP A 195 " --> pdb=" O VAL A 174 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N VAL A 174 " --> pdb=" O ASP A 195 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLU A 197 " --> pdb=" O LEU A 172 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 100 removed outlier: 7.577A pdb=" N GLU A 135 " --> pdb=" O ILE A 56 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N ILE A 56 " --> pdb=" O GLU A 135 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N GLU A 137 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ILE A 54 " --> pdb=" O GLU A 137 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N VAL A 139 " --> pdb=" O THR A 52 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 85 through 86 removed outlier: 3.508A pdb=" N THR A 117 " --> pdb=" O SER A 86 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 103 through 106 Processing sheet with id=AA5, first strand: chain 'A' and resid 145 through 147 Processing sheet with id=AA6, first strand: chain 'B' and resid 8 through 12 removed outlier: 3.632A pdb=" N GLU B 24 " --> pdb=" O THR B 8 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL B 22 " --> pdb=" O SER B 10 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N ASP B 190 " --> pdb=" O PRO B 25 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N LYS B 191 " --> pdb=" O VAL B 178 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N VAL B 178 " --> pdb=" O LYS B 191 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ILE B 193 " --> pdb=" O TYR B 176 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N TYR B 176 " --> pdb=" O ILE B 193 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ASP B 195 " --> pdb=" O VAL B 174 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N VAL B 174 " --> pdb=" O ASP B 195 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N GLU B 197 " --> pdb=" O LEU B 172 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 93 through 99 removed outlier: 7.889A pdb=" N GLU B 135 " --> pdb=" O ILE B 56 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N ILE B 56 " --> pdb=" O GLU B 135 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N GLU B 137 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ILE B 54 " --> pdb=" O GLU B 137 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N VAL B 139 " --> pdb=" O THR B 52 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 85 through 86 Processing sheet with id=AA9, first strand: chain 'B' and resid 103 through 106 Processing sheet with id=AB1, first strand: chain 'B' and resid 146 through 147 removed outlier: 3.543A pdb=" N SER B 166 " --> pdb=" O VAL B 147 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 39 through 40 removed outlier: 6.455A pdb=" N VAL C 39 " --> pdb=" O SER C 973 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY C 627 " --> pdb=" O VAL C 972 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 96 through 97 removed outlier: 5.496A pdb=" N LEU C 105 " --> pdb=" O ILE C 140 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N ILE C 140 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N PHE C 107 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N GLU C 138 " --> pdb=" O PHE C 107 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N ASP C 109 " --> pdb=" O THR C 136 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N THR C 136 " --> pdb=" O ASP C 109 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N ALA C 131 " --> pdb=" O ASP C 156 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ASP C 156 " --> pdb=" O ALA C 131 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N LEU C 133 " --> pdb=" O MET C 154 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 166 through 168 Processing sheet with id=AB5, first strand: chain 'C' and resid 376 through 379 Processing sheet with id=AB6, first strand: chain 'C' and resid 184 through 191 Processing sheet with id=AB7, first strand: chain 'C' and resid 354 through 355 Processing sheet with id=AB8, first strand: chain 'C' and resid 505 through 506 removed outlier: 3.650A pdb=" N LYS C 518 " --> pdb=" O GLU C 527 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N GLU C 527 " --> pdb=" O LYS C 518 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N VAL C 520 " --> pdb=" O SER C 525 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N SER C 525 " --> pdb=" O VAL C 520 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 505 through 506 Processing sheet with id=AC1, first strand: chain 'C' and resid 541 through 542 removed outlier: 3.510A pdb=" N VAL C 541 " --> pdb=" O ARG C 562 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N VAL C 561 " --> pdb=" O GLU C 569 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 548 through 549 removed outlier: 4.400A pdb=" N ARG C 553 " --> pdb=" O ASP C 549 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 642 through 643 removed outlier: 6.662A pdb=" N VAL C 642 " --> pdb=" O ILE C 702 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 648 through 654 removed outlier: 5.608A pdb=" N ILE C 650 " --> pdb=" O MET C 661 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N MET C 661 " --> pdb=" O ILE C 650 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 708 through 709 Processing sheet with id=AC6, first strand: chain 'C' and resid 1007 through 1008 removed outlier: 7.609A pdb=" N LEU C 737 " --> pdb=" O GLY C 896 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N ILE C 898 " --> pdb=" O LEU C 737 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ILE C 736 " --> pdb=" O ILE C 916 " (cutoff:3.500A) removed outlier: 8.426A pdb=" N ILE C 915 " --> pdb=" O ASN C 718 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N LEU C 720 " --> pdb=" O ILE C 915 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 765 through 766 removed outlier: 3.536A pdb=" N GLY C 765 " --> pdb=" O THR C 762 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ASP C 761 " --> pdb=" O VAL C 865 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N VAL C 865 " --> pdb=" O ASP C 761 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLY C 849 " --> pdb=" O TYR C 872 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ALA C 874 " --> pdb=" O VAL C 847 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N VAL C 847 " --> pdb=" O ALA C 874 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 768 through 769 Processing sheet with id=AC9, first strand: chain 'C' and resid 801 through 803 removed outlier: 6.584A pdb=" N LEU C 837 " --> pdb=" O LEU C 802 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 1042 through 1044 removed outlier: 6.306A pdb=" N CYS D 441 " --> pdb=" O MET D 515 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL D 517 " --> pdb=" O CYS D 441 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N LEU D 443 " --> pdb=" O VAL D 517 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 1042 through 1044 Processing sheet with id=AD3, first strand: chain 'C' and resid 1067 through 1068 Processing sheet with id=AD4, first strand: chain 'C' and resid 1136 through 1138 Processing sheet with id=AD5, first strand: chain 'D' and resid 94 through 102 removed outlier: 10.477A pdb=" N LEU D 97 " --> pdb=" O PRO D 318 " (cutoff:3.500A) removed outlier: 10.637A pdb=" N ALA D 99 " --> pdb=" O ALA D 316 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N ALA D 316 " --> pdb=" O ALA D 99 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 135 through 139 removed outlier: 6.643A pdb=" N THR D 253 " --> pdb=" O THR D 137 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 334 through 337 removed outlier: 3.631A pdb=" N SER J 9 " --> pdb=" O GLN D 329 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 632 through 637 Processing sheet with id=AD9, first strand: chain 'D' and resid 886 through 888 Processing sheet with id=AE1, first strand: chain 'D' and resid 897 through 899 removed outlier: 3.956A pdb=" N VAL D 960 " --> pdb=" O VAL D 899 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N THR D 924 " --> pdb=" O ARG D 963 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 1075 through 1077 Processing sheet with id=AE3, first strand: chain 'D' and resid 1180 through 1182 removed outlier: 4.731A pdb=" N ARG D1164 " --> pdb=" O VAL D1206 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ALA D1202 " --> pdb=" O ILE D1168 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 1271 through 1274 Processing sheet with id=AE5, first strand: chain 'J' and resid 39 through 45 993 hydrogen bonds defined for protein. 2808 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 89 hydrogen bonds 178 hydrogen bond angles 0 basepair planarities 39 basepair parallelities 78 stacking parallelities Total time for adding SS restraints: 12.29 Time building geometry restraints manager: 11.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.06 - 1.21: 81 1.21 - 1.36: 9496 1.36 - 1.51: 9777 1.51 - 1.66: 9122 1.66 - 1.81: 175 Bond restraints: 28651 Sorted by residual: bond pdb=" C MET D 92 " pdb=" O MET D 92 " ideal model delta sigma weight residual 1.235 1.066 0.169 1.26e-02 6.30e+03 1.80e+02 bond pdb=" C ARG D 88 " pdb=" O ARG D 88 " ideal model delta sigma weight residual 1.236 1.060 0.176 1.32e-02 5.74e+03 1.78e+02 bond pdb=" C PHE D 52 " pdb=" O PHE D 52 " ideal model delta sigma weight residual 1.236 1.072 0.165 1.32e-02 5.74e+03 1.56e+02 bond pdb=" C VAL B 147 " pdb=" O VAL B 147 " ideal model delta sigma weight residual 1.241 1.094 0.146 1.22e-02 6.72e+03 1.44e+02 bond pdb=" C ILE D 51 " pdb=" O ILE D 51 " ideal model delta sigma weight residual 1.234 1.114 0.120 1.09e-02 8.42e+03 1.21e+02 ... (remaining 28646 not shown) Histogram of bond angle deviations from ideal: 74.89 - 95.91: 6 95.91 - 116.92: 20754 116.92 - 137.93: 18454 137.93 - 158.94: 3 158.94 - 179.95: 1 Bond angle restraints: 39218 Sorted by residual: angle pdb=" C PRO J 77 " pdb=" N PRO J 78 " pdb=" CA PRO J 78 " ideal model delta sigma weight residual 119.84 179.95 -60.11 1.25e+00 6.40e-01 2.31e+03 angle pdb=" N THR D1011 " pdb=" CA THR D1011 " pdb=" C THR D1011 " ideal model delta sigma weight residual 111.28 125.95 -14.67 1.09e+00 8.42e-01 1.81e+02 angle pdb=" C ALA J 25 " pdb=" N PRO J 26 " pdb=" CA PRO J 26 " ideal model delta sigma weight residual 119.85 132.28 -12.43 1.01e+00 9.80e-01 1.52e+02 angle pdb=" C PRO J 77 " pdb=" N PRO J 78 " pdb=" CD PRO J 78 " ideal model delta sigma weight residual 125.00 74.89 50.11 4.10e+00 5.95e-02 1.49e+02 angle pdb=" N LYS C 148 " pdb=" CA LYS C 148 " pdb=" C LYS C 148 " ideal model delta sigma weight residual 108.34 89.72 18.62 1.64e+00 3.72e-01 1.29e+02 ... (remaining 39213 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.86: 16311 35.86 - 71.72: 981 71.72 - 107.58: 21 107.58 - 143.44: 0 143.44 - 179.31: 3 Dihedral angle restraints: 17316 sinusoidal: 7720 harmonic: 9596 Sorted by residual: dihedral pdb=" CA ASP D 907 " pdb=" C ASP D 907 " pdb=" N GLY D 908 " pdb=" CA GLY D 908 " ideal model delta harmonic sigma weight residual 180.00 102.21 77.79 0 5.00e+00 4.00e-02 2.42e+02 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 -125.63 -54.37 0 5.00e+00 4.00e-02 1.18e+02 dihedral pdb=" CA ALA D 933 " pdb=" C ALA D 933 " pdb=" N GLY D 934 " pdb=" CA GLY D 934 " ideal model delta harmonic sigma weight residual 180.00 134.00 46.00 0 5.00e+00 4.00e-02 8.46e+01 ... (remaining 17313 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.188: 4411 0.188 - 0.376: 38 0.376 - 0.564: 12 0.564 - 0.752: 3 0.752 - 0.940: 1 Chirality restraints: 4465 Sorted by residual: chirality pdb=" CA ASN J 21 " pdb=" N ASN J 21 " pdb=" C ASN J 21 " pdb=" CB ASN J 21 " both_signs ideal model delta sigma weight residual False 2.51 1.57 0.94 2.00e-01 2.50e+01 2.21e+01 chirality pdb=" CA GLU D 90 " pdb=" N GLU D 90 " pdb=" C GLU D 90 " pdb=" CB GLU D 90 " both_signs ideal model delta sigma weight residual False 2.51 1.81 0.70 2.00e-01 2.50e+01 1.21e+01 chirality pdb=" CA THR D1011 " pdb=" N THR D1011 " pdb=" C THR D1011 " pdb=" CB THR D1011 " both_signs ideal model delta sigma weight residual False 2.53 1.90 0.62 2.00e-01 2.50e+01 9.76e+00 ... (remaining 4462 not shown) Planarity restraints: 4824 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR E 68 " 0.027 2.00e-02 2.50e+03 5.37e-02 2.89e+01 pdb=" C TYR E 68 " -0.093 2.00e-02 2.50e+03 pdb=" O TYR E 68 " 0.034 2.00e-02 2.50e+03 pdb=" N ASN E 69 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR C 807 " 0.069 5.00e-02 4.00e+02 1.05e-01 1.78e+01 pdb=" N PRO C 808 " -0.182 5.00e-02 4.00e+02 pdb=" CA PRO C 808 " 0.057 5.00e-02 4.00e+02 pdb=" CD PRO C 808 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN D 600 " 0.066 5.00e-02 4.00e+02 1.02e-01 1.66e+01 pdb=" N PRO D 601 " -0.176 5.00e-02 4.00e+02 pdb=" CA PRO D 601 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO D 601 " 0.054 5.00e-02 4.00e+02 ... (remaining 4821 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 167 2.46 - 3.07: 16902 3.07 - 3.68: 41810 3.68 - 4.29: 59926 4.29 - 4.90: 100066 Nonbonded interactions: 218871 Sorted by model distance: nonbonded pdb=" N GLU J 17 " pdb=" OE1 GLU J 17 " model vdw 1.850 2.520 nonbonded pdb=" N LEU D1055 " pdb=" OD2 ASP D1101 " model vdw 1.863 2.520 nonbonded pdb=" N GLU F 210 " pdb=" OE1 GLU F 210 " model vdw 1.863 2.520 nonbonded pdb=" NZ LYS C 809 " pdb=" O GLU C 831 " model vdw 1.899 2.520 nonbonded pdb=" CE2 PHE D1089 " pdb=" NE2 GLN D1109 " model vdw 1.915 3.420 ... (remaining 218866 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: 0.010 Normalize map: mean=0, sd=1: 1.310 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: 7.100 Check model and map are aligned: 0.440 Set scattering table: 0.260 Process input model: 83.140 Find NCS groups from input model: 0.990 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 96.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 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 : 0.011 0.176 28651 Z= 0.705 Angle : 1.132 60.109 39218 Z= 0.678 Chirality : 0.066 0.940 4465 Planarity : 0.008 0.105 4824 Dihedral : 19.081 179.306 11144 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.45 % Allowed : 7.98 % Favored : 91.57 % Rotamer: Outliers : 14.33 % Allowed : 11.90 % Favored : 73.77 % Cbeta Deviations : 0.65 % Peptide Plane: Cis-proline : 5.23 % Cis-general : 0.09 % Twisted Proline : 0.58 % Twisted General : 0.19 % 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: -4.23 (0.11), residues: 3333 helix: -3.06 (0.10), residues: 1249 sheet: -1.91 (0.23), residues: 425 loop : -2.83 (0.12), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP J 82 HIS 0.017 0.001 HIS J 22 PHE 0.032 0.003 PHE D 52 TYR 0.022 0.002 TYR A 168 ARG 0.024 0.001 ARG D 88 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 695 residues out of total 2833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 400 poor density : 295 time to evaluate : 3.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 ASP cc_start: 0.8422 (OUTLIER) cc_final: 0.8088 (p0) REVERT: B 32 TYR cc_start: 0.9199 (m-80) cc_final: 0.8921 (m-80) REVERT: B 36 ASN cc_start: 0.8421 (t0) cc_final: 0.8135 (t0) REVERT: B 70 LYS cc_start: 0.8280 (OUTLIER) cc_final: 0.8044 (mptt) REVERT: B 123 MET cc_start: 0.8917 (OUTLIER) cc_final: 0.8709 (ttt) REVERT: B 142 ARG cc_start: 0.8417 (OUTLIER) cc_final: 0.6342 (mtp180) REVERT: B 144 ARG cc_start: 0.9354 (OUTLIER) cc_final: 0.8557 (mtt-85) REVERT: B 177 LYS cc_start: 0.8511 (OUTLIER) cc_final: 0.8280 (ptmm) REVERT: B 213 LYS cc_start: 0.8263 (ttpp) cc_final: 0.8026 (tttp) REVERT: C 81 ASN cc_start: 0.6684 (OUTLIER) cc_final: 0.5815 (p0) REVERT: C 127 MET cc_start: 0.8687 (ptp) cc_final: 0.8425 (ptp) REVERT: C 285 GLU cc_start: 0.5986 (OUTLIER) cc_final: 0.5323 (mm-30) REVERT: C 421 ARG cc_start: 0.8357 (OUTLIER) cc_final: 0.8022 (tmm-80) REVERT: C 673 ARG cc_start: 0.8399 (OUTLIER) cc_final: 0.7965 (ptm160) REVERT: C 797 ARG cc_start: 0.8200 (OUTLIER) cc_final: 0.7968 (ptm-80) REVERT: C 1101 LYS cc_start: 0.9018 (OUTLIER) cc_final: 0.8713 (mtmt) REVERT: D 1 MET cc_start: 0.7238 (pmm) cc_final: 0.6589 (ppp) REVERT: D 67 ARG cc_start: 0.7835 (OUTLIER) cc_final: 0.7353 (tpm170) REVERT: D 143 MET cc_start: 0.7105 (mtp) cc_final: 0.6875 (ttm) REVERT: D 147 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.7096 (mp0) REVERT: D 155 MET cc_start: 0.7768 (tpt) cc_final: 0.7280 (tpp) REVERT: D 206 ARG cc_start: 0.5779 (OUTLIER) cc_final: 0.5242 (ttm-80) REVERT: D 211 ARG cc_start: 0.7550 (ttm170) cc_final: 0.6882 (ttp80) REVERT: D 214 ARG cc_start: 0.7762 (ttp-110) cc_final: 0.7520 (ttp-110) REVERT: D 219 LEU cc_start: 0.8195 (OUTLIER) cc_final: 0.7737 (mm) REVERT: D 225 THR cc_start: 0.8280 (m) cc_final: 0.8044 (p) REVERT: D 251 TYR cc_start: 0.8070 (m-80) cc_final: 0.7866 (m-80) REVERT: D 449 LEU cc_start: 0.9239 (OUTLIER) cc_final: 0.9008 (tp) REVERT: D 504 LEU cc_start: 0.9282 (OUTLIER) cc_final: 0.9005 (mp) REVERT: D 506 ARG cc_start: 0.9277 (OUTLIER) cc_final: 0.8946 (ptt180) REVERT: D 636 ARG cc_start: 0.8728 (OUTLIER) cc_final: 0.8129 (ttt180) REVERT: D 638 THR cc_start: 0.9156 (p) cc_final: 0.8927 (t) REVERT: D 639 GLN cc_start: 0.9032 (OUTLIER) cc_final: 0.8762 (tp40) REVERT: D 795 ASP cc_start: 0.8463 (OUTLIER) cc_final: 0.8174 (m-30) REVERT: D 862 ASP cc_start: 0.7657 (OUTLIER) cc_final: 0.7423 (t0) REVERT: D 865 LEU cc_start: 0.8242 (OUTLIER) cc_final: 0.7935 (mp) REVERT: D 1012 MET cc_start: 0.6422 (ttt) cc_final: 0.6103 (ttp) REVERT: D 1024 ILE cc_start: 0.6636 (OUTLIER) cc_final: 0.6116 (tp) REVERT: D 1120 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7826 (mt-10) REVERT: D 1189 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7737 (mm-30) REVERT: D 1191 ARG cc_start: 0.8235 (OUTLIER) cc_final: 0.7849 (mtt180) REVERT: D 1249 LYS cc_start: 0.9238 (OUTLIER) cc_final: 0.8477 (ttpp) REVERT: F 397 GLU cc_start: 0.7370 (OUTLIER) cc_final: 0.7148 (pp20) REVERT: F 429 ASP cc_start: 0.6828 (OUTLIER) cc_final: 0.6379 (t0) REVERT: F 511 MET cc_start: 0.8525 (mmm) cc_final: 0.8157 (tpp) REVERT: J 10 ARG cc_start: 0.9174 (OUTLIER) cc_final: 0.8653 (ptt-90) REVERT: J 17 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7216 (mp0) REVERT: J 96 GLU cc_start: 0.8522 (OUTLIER) cc_final: 0.7886 (tm-30) REVERT: J 99 LYS cc_start: 0.8543 (mttt) cc_final: 0.8284 (mmtt) outliers start: 400 outliers final: 165 residues processed: 641 average time/residue: 0.4381 time to fit residues: 425.5670 Evaluate side-chains 386 residues out of total 2833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 187 time to evaluate : 3.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 LEU Chi-restraints excluded: chain A residue 10 SER Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 88 GLU Chi-restraints excluded: chain A residue 90 ASP 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 130 ASP Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 165 ASP Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 61 HIS Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 142 ARG Chi-restraints excluded: chain B residue 144 ARG Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 161 ARG Chi-restraints excluded: chain B residue 177 LYS Chi-restraints excluded: chain B residue 182 ARG Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 285 GLU Chi-restraints excluded: chain C residue 291 SER Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 413 THR Chi-restraints excluded: chain C residue 415 GLN Chi-restraints excluded: chain C residue 421 ARG Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 532 THR Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 649 VAL Chi-restraints excluded: chain C residue 660 VAL Chi-restraints excluded: chain C residue 672 MET Chi-restraints excluded: chain C residue 673 ARG Chi-restraints excluded: chain C residue 736 ILE Chi-restraints excluded: chain C residue 790 VAL Chi-restraints excluded: chain C residue 797 ARG Chi-restraints excluded: chain C residue 806 VAL Chi-restraints excluded: chain C residue 811 GLU Chi-restraints excluded: chain C residue 814 LEU Chi-restraints excluded: chain C residue 852 VAL Chi-restraints excluded: chain C residue 869 VAL Chi-restraints excluded: chain C residue 888 ARG Chi-restraints excluded: chain C residue 933 GLU Chi-restraints excluded: chain C residue 950 LYS Chi-restraints excluded: chain C residue 962 GLU Chi-restraints excluded: chain C residue 965 GLU Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1050 SER Chi-restraints excluded: chain C residue 1053 THR Chi-restraints excluded: chain C residue 1057 LEU Chi-restraints excluded: chain C residue 1063 PHE Chi-restraints excluded: chain C residue 1101 LYS Chi-restraints excluded: chain C residue 1114 GLU Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 36 TYR Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 56 ARG Chi-restraints excluded: chain D residue 67 ARG Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 84 ARG Chi-restraints excluded: chain D residue 86 LYS Chi-restraints excluded: chain D residue 88 ARG Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 147 GLU Chi-restraints excluded: chain D residue 206 ARG Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 263 LYS Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain D residue 485 ASP Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 505 HIS Chi-restraints excluded: chain D residue 506 ARG Chi-restraints excluded: chain D residue 566 LEU Chi-restraints excluded: chain D residue 588 LEU Chi-restraints excluded: chain D residue 603 SER Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain D residue 636 ARG Chi-restraints excluded: chain D residue 639 GLN Chi-restraints excluded: chain D residue 676 LEU Chi-restraints excluded: chain D residue 738 VAL Chi-restraints excluded: chain D residue 795 ASP Chi-restraints excluded: chain D residue 817 LEU Chi-restraints excluded: chain D residue 834 ARG Chi-restraints excluded: chain D residue 862 ASP Chi-restraints excluded: chain D residue 865 LEU Chi-restraints excluded: chain D residue 880 VAL Chi-restraints excluded: chain D residue 910 LEU Chi-restraints excluded: chain D residue 911 ILE Chi-restraints excluded: chain D residue 953 LEU Chi-restraints excluded: chain D residue 1024 ILE Chi-restraints excluded: chain D residue 1025 THR Chi-restraints excluded: chain D residue 1053 VAL Chi-restraints excluded: chain D residue 1054 ARG Chi-restraints excluded: chain D residue 1057 ASP Chi-restraints excluded: chain D residue 1069 ASP Chi-restraints excluded: chain D residue 1086 LEU Chi-restraints excluded: chain D residue 1087 ARG Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1089 PHE Chi-restraints excluded: chain D residue 1090 LYS 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 1100 SER Chi-restraints excluded: chain D residue 1120 GLU Chi-restraints excluded: chain D residue 1181 ILE Chi-restraints excluded: chain D residue 1189 GLU Chi-restraints excluded: chain D residue 1191 ARG Chi-restraints excluded: chain D residue 1193 VAL Chi-restraints excluded: chain D residue 1204 ARG Chi-restraints excluded: chain D residue 1249 LYS Chi-restraints excluded: chain D residue 1257 LEU Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 70 GLN Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain F residue 242 ASN Chi-restraints excluded: chain F residue 257 LEU Chi-restraints excluded: chain F residue 266 LEU Chi-restraints excluded: chain F residue 282 MET Chi-restraints excluded: chain F residue 285 CYS Chi-restraints excluded: chain F residue 328 LEU Chi-restraints excluded: chain F residue 332 VAL Chi-restraints excluded: chain F residue 365 THR Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 395 THR Chi-restraints excluded: chain F residue 397 GLU Chi-restraints excluded: chain F residue 405 ILE Chi-restraints excluded: chain F residue 429 ASP Chi-restraints excluded: chain F residue 449 ASP Chi-restraints excluded: chain F residue 482 THR Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 6 LEU Chi-restraints excluded: chain J residue 10 ARG Chi-restraints excluded: chain J residue 17 GLU Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 27 ARG Chi-restraints excluded: chain J residue 75 VAL Chi-restraints excluded: chain J residue 79 ARG Chi-restraints excluded: chain J residue 82 TRP Chi-restraints excluded: chain J residue 87 GLU Chi-restraints excluded: chain J residue 88 ARG Chi-restraints excluded: chain J residue 95 GLU Chi-restraints excluded: chain J residue 96 GLU Chi-restraints excluded: chain J residue 105 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 286 optimal weight: 6.9990 chunk 256 optimal weight: 0.5980 chunk 142 optimal weight: 0.8980 chunk 87 optimal weight: 0.5980 chunk 173 optimal weight: 20.0000 chunk 137 optimal weight: 0.9990 chunk 265 optimal weight: 0.9990 chunk 102 optimal weight: 7.9990 chunk 161 optimal weight: 2.9990 chunk 197 optimal weight: 4.9990 chunk 307 optimal weight: 9.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN B 124 HIS C 57 GLN C 142 ASN C 169 ASN C 200 HIS ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 349 HIS C 442 GLN C 585 GLN C 920 HIS C 935 HIS C1035 HIS C1062 GLN D 145 HIS D 287 GLN D 329 GLN D 368 ASN D 410 GLN D 468 ASN D 494 HIS D 606 HIS D 639 GLN D 693 GLN D 766 ASN D1145 GLN ** E 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 261 GLN F 425 GLN F 457 GLN F 516 HIS Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.100 28651 Z= 0.193 Angle : 0.630 29.140 39218 Z= 0.327 Chirality : 0.042 0.178 4465 Planarity : 0.006 0.214 4824 Dihedral : 18.444 179.878 5187 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.49 % Favored : 94.36 % Rotamer: Outliers : 7.88 % Allowed : 15.98 % Favored : 76.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.23 % Cis-general : 0.09 % 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: -2.62 (0.13), residues: 3333 helix: -1.14 (0.13), residues: 1266 sheet: -1.19 (0.25), residues: 401 loop : -2.38 (0.13), residues: 1666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 656 HIS 0.005 0.001 HIS J 22 PHE 0.014 0.001 PHE D1061 TYR 0.018 0.001 TYR D 248 ARG 0.007 0.000 ARG J 20 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 2833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 220 poor density : 221 time to evaluate : 2.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 GLN cc_start: 0.8254 (mm-40) cc_final: 0.7977 (mm-40) REVERT: B 32 TYR cc_start: 0.9098 (m-80) cc_final: 0.8833 (m-80) REVERT: B 144 ARG cc_start: 0.9221 (OUTLIER) cc_final: 0.8519 (mtt-85) REVERT: B 185 GLN cc_start: 0.6134 (tm-30) cc_final: 0.5799 (tt0) REVERT: B 213 LYS cc_start: 0.8224 (ttpp) cc_final: 0.7995 (ttmm) REVERT: C 127 MET cc_start: 0.8588 (ptp) cc_final: 0.8293 (ptp) REVERT: C 191 ILE cc_start: 0.8731 (mt) cc_final: 0.8529 (tp) REVERT: C 275 LEU cc_start: 0.8229 (OUTLIER) cc_final: 0.7989 (pp) REVERT: C 279 ARG cc_start: 0.8156 (ttm170) cc_final: 0.7755 (mtm180) REVERT: C 302 LYS cc_start: 0.8530 (mtmt) cc_final: 0.8200 (mtmt) REVERT: C 396 MET cc_start: 0.8847 (tmm) cc_final: 0.8616 (tmm) REVERT: C 673 ARG cc_start: 0.8421 (OUTLIER) cc_final: 0.8197 (ptm-80) REVERT: C 723 ILE cc_start: 0.8803 (OUTLIER) cc_final: 0.8381 (mm) REVERT: C 903 ASP cc_start: 0.8088 (p0) cc_final: 0.7863 (p0) REVERT: C 962 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.7204 (pp20) REVERT: C 1101 LYS cc_start: 0.9023 (OUTLIER) cc_final: 0.8720 (mtpt) REVERT: D 1 MET cc_start: 0.7170 (pmm) cc_final: 0.6525 (ppp) REVERT: D 56 ARG cc_start: 0.8010 (OUTLIER) cc_final: 0.7800 (mmm-85) REVERT: D 86 LYS cc_start: 0.8992 (OUTLIER) cc_final: 0.8696 (pttp) REVERT: D 155 MET cc_start: 0.7805 (tpt) cc_final: 0.7408 (tpp) REVERT: D 192 ASP cc_start: 0.0813 (OUTLIER) cc_final: 0.0390 (m-30) REVERT: D 206 ARG cc_start: 0.6079 (OUTLIER) cc_final: 0.5433 (ttm-80) REVERT: D 211 ARG cc_start: 0.7554 (ttm170) cc_final: 0.6853 (ttp80) REVERT: D 213 GLN cc_start: 0.8561 (tp-100) cc_final: 0.8346 (tp-100) REVERT: D 214 ARG cc_start: 0.7810 (ttp-110) cc_final: 0.7571 (ttp-110) REVERT: D 504 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8930 (mp) REVERT: D 506 ARG cc_start: 0.9216 (OUTLIER) cc_final: 0.8525 (ptt180) REVERT: D 717 LYS cc_start: 0.8929 (OUTLIER) cc_final: 0.8643 (pttp) REVERT: D 795 ASP cc_start: 0.8324 (OUTLIER) cc_final: 0.8082 (m-30) REVERT: D 834 ARG cc_start: 0.7788 (OUTLIER) cc_final: 0.5917 (mmp-170) REVERT: D 862 ASP cc_start: 0.7595 (OUTLIER) cc_final: 0.7265 (t0) REVERT: D 865 LEU cc_start: 0.8186 (OUTLIER) cc_final: 0.7889 (mp) REVERT: D 1191 ARG cc_start: 0.8181 (OUTLIER) cc_final: 0.7954 (mtt180) REVERT: F 242 ASN cc_start: 0.8958 (OUTLIER) cc_final: 0.8599 (p0) REVERT: F 264 THR cc_start: 0.8874 (m) cc_final: 0.8435 (p) REVERT: F 282 MET cc_start: 0.8284 (OUTLIER) cc_final: 0.7987 (mmm) REVERT: F 429 ASP cc_start: 0.6903 (OUTLIER) cc_final: 0.6466 (t0) REVERT: F 500 ARG cc_start: 0.7373 (OUTLIER) cc_final: 0.6889 (mtm-85) REVERT: J 6 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.7827 (pp) REVERT: J 21 ASN cc_start: 0.8155 (t0) cc_final: 0.7616 (t0) REVERT: J 95 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.7965 (mt-10) REVERT: J 96 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.7814 (tm-30) REVERT: J 99 LYS cc_start: 0.8734 (mttt) cc_final: 0.8485 (mmtt) outliers start: 220 outliers final: 120 residues processed: 423 average time/residue: 0.4361 time to fit residues: 287.7735 Evaluate side-chains 325 residues out of total 2833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 180 time to evaluate : 3.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 LEU Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 10 SER Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 88 GLU Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 61 HIS Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 144 ARG Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 161 ARG Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 254 PHE Chi-restraints excluded: chain C residue 266 ASN Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 303 GLU Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 532 THR Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 649 VAL Chi-restraints excluded: chain C residue 660 VAL Chi-restraints excluded: chain C residue 672 MET Chi-restraints excluded: chain C residue 673 ARG Chi-restraints excluded: chain C residue 723 ILE Chi-restraints excluded: chain C residue 736 ILE Chi-restraints excluded: chain C residue 776 ILE Chi-restraints excluded: chain C residue 790 VAL Chi-restraints excluded: chain C residue 806 VAL Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 841 HIS Chi-restraints excluded: chain C residue 852 VAL Chi-restraints excluded: chain C residue 869 VAL Chi-restraints excluded: chain C residue 888 ARG Chi-restraints excluded: chain C residue 933 GLU Chi-restraints excluded: chain C residue 950 LYS Chi-restraints excluded: chain C residue 962 GLU Chi-restraints excluded: chain C residue 965 GLU Chi-restraints excluded: chain C residue 991 CYS Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1050 SER Chi-restraints excluded: chain C residue 1063 PHE Chi-restraints excluded: chain C residue 1101 LYS Chi-restraints excluded: chain C residue 1114 GLU Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 56 ARG Chi-restraints excluded: chain D residue 84 ARG Chi-restraints excluded: chain D residue 86 LYS Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 147 GLU Chi-restraints excluded: chain D residue 192 ASP Chi-restraints excluded: chain D residue 206 ARG Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 238 GLU Chi-restraints excluded: chain D residue 263 LYS Chi-restraints excluded: chain D residue 485 ASP Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 506 ARG Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 676 LEU Chi-restraints excluded: chain D residue 679 LEU Chi-restraints excluded: chain D residue 717 LYS Chi-restraints excluded: chain D residue 795 ASP Chi-restraints excluded: chain D residue 817 LEU Chi-restraints excluded: chain D residue 834 ARG Chi-restraints excluded: chain D residue 862 ASP Chi-restraints excluded: chain D residue 865 LEU Chi-restraints excluded: chain D residue 910 LEU Chi-restraints excluded: chain D residue 911 ILE Chi-restraints excluded: chain D residue 937 ILE Chi-restraints excluded: chain D residue 953 LEU Chi-restraints excluded: chain D residue 1025 THR Chi-restraints excluded: chain D residue 1053 VAL Chi-restraints excluded: chain D residue 1054 ARG Chi-restraints excluded: chain D residue 1057 ASP Chi-restraints excluded: chain D residue 1069 ASP Chi-restraints excluded: chain D residue 1075 VAL Chi-restraints excluded: chain D residue 1089 PHE Chi-restraints excluded: chain D residue 1090 LYS Chi-restraints excluded: chain D residue 1191 ARG Chi-restraints excluded: chain D residue 1193 VAL Chi-restraints excluded: chain D residue 1204 ARG Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain F residue 242 ASN Chi-restraints excluded: chain F residue 257 LEU Chi-restraints excluded: chain F residue 266 LEU Chi-restraints excluded: chain F residue 282 MET Chi-restraints excluded: chain F residue 285 CYS Chi-restraints excluded: chain F residue 328 LEU Chi-restraints excluded: chain F residue 368 ILE Chi-restraints excluded: chain F residue 395 THR Chi-restraints excluded: chain F residue 405 ILE Chi-restraints excluded: chain F residue 429 ASP Chi-restraints excluded: chain F residue 449 ASP Chi-restraints excluded: chain F residue 482 THR Chi-restraints excluded: chain F residue 500 ARG Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 6 LEU Chi-restraints excluded: chain J residue 10 ARG Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 64 LEU Chi-restraints excluded: chain J residue 86 LEU Chi-restraints excluded: chain J residue 87 GLU Chi-restraints excluded: chain J residue 88 ARG Chi-restraints excluded: chain J residue 95 GLU Chi-restraints excluded: chain J residue 96 GLU Chi-restraints excluded: chain J residue 105 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 171 optimal weight: 10.0000 chunk 95 optimal weight: 4.9990 chunk 256 optimal weight: 0.7980 chunk 209 optimal weight: 4.9990 chunk 84 optimal weight: 10.0000 chunk 308 optimal weight: 10.0000 chunk 333 optimal weight: 7.9990 chunk 274 optimal weight: 4.9990 chunk 305 optimal weight: 7.9990 chunk 105 optimal weight: 0.9990 chunk 247 optimal weight: 7.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 HIS A 185 GLN ** B 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 232 GLN C 317 ASN D 468 ASN E 70 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.118 28651 Z= 0.408 Angle : 0.675 19.348 39218 Z= 0.352 Chirality : 0.045 0.158 4465 Planarity : 0.006 0.188 4824 Dihedral : 18.009 178.865 5020 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.38 % Favored : 92.47 % Rotamer: Outliers : 7.95 % Allowed : 17.13 % Favored : 74.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.23 % Cis-general : 0.09 % Twisted Proline : 1.16 % Twisted General : 0.09 % 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: -1.96 (0.14), residues: 3333 helix: -0.26 (0.15), residues: 1238 sheet: -1.12 (0.25), residues: 424 loop : -2.20 (0.14), residues: 1671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 656 HIS 0.006 0.001 HIS D 94 PHE 0.023 0.002 PHE D1061 TYR 0.014 0.002 TYR C 129 ARG 0.009 0.000 ARG B 182 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 2833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 222 poor density : 183 time to evaluate : 3.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 144 ARG cc_start: 0.9191 (OUTLIER) cc_final: 0.8480 (mtt-85) REVERT: B 213 LYS cc_start: 0.8335 (ttpp) cc_final: 0.8092 (tttp) REVERT: C 103 MET cc_start: 0.7582 (ptp) cc_final: 0.7188 (ptm) REVERT: C 127 MET cc_start: 0.8661 (ptp) cc_final: 0.8381 (ptp) REVERT: C 302 LYS cc_start: 0.8613 (mtmt) cc_final: 0.8191 (mtmt) REVERT: C 723 ILE cc_start: 0.8971 (OUTLIER) cc_final: 0.8762 (mm) REVERT: C 962 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.6994 (pp20) REVERT: D 1 MET cc_start: 0.7047 (pmm) cc_final: 0.6413 (ppp) REVERT: D 56 ARG cc_start: 0.8039 (OUTLIER) cc_final: 0.7029 (ptp90) REVERT: D 84 ARG cc_start: 0.8490 (OUTLIER) cc_final: 0.8271 (tpp-160) REVERT: D 155 MET cc_start: 0.7789 (tpt) cc_final: 0.7376 (tpp) REVERT: D 192 ASP cc_start: 0.0827 (OUTLIER) cc_final: 0.0421 (m-30) REVERT: D 206 ARG cc_start: 0.6108 (OUTLIER) cc_final: 0.5179 (ttm-80) REVERT: D 213 GLN cc_start: 0.8620 (tp-100) cc_final: 0.8375 (tp-100) REVERT: D 443 LEU cc_start: 0.9015 (OUTLIER) cc_final: 0.8640 (mp) REVERT: D 506 ARG cc_start: 0.9343 (OUTLIER) cc_final: 0.8922 (ptt-90) REVERT: D 636 ARG cc_start: 0.8859 (OUTLIER) cc_final: 0.8149 (ttt180) REVERT: D 717 LYS cc_start: 0.9026 (OUTLIER) cc_final: 0.8778 (pttp) REVERT: D 795 ASP cc_start: 0.8388 (OUTLIER) cc_final: 0.8045 (m-30) REVERT: D 834 ARG cc_start: 0.7857 (OUTLIER) cc_final: 0.6081 (mmp-170) REVERT: D 865 LEU cc_start: 0.8252 (OUTLIER) cc_final: 0.7955 (mp) REVERT: D 983 MET cc_start: 0.8472 (mmm) cc_final: 0.8149 (mmt) REVERT: D 1054 ARG cc_start: 0.8383 (OUTLIER) cc_final: 0.7822 (mtp-110) REVERT: D 1191 ARG cc_start: 0.8274 (OUTLIER) cc_final: 0.7990 (mtm110) REVERT: F 242 ASN cc_start: 0.8950 (OUTLIER) cc_final: 0.8636 (p0) REVERT: F 264 THR cc_start: 0.8765 (m) cc_final: 0.8469 (p) REVERT: F 282 MET cc_start: 0.8216 (OUTLIER) cc_final: 0.7939 (mmm) REVERT: J 6 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.7785 (pp) REVERT: J 10 ARG cc_start: 0.9022 (OUTLIER) cc_final: 0.8460 (ptt-90) REVERT: J 21 ASN cc_start: 0.8225 (t0) cc_final: 0.7665 (t0) REVERT: J 95 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.8141 (mt-10) REVERT: J 96 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.7860 (tm-30) REVERT: J 99 LYS cc_start: 0.8874 (mttt) cc_final: 0.8549 (mmtt) outliers start: 222 outliers final: 155 residues processed: 382 average time/residue: 0.4095 time to fit residues: 246.3867 Evaluate side-chains 348 residues out of total 2833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 171 time to evaluate : 3.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 LEU Chi-restraints excluded: chain A residue 10 SER Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 61 HIS Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 88 GLU Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 165 ASP Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 61 HIS Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 144 ARG Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 161 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 39 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 196 ASP Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 266 ASN Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 291 SER Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 303 GLU Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain C residue 494 ILE Chi-restraints excluded: chain C residue 532 THR Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 649 VAL Chi-restraints excluded: chain C residue 660 VAL Chi-restraints excluded: chain C residue 672 MET Chi-restraints excluded: chain C residue 723 ILE Chi-restraints excluded: chain C residue 736 ILE Chi-restraints excluded: chain C residue 776 ILE Chi-restraints excluded: chain C residue 789 ILE Chi-restraints excluded: chain C residue 790 VAL Chi-restraints excluded: chain C residue 806 VAL Chi-restraints excluded: chain C residue 841 HIS Chi-restraints excluded: chain C residue 852 VAL Chi-restraints excluded: chain C residue 869 VAL Chi-restraints excluded: chain C residue 888 ARG Chi-restraints excluded: chain C residue 933 GLU Chi-restraints excluded: chain C residue 950 LYS Chi-restraints excluded: chain C residue 962 GLU Chi-restraints excluded: chain C residue 965 GLU Chi-restraints excluded: chain C residue 991 CYS Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1050 SER Chi-restraints excluded: chain C residue 1063 PHE Chi-restraints excluded: chain C residue 1097 VAL Chi-restraints excluded: chain C residue 1114 GLU Chi-restraints excluded: chain C residue 1117 ILE Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 56 ARG Chi-restraints excluded: chain D residue 84 ARG Chi-restraints excluded: chain D residue 86 LYS Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 147 GLU Chi-restraints excluded: chain D residue 192 ASP Chi-restraints excluded: chain D residue 206 ARG Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 227 THR Chi-restraints excluded: chain D residue 238 GLU Chi-restraints excluded: chain D residue 263 LYS Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 485 ASP Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 505 HIS Chi-restraints excluded: chain D residue 506 ARG Chi-restraints excluded: chain D residue 559 MET Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 605 ASP Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 636 ARG Chi-restraints excluded: chain D residue 638 THR Chi-restraints excluded: chain D residue 666 THR Chi-restraints excluded: chain D residue 676 LEU Chi-restraints excluded: chain D residue 717 LYS Chi-restraints excluded: chain D residue 795 ASP Chi-restraints excluded: chain D residue 817 LEU Chi-restraints excluded: chain D residue 834 ARG Chi-restraints excluded: chain D residue 841 ARG Chi-restraints excluded: chain D residue 865 LEU Chi-restraints excluded: chain D residue 880 VAL Chi-restraints excluded: chain D residue 910 LEU Chi-restraints excluded: chain D residue 911 ILE Chi-restraints excluded: chain D residue 937 ILE Chi-restraints excluded: chain D residue 953 LEU Chi-restraints excluded: chain D residue 977 THR Chi-restraints excluded: chain D residue 1025 THR Chi-restraints excluded: chain D residue 1053 VAL Chi-restraints excluded: chain D residue 1054 ARG Chi-restraints excluded: chain D residue 1057 ASP Chi-restraints excluded: chain D residue 1069 ASP Chi-restraints excluded: chain D residue 1075 VAL Chi-restraints excluded: chain D residue 1090 LYS Chi-restraints excluded: chain D residue 1099 LEU Chi-restraints excluded: chain D residue 1168 ILE Chi-restraints excluded: chain D residue 1189 GLU Chi-restraints excluded: chain D residue 1191 ARG Chi-restraints excluded: chain D residue 1193 VAL Chi-restraints excluded: chain D residue 1204 ARG Chi-restraints excluded: chain D residue 1257 LEU Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain F residue 242 ASN Chi-restraints excluded: chain F residue 257 LEU Chi-restraints excluded: chain F residue 266 LEU Chi-restraints excluded: chain F residue 282 MET Chi-restraints excluded: chain F residue 285 CYS Chi-restraints excluded: chain F residue 328 LEU Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 395 THR Chi-restraints excluded: chain F residue 449 ASP Chi-restraints excluded: chain F residue 495 VAL Chi-restraints excluded: chain F residue 500 ARG Chi-restraints excluded: chain J residue 6 LEU Chi-restraints excluded: chain J residue 10 ARG Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 34 THR Chi-restraints excluded: chain J residue 63 THR Chi-restraints excluded: chain J residue 64 LEU Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain J residue 86 LEU Chi-restraints excluded: chain J residue 87 GLU Chi-restraints excluded: chain J residue 88 ARG Chi-restraints excluded: chain J residue 95 GLU Chi-restraints excluded: chain J residue 96 GLU Chi-restraints excluded: chain J residue 105 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 304 optimal weight: 4.9990 chunk 231 optimal weight: 8.9990 chunk 160 optimal weight: 0.6980 chunk 34 optimal weight: 0.0980 chunk 147 optimal weight: 0.4980 chunk 207 optimal weight: 2.9990 chunk 309 optimal weight: 5.9990 chunk 327 optimal weight: 5.9990 chunk 161 optimal weight: 2.9990 chunk 293 optimal weight: 5.9990 chunk 88 optimal weight: 8.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 HIS D 468 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.105 28651 Z= 0.222 Angle : 0.580 15.198 39218 Z= 0.304 Chirality : 0.042 0.166 4465 Planarity : 0.005 0.177 4824 Dihedral : 17.648 175.574 4999 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.67 % Favored : 94.21 % Rotamer: Outliers : 6.92 % Allowed : 18.38 % Favored : 74.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.23 % Cis-general : 0.09 % Twisted Proline : 1.16 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.14), residues: 3333 helix: 0.21 (0.15), residues: 1248 sheet: -0.82 (0.26), residues: 407 loop : -1.98 (0.14), residues: 1678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 656 HIS 0.009 0.001 HIS A 61 PHE 0.013 0.001 PHE D 512 TYR 0.012 0.001 TYR A 168 ARG 0.006 0.000 ARG D 214 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 2833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 184 time to evaluate : 2.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 32 TYR cc_start: 0.9136 (m-80) cc_final: 0.8863 (m-80) REVERT: B 213 LYS cc_start: 0.8297 (ttpp) cc_final: 0.8070 (ttmm) REVERT: C 103 MET cc_start: 0.7554 (ptp) cc_final: 0.7133 (ptm) REVERT: C 127 MET cc_start: 0.8643 (ptp) cc_final: 0.8389 (ptp) REVERT: C 220 ASP cc_start: 0.7751 (OUTLIER) cc_final: 0.7368 (t70) REVERT: C 279 ARG cc_start: 0.7930 (ttm110) cc_final: 0.7562 (mtm180) REVERT: C 631 GLU cc_start: 0.8648 (OUTLIER) cc_final: 0.7558 (mt-10) REVERT: C 723 ILE cc_start: 0.8756 (OUTLIER) cc_final: 0.8526 (mm) REVERT: C 903 ASP cc_start: 0.8208 (OUTLIER) cc_final: 0.8006 (p0) REVERT: C 1101 LYS cc_start: 0.9008 (OUTLIER) cc_final: 0.8573 (mtmt) REVERT: D 1 MET cc_start: 0.7092 (pmm) cc_final: 0.6497 (ppp) REVERT: D 86 LYS cc_start: 0.8900 (OUTLIER) cc_final: 0.8397 (pptt) REVERT: D 155 MET cc_start: 0.7895 (tpt) cc_final: 0.7406 (tpp) REVERT: D 192 ASP cc_start: 0.0817 (OUTLIER) cc_final: 0.0440 (m-30) REVERT: D 213 GLN cc_start: 0.8658 (tp-100) cc_final: 0.8440 (tp-100) REVERT: D 214 ARG cc_start: 0.7631 (ttp-110) cc_final: 0.7336 (ttp-110) REVERT: D 449 LEU cc_start: 0.9207 (OUTLIER) cc_final: 0.8935 (tp) REVERT: D 504 LEU cc_start: 0.9158 (OUTLIER) cc_final: 0.8881 (mp) REVERT: D 506 ARG cc_start: 0.9352 (OUTLIER) cc_final: 0.8566 (ptt180) REVERT: D 636 ARG cc_start: 0.8722 (OUTLIER) cc_final: 0.8003 (ttt180) REVERT: D 717 LYS cc_start: 0.8983 (OUTLIER) cc_final: 0.8671 (pttp) REVERT: D 795 ASP cc_start: 0.8338 (OUTLIER) cc_final: 0.7975 (m-30) REVERT: D 834 ARG cc_start: 0.7768 (OUTLIER) cc_final: 0.6047 (mmp-170) REVERT: D 865 LEU cc_start: 0.8146 (OUTLIER) cc_final: 0.7909 (mp) REVERT: D 983 MET cc_start: 0.8411 (mmm) cc_final: 0.8062 (mmt) REVERT: D 1024 ILE cc_start: 0.6567 (OUTLIER) cc_final: 0.6044 (tp) REVERT: D 1054 ARG cc_start: 0.8413 (OUTLIER) cc_final: 0.7813 (mtp-110) REVERT: D 1099 LEU cc_start: 0.8178 (OUTLIER) cc_final: 0.7956 (tp) REVERT: F 242 ASN cc_start: 0.8947 (OUTLIER) cc_final: 0.8661 (p0) REVERT: F 264 THR cc_start: 0.8699 (m) cc_final: 0.8397 (p) REVERT: F 282 MET cc_start: 0.8185 (OUTLIER) cc_final: 0.7926 (mmm) REVERT: F 395 THR cc_start: 0.8499 (OUTLIER) cc_final: 0.8128 (t) REVERT: F 500 ARG cc_start: 0.7437 (OUTLIER) cc_final: 0.6871 (mtm180) REVERT: J 6 LEU cc_start: 0.8260 (OUTLIER) cc_final: 0.7710 (pp) REVERT: J 10 ARG cc_start: 0.8930 (OUTLIER) cc_final: 0.8323 (ptt-90) REVERT: J 21 ASN cc_start: 0.8113 (t0) cc_final: 0.7586 (t0) REVERT: J 96 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.7908 (tm-30) REVERT: J 99 LYS cc_start: 0.8997 (mttt) cc_final: 0.8595 (mmtt) outliers start: 193 outliers final: 133 residues processed: 360 average time/residue: 0.3973 time to fit residues: 227.7208 Evaluate side-chains 332 residues out of total 2833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 174 time to evaluate : 3.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 LEU Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 61 HIS Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 88 GLU Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 165 ASP Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 61 HIS Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 161 ARG Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 203 SER Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 220 ASP Chi-restraints excluded: chain C residue 266 ASN Chi-restraints excluded: chain C residue 271 ASP Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain C residue 494 ILE Chi-restraints excluded: chain C residue 532 THR Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 631 GLU Chi-restraints excluded: chain C residue 649 VAL Chi-restraints excluded: chain C residue 660 VAL Chi-restraints excluded: chain C residue 672 MET Chi-restraints excluded: chain C residue 723 ILE Chi-restraints excluded: chain C residue 736 ILE Chi-restraints excluded: chain C residue 776 ILE Chi-restraints excluded: chain C residue 789 ILE Chi-restraints excluded: chain C residue 790 VAL Chi-restraints excluded: chain C residue 806 VAL Chi-restraints excluded: chain C residue 841 HIS Chi-restraints excluded: chain C residue 852 VAL Chi-restraints excluded: chain C residue 869 VAL Chi-restraints excluded: chain C residue 881 ASP Chi-restraints excluded: chain C residue 888 ARG Chi-restraints excluded: chain C residue 903 ASP Chi-restraints excluded: chain C residue 933 GLU Chi-restraints excluded: chain C residue 950 LYS Chi-restraints excluded: chain C residue 991 CYS Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1050 SER Chi-restraints excluded: chain C residue 1063 PHE Chi-restraints excluded: chain C residue 1101 LYS Chi-restraints excluded: chain C residue 1114 GLU Chi-restraints excluded: chain C residue 1117 ILE Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 67 ARG Chi-restraints excluded: chain D residue 86 LYS Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 147 GLU Chi-restraints excluded: chain D residue 192 ASP Chi-restraints excluded: chain D residue 206 ARG Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 238 GLU Chi-restraints excluded: chain D residue 263 LYS Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 506 ARG Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 636 ARG Chi-restraints excluded: chain D residue 638 THR Chi-restraints excluded: chain D residue 666 THR Chi-restraints excluded: chain D residue 676 LEU Chi-restraints excluded: chain D residue 717 LYS Chi-restraints excluded: chain D residue 738 VAL Chi-restraints excluded: chain D residue 795 ASP Chi-restraints excluded: chain D residue 834 ARG Chi-restraints excluded: chain D residue 865 LEU Chi-restraints excluded: chain D residue 880 VAL Chi-restraints excluded: chain D residue 910 LEU Chi-restraints excluded: chain D residue 911 ILE Chi-restraints excluded: chain D residue 937 ILE Chi-restraints excluded: chain D residue 953 LEU Chi-restraints excluded: chain D residue 1024 ILE Chi-restraints excluded: chain D residue 1025 THR Chi-restraints excluded: chain D residue 1053 VAL Chi-restraints excluded: chain D residue 1054 ARG Chi-restraints excluded: chain D residue 1057 ASP Chi-restraints excluded: chain D residue 1069 ASP Chi-restraints excluded: chain D residue 1075 VAL Chi-restraints excluded: chain D residue 1090 LYS Chi-restraints excluded: chain D residue 1099 LEU Chi-restraints excluded: chain D residue 1168 ILE Chi-restraints excluded: chain D residue 1193 VAL Chi-restraints excluded: chain D residue 1204 ARG Chi-restraints excluded: chain D residue 1257 LEU Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain F residue 242 ASN Chi-restraints excluded: chain F residue 257 LEU Chi-restraints excluded: chain F residue 266 LEU Chi-restraints excluded: chain F residue 282 MET Chi-restraints excluded: chain F residue 285 CYS Chi-restraints excluded: chain F residue 328 LEU Chi-restraints excluded: chain F residue 382 ILE Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 395 THR Chi-restraints excluded: chain F residue 449 ASP Chi-restraints excluded: chain F residue 482 THR Chi-restraints excluded: chain F residue 495 VAL Chi-restraints excluded: chain F residue 500 ARG Chi-restraints excluded: chain J residue 6 LEU Chi-restraints excluded: chain J residue 10 ARG Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 63 THR Chi-restraints excluded: chain J residue 64 LEU Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain J residue 86 LEU Chi-restraints excluded: chain J residue 87 GLU Chi-restraints excluded: chain J residue 88 ARG Chi-restraints excluded: chain J residue 96 GLU Chi-restraints excluded: chain J residue 105 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 272 optimal weight: 5.9990 chunk 186 optimal weight: 6.9990 chunk 4 optimal weight: 0.3980 chunk 243 optimal weight: 2.9990 chunk 135 optimal weight: 2.9990 chunk 279 optimal weight: 2.9990 chunk 226 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 167 optimal weight: 0.6980 chunk 294 optimal weight: 10.0000 chunk 82 optimal weight: 8.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 HIS A 185 GLN B 61 HIS C 981 GLN D 468 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.098 28651 Z= 0.248 Angle : 0.574 13.405 39218 Z= 0.300 Chirality : 0.042 0.144 4465 Planarity : 0.005 0.171 4824 Dihedral : 17.436 174.827 4962 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.30 % Favored : 93.58 % Rotamer: Outliers : 6.88 % Allowed : 18.63 % Favored : 74.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.23 % Cis-general : 0.09 % Twisted Proline : 1.16 % Twisted General : 0.09 % 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: -1.22 (0.14), residues: 3333 helix: 0.45 (0.15), residues: 1254 sheet: -0.69 (0.26), residues: 407 loop : -1.87 (0.14), residues: 1672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 656 HIS 0.016 0.001 HIS A 61 PHE 0.015 0.001 PHE D1061 TYR 0.012 0.001 TYR C 278 ARG 0.009 0.000 ARG D1191 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 2833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 192 poor density : 183 time to evaluate : 2.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 32 TYR cc_start: 0.9140 (m-80) cc_final: 0.8818 (m-80) REVERT: B 185 GLN cc_start: 0.7158 (tm-30) cc_final: 0.6886 (tm-30) REVERT: B 213 LYS cc_start: 0.8317 (ttpp) cc_final: 0.8090 (ttmm) REVERT: C 103 MET cc_start: 0.7364 (ptp) cc_final: 0.7014 (ptm) REVERT: C 127 MET cc_start: 0.8665 (ptp) cc_final: 0.8445 (ptp) REVERT: C 220 ASP cc_start: 0.7653 (OUTLIER) cc_final: 0.7273 (t70) REVERT: C 279 ARG cc_start: 0.7961 (ttm110) cc_final: 0.7638 (mtm180) REVERT: C 607 MET cc_start: 0.8865 (mtp) cc_final: 0.8634 (mtt) REVERT: C 631 GLU cc_start: 0.8680 (OUTLIER) cc_final: 0.7601 (mt-10) REVERT: C 723 ILE cc_start: 0.8821 (OUTLIER) cc_final: 0.8580 (mm) REVERT: C 962 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.6968 (pp20) REVERT: D 1 MET cc_start: 0.7057 (pmm) cc_final: 0.6517 (ppp) REVERT: D 86 LYS cc_start: 0.8902 (OUTLIER) cc_final: 0.8391 (pptt) REVERT: D 155 MET cc_start: 0.7938 (tpt) cc_final: 0.7473 (tpp) REVERT: D 192 ASP cc_start: 0.0727 (OUTLIER) cc_final: 0.0426 (m-30) REVERT: D 206 ARG cc_start: 0.6073 (OUTLIER) cc_final: 0.5183 (ttm-80) REVERT: D 213 GLN cc_start: 0.8664 (tp-100) cc_final: 0.8393 (tp-100) REVERT: D 248 TYR cc_start: 0.6925 (OUTLIER) cc_final: 0.6663 (m-80) REVERT: D 449 LEU cc_start: 0.9201 (OUTLIER) cc_final: 0.8968 (tp) REVERT: D 504 LEU cc_start: 0.9164 (OUTLIER) cc_final: 0.8904 (mp) REVERT: D 506 ARG cc_start: 0.9353 (OUTLIER) cc_final: 0.8599 (ptt180) REVERT: D 636 ARG cc_start: 0.8743 (OUTLIER) cc_final: 0.7999 (ttt180) REVERT: D 717 LYS cc_start: 0.8995 (OUTLIER) cc_final: 0.8692 (pttp) REVERT: D 744 GLU cc_start: 0.7031 (OUTLIER) cc_final: 0.6751 (pt0) REVERT: D 795 ASP cc_start: 0.8323 (OUTLIER) cc_final: 0.7979 (m-30) REVERT: D 834 ARG cc_start: 0.7786 (OUTLIER) cc_final: 0.6080 (mmp-170) REVERT: D 862 ASP cc_start: 0.8088 (t0) cc_final: 0.7363 (t0) REVERT: D 983 MET cc_start: 0.8408 (mmm) cc_final: 0.8056 (mmt) REVERT: D 1024 ILE cc_start: 0.6612 (OUTLIER) cc_final: 0.6070 (tp) REVERT: D 1054 ARG cc_start: 0.8411 (OUTLIER) cc_final: 0.7879 (mtp-110) REVERT: D 1099 LEU cc_start: 0.8181 (OUTLIER) cc_final: 0.7950 (tp) REVERT: F 242 ASN cc_start: 0.8936 (OUTLIER) cc_final: 0.8656 (p0) REVERT: F 264 THR cc_start: 0.8688 (m) cc_final: 0.8389 (p) REVERT: F 282 MET cc_start: 0.8174 (OUTLIER) cc_final: 0.7936 (mmm) REVERT: F 395 THR cc_start: 0.8529 (OUTLIER) cc_final: 0.8196 (t) REVERT: F 500 ARG cc_start: 0.7363 (OUTLIER) cc_final: 0.6873 (mtm180) REVERT: J 6 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.7816 (pp) REVERT: J 10 ARG cc_start: 0.8894 (OUTLIER) cc_final: 0.8240 (ptt-90) REVERT: J 21 ASN cc_start: 0.8220 (t0) cc_final: 0.7641 (t0) REVERT: J 99 LYS cc_start: 0.8977 (mttt) cc_final: 0.8627 (mmtt) outliers start: 192 outliers final: 138 residues processed: 354 average time/residue: 0.4069 time to fit residues: 229.6060 Evaluate side-chains 330 residues out of total 2833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 167 time to evaluate : 3.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 LEU Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 88 GLU Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 161 ARG Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 220 ASP Chi-restraints excluded: chain C residue 266 ASN Chi-restraints excluded: chain C residue 271 ASP Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 291 SER Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain C residue 494 ILE Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 631 GLU Chi-restraints excluded: chain C residue 649 VAL Chi-restraints excluded: chain C residue 653 VAL Chi-restraints excluded: chain C residue 660 VAL Chi-restraints excluded: chain C residue 672 MET Chi-restraints excluded: chain C residue 723 ILE Chi-restraints excluded: chain C residue 736 ILE Chi-restraints excluded: chain C residue 776 ILE Chi-restraints excluded: chain C residue 789 ILE Chi-restraints excluded: chain C residue 790 VAL Chi-restraints excluded: chain C residue 806 VAL Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 841 HIS Chi-restraints excluded: chain C residue 852 VAL Chi-restraints excluded: chain C residue 869 VAL Chi-restraints excluded: chain C residue 881 ASP Chi-restraints excluded: chain C residue 888 ARG Chi-restraints excluded: chain C residue 933 GLU Chi-restraints excluded: chain C residue 950 LYS Chi-restraints excluded: chain C residue 962 GLU 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 1063 PHE Chi-restraints excluded: chain C residue 1114 GLU Chi-restraints excluded: chain C residue 1117 ILE Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 86 LYS Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 147 GLU Chi-restraints excluded: chain D residue 192 ASP Chi-restraints excluded: chain D residue 206 ARG Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 227 THR Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 238 GLU Chi-restraints excluded: chain D residue 248 TYR Chi-restraints excluded: chain D residue 263 LYS Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 506 ARG Chi-restraints excluded: chain D residue 559 MET Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 636 ARG Chi-restraints excluded: chain D residue 638 THR Chi-restraints excluded: chain D residue 666 THR Chi-restraints excluded: chain D residue 676 LEU Chi-restraints excluded: chain D residue 717 LYS Chi-restraints excluded: chain D residue 738 VAL Chi-restraints excluded: chain D residue 744 GLU Chi-restraints excluded: chain D residue 795 ASP Chi-restraints excluded: chain D residue 834 ARG Chi-restraints excluded: chain D residue 841 ARG Chi-restraints excluded: chain D residue 880 VAL Chi-restraints excluded: chain D residue 910 LEU Chi-restraints excluded: chain D residue 911 ILE Chi-restraints excluded: chain D residue 937 ILE Chi-restraints excluded: chain D residue 1024 ILE Chi-restraints excluded: chain D residue 1025 THR Chi-restraints excluded: chain D residue 1053 VAL Chi-restraints excluded: chain D residue 1054 ARG Chi-restraints excluded: chain D residue 1057 ASP Chi-restraints excluded: chain D residue 1061 PHE Chi-restraints excluded: chain D residue 1069 ASP Chi-restraints excluded: chain D residue 1090 LYS Chi-restraints excluded: chain D residue 1099 LEU Chi-restraints excluded: chain D residue 1193 VAL Chi-restraints excluded: chain D residue 1204 ARG Chi-restraints excluded: chain D residue 1257 LEU Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain F residue 242 ASN Chi-restraints excluded: chain F residue 257 LEU Chi-restraints excluded: chain F residue 266 LEU Chi-restraints excluded: chain F residue 282 MET Chi-restraints excluded: chain F residue 285 CYS Chi-restraints excluded: chain F residue 328 LEU Chi-restraints excluded: chain F residue 359 MET Chi-restraints excluded: chain F residue 382 ILE Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 395 THR Chi-restraints excluded: chain F residue 449 ASP Chi-restraints excluded: chain F residue 482 THR Chi-restraints excluded: chain F residue 495 VAL Chi-restraints excluded: chain F residue 500 ARG Chi-restraints excluded: chain J residue 6 LEU Chi-restraints excluded: chain J residue 10 ARG Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 34 THR Chi-restraints excluded: chain J residue 63 THR Chi-restraints excluded: chain J residue 64 LEU Chi-restraints excluded: chain J residue 76 LYS Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain J residue 86 LEU Chi-restraints excluded: chain J residue 87 GLU Chi-restraints excluded: chain J residue 88 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 110 optimal weight: 5.9990 chunk 295 optimal weight: 3.9990 chunk 64 optimal weight: 5.9990 chunk 192 optimal weight: 0.5980 chunk 80 optimal weight: 0.9980 chunk 327 optimal weight: 8.9990 chunk 272 optimal weight: 3.9990 chunk 151 optimal weight: 0.7980 chunk 27 optimal weight: 9.9990 chunk 108 optimal weight: 6.9990 chunk 172 optimal weight: 20.0000 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 468 ASN D1227 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 28651 Z= 0.271 Angle : 0.579 11.865 39218 Z= 0.303 Chirality : 0.042 0.145 4465 Planarity : 0.005 0.166 4824 Dihedral : 17.313 173.752 4946 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.03 % Favored : 93.85 % Rotamer: Outliers : 7.24 % Allowed : 18.67 % Favored : 74.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.23 % Cis-general : 0.09 % Twisted Proline : 1.16 % Twisted General : 0.06 % 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: -1.04 (0.15), residues: 3333 helix: 0.63 (0.15), residues: 1248 sheet: -0.64 (0.26), residues: 412 loop : -1.78 (0.15), residues: 1673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 656 HIS 0.004 0.001 HIS D 94 PHE 0.014 0.001 PHE D1061 TYR 0.016 0.001 TYR C 278 ARG 0.007 0.000 ARG D 214 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 202 poor density : 176 time to evaluate : 3.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 32 TYR cc_start: 0.9155 (m-80) cc_final: 0.8810 (m-80) REVERT: B 185 GLN cc_start: 0.7132 (tm-30) cc_final: 0.6864 (tm-30) REVERT: B 213 LYS cc_start: 0.8311 (ttpp) cc_final: 0.8053 (tttp) REVERT: C 103 MET cc_start: 0.7353 (ptp) cc_final: 0.7067 (ptm) REVERT: C 127 MET cc_start: 0.8681 (ptp) cc_final: 0.8426 (ptp) REVERT: C 220 ASP cc_start: 0.7701 (OUTLIER) cc_final: 0.7328 (t70) REVERT: C 279 ARG cc_start: 0.7936 (ttm110) cc_final: 0.7586 (mtm180) REVERT: C 282 ARG cc_start: 0.7843 (OUTLIER) cc_final: 0.7523 (mmp80) REVERT: C 285 GLU cc_start: 0.6601 (OUTLIER) cc_final: 0.6380 (mm-30) REVERT: C 631 GLU cc_start: 0.8708 (OUTLIER) cc_final: 0.7621 (mt-10) REVERT: C 723 ILE cc_start: 0.8731 (OUTLIER) cc_final: 0.8513 (mm) REVERT: C 903 ASP cc_start: 0.8169 (p0) cc_final: 0.7857 (p0) REVERT: C 962 GLU cc_start: 0.8465 (OUTLIER) cc_final: 0.6925 (pp20) REVERT: C 1101 LYS cc_start: 0.9015 (OUTLIER) cc_final: 0.8461 (mtmt) REVERT: D 1 MET cc_start: 0.7021 (pmm) cc_final: 0.6470 (ppp) REVERT: D 155 MET cc_start: 0.7936 (tpt) cc_final: 0.7633 (tpp) REVERT: D 192 ASP cc_start: 0.0951 (OUTLIER) cc_final: 0.0702 (m-30) REVERT: D 213 GLN cc_start: 0.8627 (tp-100) cc_final: 0.8394 (tp-100) REVERT: D 248 TYR cc_start: 0.6974 (OUTLIER) cc_final: 0.6712 (m-80) REVERT: D 443 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8598 (mp) REVERT: D 449 LEU cc_start: 0.9215 (OUTLIER) cc_final: 0.8983 (tp) REVERT: D 504 LEU cc_start: 0.9181 (OUTLIER) cc_final: 0.8887 (mp) REVERT: D 506 ARG cc_start: 0.9358 (OUTLIER) cc_final: 0.8588 (ptt180) REVERT: D 636 ARG cc_start: 0.8752 (OUTLIER) cc_final: 0.8012 (ttt180) REVERT: D 717 LYS cc_start: 0.8963 (OUTLIER) cc_final: 0.8685 (pttp) REVERT: D 744 GLU cc_start: 0.7040 (OUTLIER) cc_final: 0.6761 (pt0) REVERT: D 795 ASP cc_start: 0.8306 (OUTLIER) cc_final: 0.7959 (m-30) REVERT: D 834 ARG cc_start: 0.7830 (OUTLIER) cc_final: 0.6160 (mmp-170) REVERT: D 862 ASP cc_start: 0.8130 (t0) cc_final: 0.7350 (t0) REVERT: D 983 MET cc_start: 0.8451 (mmm) cc_final: 0.8084 (mmt) REVERT: D 1024 ILE cc_start: 0.6855 (OUTLIER) cc_final: 0.6365 (tp) REVERT: D 1054 ARG cc_start: 0.8402 (OUTLIER) cc_final: 0.7889 (mtp-110) REVERT: F 242 ASN cc_start: 0.8934 (OUTLIER) cc_final: 0.8660 (p0) REVERT: F 264 THR cc_start: 0.8682 (m) cc_final: 0.8373 (p) REVERT: F 282 MET cc_start: 0.8203 (OUTLIER) cc_final: 0.7973 (mmm) REVERT: F 341 TYR cc_start: 0.8274 (m-80) cc_final: 0.8013 (m-80) REVERT: F 395 THR cc_start: 0.8485 (OUTLIER) cc_final: 0.8240 (t) REVERT: F 500 ARG cc_start: 0.7327 (OUTLIER) cc_final: 0.6855 (mtm180) REVERT: J 6 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.7924 (pp) REVERT: J 10 ARG cc_start: 0.8944 (OUTLIER) cc_final: 0.8310 (ptt-90) REVERT: J 21 ASN cc_start: 0.8227 (t0) cc_final: 0.7684 (t0) REVERT: J 99 LYS cc_start: 0.9025 (mttt) cc_final: 0.8675 (mmtt) outliers start: 202 outliers final: 148 residues processed: 358 average time/residue: 0.4094 time to fit residues: 232.9623 Evaluate side-chains 339 residues out of total 2833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 165 time to evaluate : 3.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 LEU Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 88 GLU Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 165 ASP Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 161 ARG Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 203 SER Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 220 ASP Chi-restraints excluded: chain C residue 266 ASN Chi-restraints excluded: chain C residue 271 ASP Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 282 ARG Chi-restraints excluded: chain C residue 285 GLU Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 413 THR Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain C residue 494 ILE Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 631 GLU Chi-restraints excluded: chain C residue 649 VAL Chi-restraints excluded: chain C residue 653 VAL Chi-restraints excluded: chain C residue 660 VAL Chi-restraints excluded: chain C residue 672 MET Chi-restraints excluded: chain C residue 723 ILE Chi-restraints excluded: chain C residue 736 ILE Chi-restraints excluded: chain C residue 776 ILE Chi-restraints excluded: chain C residue 789 ILE Chi-restraints excluded: chain C residue 806 VAL Chi-restraints excluded: chain C residue 835 THR Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 841 HIS Chi-restraints excluded: chain C residue 852 VAL Chi-restraints excluded: chain C residue 869 VAL Chi-restraints excluded: chain C residue 881 ASP Chi-restraints excluded: chain C residue 888 ARG Chi-restraints excluded: chain C residue 933 GLU Chi-restraints excluded: chain C residue 950 LYS Chi-restraints excluded: chain C residue 962 GLU Chi-restraints excluded: chain C residue 965 GLU 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 1063 PHE Chi-restraints excluded: chain C residue 1097 VAL Chi-restraints excluded: chain C residue 1101 LYS Chi-restraints excluded: chain C residue 1114 GLU Chi-restraints excluded: chain C residue 1117 ILE Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 147 GLU Chi-restraints excluded: chain D residue 192 ASP Chi-restraints excluded: chain D residue 206 ARG Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 227 THR Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 238 GLU Chi-restraints excluded: chain D residue 248 TYR Chi-restraints excluded: chain D residue 263 LYS Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain D residue 485 ASP Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 506 ARG Chi-restraints excluded: chain D residue 559 MET Chi-restraints excluded: chain D residue 576 MET Chi-restraints excluded: chain D residue 605 ASP Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 636 ARG Chi-restraints excluded: chain D residue 638 THR Chi-restraints excluded: chain D residue 666 THR Chi-restraints excluded: chain D residue 676 LEU Chi-restraints excluded: chain D residue 717 LYS Chi-restraints excluded: chain D residue 738 VAL Chi-restraints excluded: chain D residue 744 GLU Chi-restraints excluded: chain D residue 795 ASP Chi-restraints excluded: chain D residue 834 ARG Chi-restraints excluded: chain D residue 841 ARG Chi-restraints excluded: chain D residue 880 VAL Chi-restraints excluded: chain D residue 910 LEU Chi-restraints excluded: chain D residue 911 ILE Chi-restraints excluded: chain D residue 937 ILE Chi-restraints excluded: chain D residue 977 THR Chi-restraints excluded: chain D residue 1024 ILE Chi-restraints excluded: chain D residue 1025 THR Chi-restraints excluded: chain D residue 1053 VAL Chi-restraints excluded: chain D residue 1054 ARG Chi-restraints excluded: chain D residue 1057 ASP Chi-restraints excluded: chain D residue 1059 GLU Chi-restraints excluded: chain D residue 1069 ASP Chi-restraints excluded: chain D residue 1090 LYS Chi-restraints excluded: chain D residue 1168 ILE Chi-restraints excluded: chain D residue 1193 VAL Chi-restraints excluded: chain D residue 1204 ARG Chi-restraints excluded: chain D residue 1257 LEU Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain F residue 242 ASN Chi-restraints excluded: chain F residue 257 LEU Chi-restraints excluded: chain F residue 282 MET Chi-restraints excluded: chain F residue 285 CYS Chi-restraints excluded: chain F residue 328 LEU Chi-restraints excluded: chain F residue 332 VAL Chi-restraints excluded: chain F residue 382 ILE Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 395 THR Chi-restraints excluded: chain F residue 449 ASP Chi-restraints excluded: chain F residue 482 THR Chi-restraints excluded: chain F residue 495 VAL Chi-restraints excluded: chain F residue 500 ARG Chi-restraints excluded: chain J residue 6 LEU Chi-restraints excluded: chain J residue 10 ARG Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 34 THR Chi-restraints excluded: chain J residue 63 THR Chi-restraints excluded: chain J residue 64 LEU Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain J residue 86 LEU Chi-restraints excluded: chain J residue 88 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 316 optimal weight: 8.9990 chunk 36 optimal weight: 3.9990 chunk 186 optimal weight: 0.7980 chunk 239 optimal weight: 4.9990 chunk 185 optimal weight: 5.9990 chunk 276 optimal weight: 6.9990 chunk 183 optimal weight: 0.7980 chunk 326 optimal weight: 7.9990 chunk 204 optimal weight: 1.9990 chunk 199 optimal weight: 0.5980 chunk 150 optimal weight: 4.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN C 141 ASN D 165 GLN D 468 ASN D 657 GLN E 69 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 28651 Z= 0.227 Angle : 0.558 10.451 39218 Z= 0.291 Chirality : 0.042 0.143 4465 Planarity : 0.005 0.161 4824 Dihedral : 17.109 172.679 4936 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.73 % Favored : 94.18 % Rotamer: Outliers : 6.74 % Allowed : 19.03 % Favored : 74.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.23 % Cis-general : 0.09 % Twisted Proline : 1.16 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.15), residues: 3333 helix: 0.80 (0.15), residues: 1251 sheet: -0.39 (0.26), residues: 404 loop : -1.70 (0.15), residues: 1678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 656 HIS 0.003 0.001 HIS D 94 PHE 0.016 0.001 PHE D1061 TYR 0.013 0.001 TYR C 278 ARG 0.008 0.000 ARG D 214 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 2833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 180 time to evaluate : 3.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 32 TYR cc_start: 0.9135 (m-80) cc_final: 0.8792 (m-80) REVERT: B 185 GLN cc_start: 0.7056 (tm-30) cc_final: 0.6815 (tm-30) REVERT: B 213 LYS cc_start: 0.8297 (ttpp) cc_final: 0.8076 (ttmm) REVERT: C 103 MET cc_start: 0.7374 (ptp) cc_final: 0.7068 (ptm) REVERT: C 127 MET cc_start: 0.8686 (ptp) cc_final: 0.8462 (ptp) REVERT: C 220 ASP cc_start: 0.7734 (OUTLIER) cc_final: 0.7351 (t70) REVERT: C 279 ARG cc_start: 0.7932 (ttm110) cc_final: 0.7586 (mtm180) REVERT: C 282 ARG cc_start: 0.7796 (OUTLIER) cc_final: 0.7492 (mmp80) REVERT: C 285 GLU cc_start: 0.6613 (OUTLIER) cc_final: 0.6390 (mm-30) REVERT: C 607 MET cc_start: 0.8868 (mtp) cc_final: 0.8614 (mtt) REVERT: C 631 GLU cc_start: 0.8696 (OUTLIER) cc_final: 0.7636 (mt-10) REVERT: C 672 MET cc_start: 0.9344 (OUTLIER) cc_final: 0.8679 (mmp) REVERT: C 723 ILE cc_start: 0.8789 (OUTLIER) cc_final: 0.8558 (mm) REVERT: C 962 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.6945 (pp20) REVERT: C 1101 LYS cc_start: 0.9004 (OUTLIER) cc_final: 0.8475 (mtmt) REVERT: D 1 MET cc_start: 0.6969 (pmm) cc_final: 0.6439 (ppp) REVERT: D 155 MET cc_start: 0.7928 (tpt) cc_final: 0.7703 (tpp) REVERT: D 192 ASP cc_start: 0.1189 (OUTLIER) cc_final: 0.0942 (m-30) REVERT: D 213 GLN cc_start: 0.8602 (tp-100) cc_final: 0.8362 (tp-100) REVERT: D 225 THR cc_start: 0.8939 (OUTLIER) cc_final: 0.8679 (p) REVERT: D 248 TYR cc_start: 0.6996 (OUTLIER) cc_final: 0.6705 (m-80) REVERT: D 449 LEU cc_start: 0.9211 (OUTLIER) cc_final: 0.8986 (tp) REVERT: D 504 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8866 (mp) REVERT: D 636 ARG cc_start: 0.8729 (OUTLIER) cc_final: 0.7977 (ttt180) REVERT: D 717 LYS cc_start: 0.8980 (OUTLIER) cc_final: 0.8672 (pttp) REVERT: D 744 GLU cc_start: 0.7021 (OUTLIER) cc_final: 0.6741 (pt0) REVERT: D 795 ASP cc_start: 0.8298 (OUTLIER) cc_final: 0.7948 (m-30) REVERT: D 834 ARG cc_start: 0.7805 (OUTLIER) cc_final: 0.6161 (mmp-170) REVERT: D 862 ASP cc_start: 0.8109 (t0) cc_final: 0.7341 (t0) REVERT: D 983 MET cc_start: 0.8447 (mmm) cc_final: 0.8111 (mmt) REVERT: D 1024 ILE cc_start: 0.6825 (OUTLIER) cc_final: 0.6346 (tp) REVERT: D 1054 ARG cc_start: 0.8386 (OUTLIER) cc_final: 0.7804 (mtp-110) REVERT: F 242 ASN cc_start: 0.8918 (OUTLIER) cc_final: 0.8699 (p0) REVERT: F 264 THR cc_start: 0.8690 (m) cc_final: 0.8378 (p) REVERT: F 282 MET cc_start: 0.8240 (OUTLIER) cc_final: 0.8038 (mmm) REVERT: F 341 TYR cc_start: 0.8236 (m-80) cc_final: 0.7981 (m-80) REVERT: F 500 ARG cc_start: 0.7290 (OUTLIER) cc_final: 0.7032 (mtm110) REVERT: J 6 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.7972 (pp) REVERT: J 10 ARG cc_start: 0.8924 (OUTLIER) cc_final: 0.8253 (ptt-90) REVERT: J 21 ASN cc_start: 0.8182 (t0) cc_final: 0.7646 (t0) REVERT: J 90 SER cc_start: 0.7789 (m) cc_final: 0.7445 (p) REVERT: J 99 LYS cc_start: 0.8994 (mttt) cc_final: 0.8631 (mmtt) outliers start: 188 outliers final: 137 residues processed: 347 average time/residue: 0.4020 time to fit residues: 223.2630 Evaluate side-chains 329 residues out of total 2833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 167 time to evaluate : 3.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 LEU Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 165 ASP Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 161 ARG Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 203 SER Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 196 ASP Chi-restraints excluded: chain C residue 220 ASP Chi-restraints excluded: chain C residue 266 ASN Chi-restraints excluded: chain C residue 271 ASP Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 282 ARG Chi-restraints excluded: chain C residue 285 GLU Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 413 THR Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain C residue 494 ILE Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 631 GLU Chi-restraints excluded: chain C residue 649 VAL Chi-restraints excluded: chain C residue 660 VAL Chi-restraints excluded: chain C residue 672 MET Chi-restraints excluded: chain C residue 723 ILE Chi-restraints excluded: chain C residue 736 ILE Chi-restraints excluded: chain C residue 776 ILE Chi-restraints excluded: chain C residue 789 ILE Chi-restraints excluded: chain C residue 806 VAL Chi-restraints excluded: chain C residue 835 THR Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 841 HIS Chi-restraints excluded: chain C residue 852 VAL Chi-restraints excluded: chain C residue 869 VAL Chi-restraints excluded: chain C residue 881 ASP Chi-restraints excluded: chain C residue 888 ARG Chi-restraints excluded: chain C residue 933 GLU Chi-restraints excluded: chain C residue 950 LYS Chi-restraints excluded: chain C residue 962 GLU Chi-restraints excluded: chain C residue 965 GLU Chi-restraints excluded: chain C residue 991 CYS Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1063 PHE Chi-restraints excluded: chain C residue 1097 VAL Chi-restraints excluded: chain C residue 1101 LYS Chi-restraints excluded: chain C residue 1114 GLU Chi-restraints excluded: chain C residue 1117 ILE Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 147 GLU Chi-restraints excluded: chain D residue 192 ASP Chi-restraints excluded: chain D residue 206 ARG Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 227 THR Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 238 GLU Chi-restraints excluded: chain D residue 248 TYR Chi-restraints excluded: chain D residue 263 LYS Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain D residue 485 ASP Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 559 MET Chi-restraints excluded: chain D residue 605 ASP Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 636 ARG Chi-restraints excluded: chain D residue 638 THR Chi-restraints excluded: chain D residue 666 THR Chi-restraints excluded: chain D residue 676 LEU Chi-restraints excluded: chain D residue 717 LYS Chi-restraints excluded: chain D residue 738 VAL Chi-restraints excluded: chain D residue 744 GLU Chi-restraints excluded: chain D residue 795 ASP Chi-restraints excluded: chain D residue 834 ARG Chi-restraints excluded: chain D residue 841 ARG Chi-restraints excluded: chain D residue 880 VAL Chi-restraints excluded: chain D residue 910 LEU Chi-restraints excluded: chain D residue 911 ILE Chi-restraints excluded: chain D residue 937 ILE Chi-restraints excluded: chain D residue 1024 ILE Chi-restraints excluded: chain D residue 1025 THR Chi-restraints excluded: chain D residue 1053 VAL Chi-restraints excluded: chain D residue 1054 ARG Chi-restraints excluded: chain D residue 1059 GLU Chi-restraints excluded: chain D residue 1069 ASP Chi-restraints excluded: chain D residue 1090 LYS Chi-restraints excluded: chain D residue 1168 ILE Chi-restraints excluded: chain D residue 1193 VAL Chi-restraints excluded: chain D residue 1204 ARG Chi-restraints excluded: chain D residue 1207 LEU Chi-restraints excluded: chain D residue 1257 LEU Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain F residue 242 ASN Chi-restraints excluded: chain F residue 257 LEU Chi-restraints excluded: chain F residue 266 LEU Chi-restraints excluded: chain F residue 282 MET Chi-restraints excluded: chain F residue 285 CYS Chi-restraints excluded: chain F residue 328 LEU Chi-restraints excluded: chain F residue 382 ILE Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 449 ASP Chi-restraints excluded: chain F residue 495 VAL Chi-restraints excluded: chain F residue 500 ARG Chi-restraints excluded: chain J residue 6 LEU Chi-restraints excluded: chain J residue 10 ARG Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 34 THR Chi-restraints excluded: chain J residue 63 THR Chi-restraints excluded: chain J residue 64 LEU Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain J residue 86 LEU Chi-restraints excluded: chain J residue 88 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 202 optimal weight: 5.9990 chunk 130 optimal weight: 0.9990 chunk 195 optimal weight: 20.0000 chunk 98 optimal weight: 5.9990 chunk 64 optimal weight: 0.6980 chunk 63 optimal weight: 7.9990 chunk 207 optimal weight: 0.0980 chunk 222 optimal weight: 0.7980 chunk 161 optimal weight: 0.8980 chunk 30 optimal weight: 4.9990 chunk 256 optimal weight: 2.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 468 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.2840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.068 28651 Z= 0.156 Angle : 0.548 28.586 39218 Z= 0.279 Chirality : 0.041 0.163 4465 Planarity : 0.005 0.213 4824 Dihedral : 16.856 173.027 4916 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.92 % Favored : 94.96 % Rotamer: Outliers : 5.48 % Allowed : 20.03 % Favored : 74.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.23 % Cis-general : 0.09 % Twisted Proline : 1.16 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.15), residues: 3333 helix: 1.01 (0.15), residues: 1256 sheet: -0.18 (0.27), residues: 394 loop : -1.59 (0.15), residues: 1683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 656 HIS 0.002 0.000 HIS C1042 PHE 0.014 0.001 PHE D1061 TYR 0.012 0.001 TYR D 248 ARG 0.010 0.000 ARG D 214 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 189 time to evaluate : 3.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 32 TYR cc_start: 0.9125 (m-80) cc_final: 0.8862 (m-80) REVERT: B 213 LYS cc_start: 0.8274 (ttpp) cc_final: 0.8059 (ttmm) REVERT: C 103 MET cc_start: 0.7332 (ptp) cc_final: 0.7012 (ptm) REVERT: C 127 MET cc_start: 0.8653 (ptp) cc_final: 0.8381 (ptp) REVERT: C 220 ASP cc_start: 0.7675 (OUTLIER) cc_final: 0.7343 (t70) REVERT: C 631 GLU cc_start: 0.8652 (OUTLIER) cc_final: 0.7695 (mt-10) REVERT: C 672 MET cc_start: 0.9343 (OUTLIER) cc_final: 0.8644 (mmp) REVERT: C 723 ILE cc_start: 0.8607 (OUTLIER) cc_final: 0.8364 (mm) REVERT: C 903 ASP cc_start: 0.7840 (p0) cc_final: 0.7574 (p0) REVERT: C 962 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.6878 (pp20) REVERT: C 1101 LYS cc_start: 0.9016 (OUTLIER) cc_final: 0.8561 (mtmt) REVERT: D 1 MET cc_start: 0.6951 (pmm) cc_final: 0.6497 (ptm) REVERT: D 155 MET cc_start: 0.8044 (tpt) cc_final: 0.7806 (tpp) REVERT: D 206 ARG cc_start: 0.6103 (OUTLIER) cc_final: 0.5420 (ttm-80) REVERT: D 213 GLN cc_start: 0.8594 (tp-100) cc_final: 0.8287 (tp-100) REVERT: D 225 THR cc_start: 0.8922 (OUTLIER) cc_final: 0.8693 (p) REVERT: D 248 TYR cc_start: 0.6965 (OUTLIER) cc_final: 0.6684 (m-80) REVERT: D 449 LEU cc_start: 0.9191 (OUTLIER) cc_final: 0.8985 (tp) REVERT: D 504 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8825 (mp) REVERT: D 506 ARG cc_start: 0.9294 (OUTLIER) cc_final: 0.8759 (ptt180) REVERT: D 636 ARG cc_start: 0.8636 (OUTLIER) cc_final: 0.8434 (ttp-170) REVERT: D 744 GLU cc_start: 0.6995 (OUTLIER) cc_final: 0.6777 (pt0) REVERT: D 776 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7678 (mp0) REVERT: D 795 ASP cc_start: 0.8193 (OUTLIER) cc_final: 0.7916 (m-30) REVERT: D 862 ASP cc_start: 0.7913 (t0) cc_final: 0.7230 (t0) REVERT: D 983 MET cc_start: 0.8385 (mmm) cc_final: 0.8066 (mmt) REVERT: D 1024 ILE cc_start: 0.6860 (OUTLIER) cc_final: 0.6408 (tp) REVERT: F 242 ASN cc_start: 0.8909 (OUTLIER) cc_final: 0.8644 (p0) REVERT: F 264 THR cc_start: 0.8637 (m) cc_final: 0.8342 (p) REVERT: F 359 MET cc_start: 0.8751 (OUTLIER) cc_final: 0.8550 (ttp) REVERT: J 6 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.7954 (pp) REVERT: J 10 ARG cc_start: 0.8880 (OUTLIER) cc_final: 0.8219 (ptt-90) REVERT: J 21 ASN cc_start: 0.8106 (t0) cc_final: 0.7629 (t0) REVERT: J 90 SER cc_start: 0.7806 (m) cc_final: 0.7512 (p) REVERT: J 99 LYS cc_start: 0.9008 (mttt) cc_final: 0.8623 (mmtt) outliers start: 153 outliers final: 102 residues processed: 326 average time/residue: 0.4117 time to fit residues: 213.0584 Evaluate side-chains 289 residues out of total 2833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 166 time to evaluate : 2.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 LEU Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 161 ARG Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 203 SER Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 196 ASP Chi-restraints excluded: chain C residue 220 ASP Chi-restraints excluded: chain C residue 266 ASN Chi-restraints excluded: chain C residue 271 ASP Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 413 THR Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain C residue 494 ILE Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 631 GLU Chi-restraints excluded: chain C residue 660 VAL Chi-restraints excluded: chain C residue 672 MET Chi-restraints excluded: chain C residue 723 ILE Chi-restraints excluded: chain C residue 736 ILE Chi-restraints excluded: chain C residue 776 ILE Chi-restraints excluded: chain C residue 789 ILE Chi-restraints excluded: chain C residue 806 VAL Chi-restraints excluded: chain C residue 835 THR Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 852 VAL Chi-restraints excluded: chain C residue 869 VAL Chi-restraints excluded: chain C residue 881 ASP Chi-restraints excluded: chain C residue 888 ARG Chi-restraints excluded: chain C residue 933 GLU Chi-restraints excluded: chain C residue 950 LYS Chi-restraints excluded: chain C residue 962 GLU Chi-restraints excluded: chain C residue 965 GLU Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1063 PHE Chi-restraints excluded: chain C residue 1101 LYS Chi-restraints excluded: chain C residue 1117 ILE Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 147 GLU Chi-restraints excluded: chain D residue 206 ARG Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 238 GLU Chi-restraints excluded: chain D residue 248 TYR Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain D residue 485 ASP Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 506 ARG Chi-restraints excluded: chain D residue 590 THR Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 636 ARG Chi-restraints excluded: chain D residue 638 THR Chi-restraints excluded: chain D residue 676 LEU Chi-restraints excluded: chain D residue 679 LEU Chi-restraints excluded: chain D residue 738 VAL Chi-restraints excluded: chain D residue 744 GLU Chi-restraints excluded: chain D residue 776 GLU Chi-restraints excluded: chain D residue 795 ASP Chi-restraints excluded: chain D residue 834 ARG Chi-restraints excluded: chain D residue 910 LEU Chi-restraints excluded: chain D residue 911 ILE Chi-restraints excluded: chain D residue 937 ILE Chi-restraints excluded: chain D residue 1024 ILE Chi-restraints excluded: chain D residue 1053 VAL Chi-restraints excluded: chain D residue 1059 GLU Chi-restraints excluded: chain D residue 1061 PHE Chi-restraints excluded: chain D residue 1069 ASP Chi-restraints excluded: chain D residue 1090 LYS Chi-restraints excluded: chain D residue 1168 ILE Chi-restraints excluded: chain D residue 1193 VAL Chi-restraints excluded: chain D residue 1257 LEU Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain F residue 242 ASN Chi-restraints excluded: chain F residue 266 LEU Chi-restraints excluded: chain F residue 285 CYS Chi-restraints excluded: chain F residue 328 LEU Chi-restraints excluded: chain F residue 332 VAL Chi-restraints excluded: chain F residue 359 MET Chi-restraints excluded: chain F residue 482 THR Chi-restraints excluded: chain F residue 495 VAL Chi-restraints excluded: chain F residue 500 ARG Chi-restraints excluded: chain J residue 6 LEU Chi-restraints excluded: chain J residue 10 ARG Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 34 THR Chi-restraints excluded: chain J residue 64 LEU Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain J residue 86 LEU Chi-restraints excluded: chain J residue 88 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 297 optimal weight: 3.9990 chunk 313 optimal weight: 0.9980 chunk 285 optimal weight: 5.9990 chunk 304 optimal weight: 5.9990 chunk 312 optimal weight: 9.9990 chunk 183 optimal weight: 8.9990 chunk 132 optimal weight: 0.9990 chunk 239 optimal weight: 2.9990 chunk 93 optimal weight: 5.9990 chunk 275 optimal weight: 3.9990 chunk 287 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN C 935 HIS D 145 HIS D 468 ASN E 69 ASN F 299 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 28651 Z= 0.301 Angle : 0.605 28.588 39218 Z= 0.308 Chirality : 0.043 0.164 4465 Planarity : 0.005 0.212 4824 Dihedral : 16.873 175.322 4882 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.24 % Favored : 93.64 % Rotamer: Outliers : 5.27 % Allowed : 20.49 % Favored : 74.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.23 % Cis-general : 0.09 % Twisted Proline : 1.16 % Twisted General : 0.06 % 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: -0.62 (0.15), residues: 3333 helix: 0.98 (0.15), residues: 1250 sheet: -0.36 (0.26), residues: 415 loop : -1.56 (0.15), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 656 HIS 0.007 0.001 HIS D 145 PHE 0.014 0.001 PHE D 512 TYR 0.018 0.001 TYR C 278 ARG 0.008 0.000 ARG D 211 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 171 time to evaluate : 3.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 185 GLN cc_start: 0.6417 (tm-30) cc_final: 0.6032 (tm-30) REVERT: B 213 LYS cc_start: 0.8296 (ttpp) cc_final: 0.8067 (ttmm) REVERT: C 103 MET cc_start: 0.7363 (ptp) cc_final: 0.7078 (ptm) REVERT: C 127 MET cc_start: 0.8694 (ptp) cc_final: 0.8454 (ptp) REVERT: C 220 ASP cc_start: 0.7760 (OUTLIER) cc_final: 0.7409 (t70) REVERT: C 607 MET cc_start: 0.8852 (mtp) cc_final: 0.8596 (mtt) REVERT: C 631 GLU cc_start: 0.8741 (OUTLIER) cc_final: 0.7613 (mt-10) REVERT: C 672 MET cc_start: 0.9340 (OUTLIER) cc_final: 0.8668 (mmp) REVERT: C 723 ILE cc_start: 0.8908 (OUTLIER) cc_final: 0.8694 (mm) REVERT: C 903 ASP cc_start: 0.8123 (p0) cc_final: 0.7783 (p0) REVERT: C 962 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.6938 (pp20) REVERT: C 1101 LYS cc_start: 0.9019 (OUTLIER) cc_final: 0.8463 (mtmt) REVERT: D 1 MET cc_start: 0.6959 (pmm) cc_final: 0.6503 (ptm) REVERT: D 155 MET cc_start: 0.7875 (tpt) cc_final: 0.7589 (tpp) REVERT: D 206 ARG cc_start: 0.6099 (OUTLIER) cc_final: 0.5439 (ttm-80) REVERT: D 213 GLN cc_start: 0.8698 (tp-100) cc_final: 0.8409 (tp-100) REVERT: D 225 THR cc_start: 0.8934 (OUTLIER) cc_final: 0.8675 (p) REVERT: D 248 TYR cc_start: 0.7036 (OUTLIER) cc_final: 0.6769 (m-80) REVERT: D 504 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8896 (mp) REVERT: D 506 ARG cc_start: 0.9381 (OUTLIER) cc_final: 0.8654 (ptt180) REVERT: D 636 ARG cc_start: 0.8744 (OUTLIER) cc_final: 0.7963 (ttt180) REVERT: D 744 GLU cc_start: 0.7013 (OUTLIER) cc_final: 0.6730 (pt0) REVERT: D 776 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.7742 (mp0) REVERT: D 795 ASP cc_start: 0.8265 (OUTLIER) cc_final: 0.7934 (m-30) REVERT: D 834 ARG cc_start: 0.7831 (OUTLIER) cc_final: 0.6208 (mmp-170) REVERT: D 862 ASP cc_start: 0.8145 (t0) cc_final: 0.7392 (t0) REVERT: D 983 MET cc_start: 0.8471 (mmm) cc_final: 0.8139 (mmt) REVERT: D 1024 ILE cc_start: 0.6871 (OUTLIER) cc_final: 0.6413 (tp) REVERT: F 242 ASN cc_start: 0.8906 (OUTLIER) cc_final: 0.8633 (p0) REVERT: F 264 THR cc_start: 0.8676 (m) cc_final: 0.8371 (p) REVERT: J 6 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8063 (pp) REVERT: J 10 ARG cc_start: 0.8941 (OUTLIER) cc_final: 0.8350 (ptt-90) REVERT: J 90 SER cc_start: 0.7871 (m) cc_final: 0.7523 (p) REVERT: J 99 LYS cc_start: 0.9031 (mttt) cc_final: 0.8655 (mmtt) outliers start: 147 outliers final: 112 residues processed: 306 average time/residue: 0.3892 time to fit residues: 192.6217 Evaluate side-chains 299 residues out of total 2833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 167 time to evaluate : 3.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 LEU Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 165 ASP Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 161 ARG Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 203 SER Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 148 LYS Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 196 ASP Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 220 ASP Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 266 ASN Chi-restraints excluded: chain C residue 271 ASP Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain C residue 494 ILE Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 631 GLU Chi-restraints excluded: chain C residue 660 VAL Chi-restraints excluded: chain C residue 672 MET Chi-restraints excluded: chain C residue 723 ILE Chi-restraints excluded: chain C residue 736 ILE Chi-restraints excluded: chain C residue 776 ILE Chi-restraints excluded: chain C residue 789 ILE Chi-restraints excluded: chain C residue 806 VAL Chi-restraints excluded: chain C residue 814 LEU Chi-restraints excluded: chain C residue 835 THR Chi-restraints excluded: chain C residue 852 VAL Chi-restraints excluded: chain C residue 869 VAL Chi-restraints excluded: chain C residue 881 ASP Chi-restraints excluded: chain C residue 888 ARG Chi-restraints excluded: chain C residue 933 GLU Chi-restraints excluded: chain C residue 950 LYS Chi-restraints excluded: chain C residue 962 GLU Chi-restraints excluded: chain C residue 965 GLU Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1063 PHE Chi-restraints excluded: chain C residue 1097 VAL Chi-restraints excluded: chain C residue 1101 LYS Chi-restraints excluded: chain C residue 1117 ILE Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 147 GLU Chi-restraints excluded: chain D residue 206 ARG Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 227 THR Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 238 GLU Chi-restraints excluded: chain D residue 248 TYR Chi-restraints excluded: chain D residue 485 ASP Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 506 ARG Chi-restraints excluded: chain D residue 590 THR Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 636 ARG Chi-restraints excluded: chain D residue 638 THR Chi-restraints excluded: chain D residue 676 LEU Chi-restraints excluded: chain D residue 738 VAL Chi-restraints excluded: chain D residue 744 GLU Chi-restraints excluded: chain D residue 776 GLU Chi-restraints excluded: chain D residue 795 ASP Chi-restraints excluded: chain D residue 834 ARG Chi-restraints excluded: chain D residue 910 LEU Chi-restraints excluded: chain D residue 911 ILE Chi-restraints excluded: chain D residue 937 ILE Chi-restraints excluded: chain D residue 1024 ILE Chi-restraints excluded: chain D residue 1053 VAL Chi-restraints excluded: chain D residue 1059 GLU Chi-restraints excluded: chain D residue 1069 ASP Chi-restraints excluded: chain D residue 1090 LYS Chi-restraints excluded: chain D residue 1099 LEU Chi-restraints excluded: chain D residue 1168 ILE Chi-restraints excluded: chain D residue 1193 VAL Chi-restraints excluded: chain D residue 1207 LEU Chi-restraints excluded: chain D residue 1257 LEU Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain F residue 242 ASN Chi-restraints excluded: chain F residue 266 LEU Chi-restraints excluded: chain F residue 285 CYS Chi-restraints excluded: chain F residue 328 LEU Chi-restraints excluded: chain F residue 332 VAL Chi-restraints excluded: chain F residue 382 ILE Chi-restraints excluded: chain F residue 482 THR Chi-restraints excluded: chain F residue 495 VAL Chi-restraints excluded: chain F residue 500 ARG Chi-restraints excluded: chain J residue 6 LEU Chi-restraints excluded: chain J residue 10 ARG Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 34 THR Chi-restraints excluded: chain J residue 63 THR Chi-restraints excluded: chain J residue 64 LEU Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain J residue 86 LEU Chi-restraints excluded: chain J residue 88 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 303 optimal weight: 5.9990 chunk 199 optimal weight: 4.9990 chunk 321 optimal weight: 6.9990 chunk 196 optimal weight: 2.9990 chunk 152 optimal weight: 2.9990 chunk 223 optimal weight: 1.9990 chunk 337 optimal weight: 10.0000 chunk 310 optimal weight: 2.9990 chunk 268 optimal weight: 3.9990 chunk 27 optimal weight: 7.9990 chunk 207 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 145 HIS D 468 ASN E 69 ASN J 21 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.2799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 28651 Z= 0.344 Angle : 0.624 28.490 39218 Z= 0.318 Chirality : 0.044 0.153 4465 Planarity : 0.005 0.209 4824 Dihedral : 16.941 176.047 4882 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.24 % Favored : 93.64 % Rotamer: Outliers : 5.27 % Allowed : 20.35 % Favored : 74.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.23 % Cis-general : 0.09 % Twisted Proline : 1.16 % Twisted General : 0.06 % 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: -0.70 (0.15), residues: 3333 helix: 0.90 (0.15), residues: 1257 sheet: -0.47 (0.26), residues: 427 loop : -1.58 (0.15), residues: 1649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 656 HIS 0.006 0.001 HIS D 145 PHE 0.015 0.001 PHE D 512 TYR 0.034 0.001 TYR C 278 ARG 0.005 0.000 ARG D 214 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 167 time to evaluate : 3.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 VAL cc_start: 0.9458 (OUTLIER) cc_final: 0.9226 (m) REVERT: B 32 TYR cc_start: 0.9191 (m-80) cc_final: 0.8836 (m-80) REVERT: B 185 GLN cc_start: 0.6595 (tm-30) cc_final: 0.6194 (tm-30) REVERT: B 213 LYS cc_start: 0.8306 (ttpp) cc_final: 0.8078 (ttmm) REVERT: C 103 MET cc_start: 0.7377 (ptp) cc_final: 0.7093 (ptm) REVERT: C 127 MET cc_start: 0.8701 (ptp) cc_final: 0.8456 (ptp) REVERT: C 220 ASP cc_start: 0.7702 (OUTLIER) cc_final: 0.7351 (t70) REVERT: C 607 MET cc_start: 0.8862 (mtp) cc_final: 0.8577 (mtt) REVERT: C 631 GLU cc_start: 0.8764 (OUTLIER) cc_final: 0.7621 (mt-10) REVERT: C 672 MET cc_start: 0.9335 (OUTLIER) cc_final: 0.8612 (mmp) REVERT: C 903 ASP cc_start: 0.8318 (p0) cc_final: 0.7993 (p0) REVERT: C 962 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.6981 (pp20) REVERT: C 1101 LYS cc_start: 0.9029 (OUTLIER) cc_final: 0.8572 (mtmt) REVERT: D 1 MET cc_start: 0.7026 (pmm) cc_final: 0.6546 (ptm) REVERT: D 155 MET cc_start: 0.7883 (tpt) cc_final: 0.7625 (tpp) REVERT: D 213 GLN cc_start: 0.8702 (tp-100) cc_final: 0.8414 (tp-100) REVERT: D 225 THR cc_start: 0.9010 (OUTLIER) cc_final: 0.8726 (p) REVERT: D 248 TYR cc_start: 0.6924 (OUTLIER) cc_final: 0.6649 (m-80) REVERT: D 506 ARG cc_start: 0.9393 (OUTLIER) cc_final: 0.8635 (ptt180) REVERT: D 636 ARG cc_start: 0.8755 (OUTLIER) cc_final: 0.8006 (ttt180) REVERT: D 744 GLU cc_start: 0.7068 (OUTLIER) cc_final: 0.6802 (pt0) REVERT: D 776 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.7762 (mp0) REVERT: D 795 ASP cc_start: 0.8308 (OUTLIER) cc_final: 0.7919 (m-30) REVERT: D 834 ARG cc_start: 0.7854 (OUTLIER) cc_final: 0.6195 (mmp-170) REVERT: D 862 ASP cc_start: 0.8191 (t0) cc_final: 0.7413 (t0) REVERT: D 983 MET cc_start: 0.8536 (mmm) cc_final: 0.8188 (mmt) REVERT: D 1024 ILE cc_start: 0.6590 (OUTLIER) cc_final: 0.6042 (tp) REVERT: F 242 ASN cc_start: 0.8935 (OUTLIER) cc_final: 0.8637 (p0) REVERT: F 264 THR cc_start: 0.8702 (m) cc_final: 0.8371 (p) REVERT: J 6 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8102 (pp) REVERT: J 10 ARG cc_start: 0.8956 (OUTLIER) cc_final: 0.8403 (ptt-90) REVERT: J 90 SER cc_start: 0.7858 (m) cc_final: 0.7504 (p) REVERT: J 99 LYS cc_start: 0.9013 (mttt) cc_final: 0.8649 (mmtt) outliers start: 147 outliers final: 118 residues processed: 300 average time/residue: 0.3904 time to fit residues: 189.9425 Evaluate side-chains 298 residues out of total 2833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 162 time to evaluate : 3.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 LEU Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 84 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 130 ASP Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 165 ASP Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 161 ARG Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 203 SER Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 148 LYS Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 220 ASP Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 266 ASN Chi-restraints excluded: chain C residue 271 ASP Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 354 THR Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 413 THR Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain C residue 494 ILE Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 631 GLU Chi-restraints excluded: chain C residue 660 VAL Chi-restraints excluded: chain C residue 672 MET Chi-restraints excluded: chain C residue 736 ILE Chi-restraints excluded: chain C residue 776 ILE Chi-restraints excluded: chain C residue 789 ILE Chi-restraints excluded: chain C residue 806 VAL Chi-restraints excluded: chain C residue 835 THR Chi-restraints excluded: chain C residue 852 VAL Chi-restraints excluded: chain C residue 869 VAL Chi-restraints excluded: chain C residue 881 ASP Chi-restraints excluded: chain C residue 888 ARG Chi-restraints excluded: chain C residue 933 GLU Chi-restraints excluded: chain C residue 950 LYS Chi-restraints excluded: chain C residue 962 GLU Chi-restraints excluded: chain C residue 965 GLU Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1063 PHE Chi-restraints excluded: chain C residue 1097 VAL Chi-restraints excluded: chain C residue 1101 LYS Chi-restraints excluded: chain C residue 1117 ILE Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 147 GLU Chi-restraints excluded: chain D residue 206 ARG Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 227 THR Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 238 GLU Chi-restraints excluded: chain D residue 248 TYR Chi-restraints excluded: chain D residue 485 ASP Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 505 HIS Chi-restraints excluded: chain D residue 506 ARG Chi-restraints excluded: chain D residue 590 THR Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 636 ARG Chi-restraints excluded: chain D residue 638 THR Chi-restraints excluded: chain D residue 676 LEU Chi-restraints excluded: chain D residue 738 VAL Chi-restraints excluded: chain D residue 744 GLU Chi-restraints excluded: chain D residue 776 GLU Chi-restraints excluded: chain D residue 795 ASP Chi-restraints excluded: chain D residue 834 ARG Chi-restraints excluded: chain D residue 841 ARG Chi-restraints excluded: chain D residue 910 LEU Chi-restraints excluded: chain D residue 911 ILE Chi-restraints excluded: chain D residue 937 ILE Chi-restraints excluded: chain D residue 1024 ILE Chi-restraints excluded: chain D residue 1053 VAL Chi-restraints excluded: chain D residue 1059 GLU Chi-restraints excluded: chain D residue 1069 ASP Chi-restraints excluded: chain D residue 1090 LYS Chi-restraints excluded: chain D residue 1099 LEU Chi-restraints excluded: chain D residue 1112 MET Chi-restraints excluded: chain D residue 1168 ILE Chi-restraints excluded: chain D residue 1193 VAL Chi-restraints excluded: chain D residue 1207 LEU Chi-restraints excluded: chain D residue 1257 LEU Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain F residue 242 ASN Chi-restraints excluded: chain F residue 266 LEU Chi-restraints excluded: chain F residue 285 CYS Chi-restraints excluded: chain F residue 328 LEU Chi-restraints excluded: chain F residue 332 VAL Chi-restraints excluded: chain F residue 482 THR Chi-restraints excluded: chain F residue 489 LEU Chi-restraints excluded: chain F residue 495 VAL Chi-restraints excluded: chain F residue 500 ARG Chi-restraints excluded: chain J residue 6 LEU Chi-restraints excluded: chain J residue 10 ARG Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 34 THR Chi-restraints excluded: chain J residue 63 THR Chi-restraints excluded: chain J residue 64 LEU Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain J residue 86 LEU Chi-restraints excluded: chain J residue 88 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 164 optimal weight: 4.9990 chunk 213 optimal weight: 0.5980 chunk 286 optimal weight: 8.9990 chunk 82 optimal weight: 10.0000 chunk 247 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 74 optimal weight: 6.9990 chunk 269 optimal weight: 4.9990 chunk 112 optimal weight: 6.9990 chunk 276 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 145 HIS D 468 ASN E 69 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.102578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.071353 restraints weight = 52427.824| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 2.14 r_work: 0.2840 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2717 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 28651 Z= 0.274 Angle : 0.597 27.108 39218 Z= 0.305 Chirality : 0.043 0.168 4465 Planarity : 0.005 0.206 4824 Dihedral : 16.875 175.675 4882 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.97 % Favored : 93.91 % Rotamer: Outliers : 4.94 % Allowed : 20.89 % Favored : 74.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.23 % Cis-general : 0.09 % Twisted Proline : 1.16 % Twisted General : 0.06 % 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: -0.61 (0.15), residues: 3333 helix: 0.99 (0.15), residues: 1259 sheet: -0.44 (0.26), residues: 427 loop : -1.54 (0.15), residues: 1647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 656 HIS 0.007 0.001 HIS D 145 PHE 0.014 0.001 PHE D 512 TYR 0.035 0.001 TYR C 278 ARG 0.004 0.000 ARG D 214 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6279.25 seconds wall clock time: 114 minutes 11.33 seconds (6851.33 seconds total)