Starting phenix.real_space_refine on Sun Feb 25 03:29:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gzg_34397/02_2024/8gzg_34397.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gzg_34397/02_2024/8gzg_34397.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gzg_34397/02_2024/8gzg_34397.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gzg_34397/02_2024/8gzg_34397.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gzg_34397/02_2024/8gzg_34397.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gzg_34397/02_2024/8gzg_34397.pdb" } resolution = 3.13 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 19185 atoms to isotropic. 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 97 5.49 5 Mg 1 5.21 5 S 83 5.16 5 C 18250 2.51 5 N 5264 2.21 5 O 5806 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 57": "NH1" <-> "NH2" Residue "A ARG 72": "NH1" <-> "NH2" Residue "A GLU 117": "OE1" <-> "OE2" Residue "A GLU 137": "OE1" <-> "OE2" Residue "A GLU 143": "OE1" <-> "OE2" Residue "A GLU 185": "OE1" <-> "OE2" Residue "A ARG 197": "NH1" <-> "NH2" Residue "A ARG 211": "NH1" <-> "NH2" Residue "A GLU 216": "OE1" <-> "OE2" Residue "B GLU 10": "OE1" <-> "OE2" Residue "B PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 139": "OE1" <-> "OE2" Residue "B ARG 141": "NH1" <-> "NH2" Residue "B ARG 149": "NH1" <-> "NH2" Residue "B ARG 207": "NH1" <-> "NH2" Residue "B GLU 212": "OE1" <-> "OE2" Residue "C GLU 30": "OE1" <-> "OE2" Residue "C GLU 31": "OE1" <-> "OE2" Residue "C GLU 87": "OE1" <-> "OE2" Residue "C GLU 93": "OE1" <-> "OE2" Residue "C GLU 134": "OE1" <-> "OE2" Residue "C ARG 141": "NH1" <-> "NH2" Residue "C GLU 158": "OE1" <-> "OE2" Residue "C GLU 199": "OE1" <-> "OE2" Residue "C GLU 213": "OE1" <-> "OE2" Residue "C GLU 214": "OE1" <-> "OE2" Residue "C GLU 219": "OE1" <-> "OE2" Residue "C GLU 312": "OE1" <-> "OE2" Residue "C ARG 332": "NH1" <-> "NH2" Residue "C GLU 377": "OE1" <-> "OE2" Residue "C GLU 395": "OE1" <-> "OE2" Residue "C GLU 419": "OE1" <-> "OE2" Residue "C GLU 466": "OE1" <-> "OE2" Residue "C GLU 481": "OE1" <-> "OE2" Residue "C GLU 561": "OE1" <-> "OE2" Residue "C GLU 604": "OE1" <-> "OE2" Residue "C TYR 628": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 676": "OE1" <-> "OE2" Residue "C GLU 705": "OE1" <-> "OE2" Residue "C GLU 709": "OE1" <-> "OE2" Residue "C GLU 723": "OE1" <-> "OE2" Residue "C GLU 754": "OE1" <-> "OE2" Residue "C GLU 755": "OE1" <-> "OE2" Residue "C GLU 793": "OE1" <-> "OE2" Residue "C GLU 895": "OE1" <-> "OE2" Residue "C ARG 899": "NH1" <-> "NH2" Residue "C GLU 936": "OE1" <-> "OE2" Residue "C ARG 1033": "NH1" <-> "NH2" Residue "C GLU 1038": "OE1" <-> "OE2" Residue "D GLU 20": "OE1" <-> "OE2" Residue "D ARG 21": "NH1" <-> "NH2" Residue "D GLU 27": "OE1" <-> "OE2" Residue "D ARG 48": "NH1" <-> "NH2" Residue "D ARG 78": "NH1" <-> "NH2" Residue "D GLU 95": "OE1" <-> "OE2" Residue "D GLU 204": "OE1" <-> "OE2" Residue "D PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 291": "OE1" <-> "OE2" Residue "D ARG 319": "NH1" <-> "NH2" Residue "D GLU 339": "OE1" <-> "OE2" Residue "D ARG 377": "NH1" <-> "NH2" Residue "D GLU 378": "OE1" <-> "OE2" Residue "D GLU 382": "OE1" <-> "OE2" Residue "D ARG 391": "NH1" <-> "NH2" Residue "D GLU 420": "OE1" <-> "OE2" Residue "D PHE 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 450": "OE1" <-> "OE2" Residue "D ARG 559": "NH1" <-> "NH2" Residue "D GLU 563": "OE1" <-> "OE2" Residue "D GLU 578": "OE1" <-> "OE2" Residue "E GLU 17": "OE1" <-> "OE2" Residue "E GLU 39": "OE1" <-> "OE2" Residue "E ARG 58": "NH1" <-> "NH2" Residue "F GLU 79": "OE1" <-> "OE2" Residue "F ARG 82": "NH1" <-> "NH2" Residue "F ARG 84": "NH1" <-> "NH2" Residue "F ARG 87": "NH1" <-> "NH2" Residue "F ARG 96": "NH1" <-> "NH2" Residue "F GLU 105": "OE1" <-> "OE2" Residue "F ARG 180": "NH1" <-> "NH2" Residue "F ARG 187": "NH1" <-> "NH2" Residue "F ARG 188": "NH1" <-> "NH2" Residue "F ARG 228": "NH1" <-> "NH2" Residue "F GLU 231": "OE1" <-> "OE2" Residue "F ARG 255": "NH1" <-> "NH2" Residue "F GLU 295": "OE1" <-> "OE2" Residue "F ARG 332": "NH1" <-> "NH2" Residue "F GLU 345": "OE1" <-> "OE2" Residue "F GLU 347": "OE1" <-> "OE2" Residue "F GLU 368": "OE1" <-> "OE2" Residue "F GLU 404": "OE1" <-> "OE2" Residue "F ARG 412": "NH1" <-> "NH2" Residue "F GLU 422": "OE1" <-> "OE2" Residue "F ARG 425": "NH1" <-> "NH2" Residue "Z PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 23": "NH1" <-> "NH2" Residue "Z GLU 38": "OE1" <-> "OE2" Residue "Z GLU 77": "OE1" <-> "OE2" Residue "Z GLU 78": "OE1" <-> "OE2" Residue "Z ARG 79": "NH1" <-> "NH2" Residue "Z GLU 103": "OE1" <-> "OE2" Residue "Z ARG 138": "NH1" <-> "NH2" Residue "Z ARG 189": "NH1" <-> "NH2" Residue "Z ARG 221": "NH1" <-> "NH2" Residue "Z ARG 270": "NH1" <-> "NH2" Residue "Z ARG 364": "NH1" <-> "NH2" Residue "Z ARG 369": "NH1" <-> "NH2" Residue "Z GLU 372": "OE1" <-> "OE2" Residue "Z GLU 421": "OE1" <-> "OE2" Residue "Z ARG 433": "NH1" <-> "NH2" Residue "Z ARG 450": "NH1" <-> "NH2" Residue "Z GLU 455": "OE1" <-> "OE2" Residue "Z GLU 505": "OE1" <-> "OE2" Residue "Z ARG 546": "NH1" <-> "NH2" Residue "Z GLU 577": "OE1" <-> "OE2" Residue "Z ARG 592": "NH1" <-> "NH2" Residue "Z GLU 624": "OE1" <-> "OE2" Residue "Z ASP 628": "OD1" <-> "OD2" Residue "Z GLU 729": "OE1" <-> "OE2" Residue "Z GLU 730": "OE1" <-> "OE2" Residue "Z GLU 736": "OE1" <-> "OE2" Residue "Z GLU 773": "OE1" <-> "OE2" Residue "Z GLU 820": "OE1" <-> "OE2" Residue "Z ARG 857": "NH1" <-> "NH2" Residue "Z ARG 880": "NH1" <-> "NH2" Residue "Z GLU 919": "OE1" <-> "OE2" Residue "Z GLU 920": "OE1" <-> "OE2" Residue "Z GLU 926": "OE1" <-> "OE2" Residue "Z GLU 955": "OE1" <-> "OE2" Residue "Z ARG 962": "NH1" <-> "NH2" Residue "Z GLU 972": "OE1" <-> "OE2" Residue "Z GLU 987": "OE1" <-> "OE2" Residue "Z GLU 991": "OE1" <-> "OE2" Residue "Z GLU 1063": "OE1" <-> "OE2" Residue "Z ARG 1084": "NH1" <-> "NH2" Residue "Z GLU 1096": "OE1" <-> "OE2" Residue "Z PHE 1179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 1187": "OE1" <-> "OE2" Residue "Z ARG 1215": "NH1" <-> "NH2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 29503 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1628 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 205} Chain breaks: 2 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 48 Chain: "B" Number of atoms: 1569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1569 Classifications: {'peptide': 201} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 192} Chain breaks: 5 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "C" Number of atoms: 8118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1049, 8118 Classifications: {'peptide': 1049} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PCIS': 1, 'PTRANS': 61, 'TRANS': 986} Chain breaks: 5 Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 190 Unresolved non-hydrogen dihedrals: 121 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 12} Unresolved non-hydrogen planarities: 107 Chain: "D" Number of atoms: 4827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 611, 4827 Classifications: {'peptide': 611} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 2, 'PTRANS': 27, 'TRANS': 581} Chain breaks: 2 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 4, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 42 Chain: "E" Number of atoms: 450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 450 Classifications: {'peptide': 58} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 2, 'TRANS': 55} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 13 Chain: "F" Number of atoms: 2483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2483 Classifications: {'peptide': 314} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 8, 'TRANS': 305} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 130 Unresolved non-hydrogen angles: 160 Unresolved non-hydrogen dihedrals: 110 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'HIS:plan': 1, 'GLU:plan': 9, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 91 Chain: "Z" Number of atoms: 8387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1175, 8387 Classifications: {'peptide': 1175} Incomplete info: {'truncation_to_alanine': 181} Link IDs: {'PTRANS': 43, 'TRANS': 1131} Chain breaks: 9 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 699 Unresolved non-hydrogen angles: 866 Unresolved non-hydrogen dihedrals: 565 Unresolved non-hydrogen chiralities: 43 Planarities with less than four sites: {'GLN:plan1': 25, 'HIS:plan': 2, 'TYR:plan': 4, 'ASN:plan1': 4, 'TRP:plan': 2, 'ASP:plan': 15, 'PHE:plan': 1, 'GLU:plan': 33, 'ARG:plan': 18} Unresolved non-hydrogen planarities: 441 Chain: "1" Number of atoms: 1029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 1029 Classifications: {'DNA': 50} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 49} Chain: "2" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 928 Classifications: {'DNA': 45} Link IDs: {'rna3p': 44} Chain breaks: 1 Chain: "3" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 81 Classifications: {'RNA': 4} Modifications used: {'5*END': 1, 'rna3p_pur': 2, 'rna3p_pyr': 1} Link IDs: {'rna3p': 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Z" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 11843 SG CYS D 71 111.942 54.734 69.153 1.00 28.50 S ATOM 11863 SG CYS D 73 114.277 56.135 65.730 1.00 28.50 S ATOM 11972 SG CYS D 86 116.657 55.737 69.115 1.00 37.37 S ATOM 20772 SG CYS Z 214 82.509 75.799 126.351 1.00 28.50 S ATOM 21294 SG CYS Z 286 81.155 76.884 122.107 1.00 28.50 S ATOM 21366 SG CYS Z 296 78.561 76.033 124.931 1.00 28.50 S Time building chain proxies: 15.47, per 1000 atoms: 0.52 Number of scatterers: 29503 At special positions: 0 Unit cell: (152.1, 154.128, 155.142, 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 83 16.00 P 97 15.00 Mg 1 11.99 O 5806 8.00 N 5264 7.00 C 18250 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: 11.83 Conformation dependent library (CDL) restraints added in 5.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D2002 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 71 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 73 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 86 " pdb=" ZN Z2001 " pdb="ZN ZN Z2001 " - pdb=" SG CYS Z 296 " pdb="ZN ZN Z2001 " - pdb=" SG CYS Z 214 " pdb="ZN ZN Z2001 " - pdb=" SG CYS Z 286 " 7124 Ramachandran restraints generated. 3562 Oldfield, 0 Emsley, 3562 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6700 Finding SS restraints... Secondary structure from input PDB file: 109 helices and 51 sheets defined 33.1% alpha, 16.6% beta 31 base pairs and 79 stacking pairs defined. Time for finding SS restraints: 10.49 Creating SS restraints... Processing helix chain 'A' and resid 32 through 47 removed outlier: 3.615A pdb=" N GLY A 37 " --> pdb=" O GLY A 33 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA A 39 " --> pdb=" O THR A 35 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL A 43 " --> pdb=" O ALA A 39 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER A 46 " --> pdb=" O ARG A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 82 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 209 through 224 removed outlier: 3.518A pdb=" N SER A 215 " --> pdb=" O ARG A 211 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE A 220 " --> pdb=" O GLU A 216 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE A 221 " --> pdb=" O ALA A 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 46 removed outlier: 4.013A pdb=" N THR B 35 " --> pdb=" O GLY B 31 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY B 37 " --> pdb=" O GLY B 33 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA B 39 " --> pdb=" O THR B 35 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL B 43 " --> pdb=" O ALA B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 82 removed outlier: 3.631A pdb=" N ILE B 78 " --> pdb=" O ASP B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 219 Processing helix chain 'B' and resid 221 through 226 removed outlier: 4.047A pdb=" N ASP B 226 " --> pdb=" O ILE B 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 24 Processing helix chain 'C' and resid 26 through 36 removed outlier: 3.582A pdb=" N GLU C 31 " --> pdb=" O GLY C 27 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU C 32 " --> pdb=" O LEU C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 54 removed outlier: 3.841A pdb=" N TYR C 54 " --> pdb=" O GLY C 51 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 51 through 54' Processing helix chain 'C' and resid 62 through 69 removed outlier: 3.893A pdb=" N LYS C 67 " --> pdb=" O VAL C 63 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ARG C 68 " --> pdb=" O ASP C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 184 Processing helix chain 'C' and resid 188 through 193 removed outlier: 3.828A pdb=" N LEU C 192 " --> pdb=" O ASP C 188 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASP C 193 " --> pdb=" O ASN C 189 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 188 through 193' Processing helix chain 'C' and resid 199 through 201 No H-bonds generated for 'chain 'C' and resid 199 through 201' Processing helix chain 'C' and resid 202 through 207 removed outlier: 4.176A pdb=" N LYS C 207 " --> pdb=" O LYS C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 225 removed outlier: 3.758A pdb=" N LYS C 223 " --> pdb=" O GLU C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 244 removed outlier: 3.515A pdb=" N GLN C 237 " --> pdb=" O SER C 233 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU C 239 " --> pdb=" O GLY C 235 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER C 241 " --> pdb=" O GLN C 237 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ARG C 242 " --> pdb=" O LEU C 238 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N PHE C 243 " --> pdb=" O LEU C 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 263 removed outlier: 3.736A pdb=" N TYR C 257 " --> pdb=" O ARG C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 288 removed outlier: 3.746A pdb=" N ILE C 279 " --> pdb=" O THR C 275 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU C 280 " --> pdb=" O PRO C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 292 removed outlier: 3.631A pdb=" N ASP C 292 " --> pdb=" O LEU C 289 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 289 through 292' Processing helix chain 'C' and resid 309 through 330 removed outlier: 3.967A pdb=" N GLN C 315 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN C 316 " --> pdb=" O GLU C 312 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLN C 317 " --> pdb=" O LEU C 313 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ARG C 324 " --> pdb=" O VAL C 320 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG C 327 " --> pdb=" O ASN C 323 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ILE C 328 " --> pdb=" O ARG C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 346 Processing helix chain 'C' and resid 349 through 362 removed outlier: 3.516A pdb=" N ALA C 355 " --> pdb=" O PRO C 351 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE C 359 " --> pdb=" O ALA C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 381 removed outlier: 3.664A pdb=" N LYS C 381 " --> pdb=" O GLU C 377 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 403 removed outlier: 3.710A pdb=" N ARG C 402 " --> pdb=" O GLY C 398 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 409 removed outlier: 3.891A pdb=" N HIS C 409 " --> pdb=" O PRO C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 524 removed outlier: 3.686A pdb=" N MET C 523 " --> pdb=" O ALA C 520 " (cutoff:3.500A) Processing helix chain 'C' and resid 526 through 530 Processing helix chain 'C' and resid 531 through 542 removed outlier: 3.578A pdb=" N MET C 537 " --> pdb=" O ASN C 533 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASN C 540 " --> pdb=" O LEU C 536 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 545 No H-bonds generated for 'chain 'C' and resid 543 through 545' Processing helix chain 'C' and resid 560 through 567 removed outlier: 3.526A pdb=" N ALA C 564 " --> pdb=" O LEU C 560 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ARG C 566 " --> pdb=" O ALA C 562 " (cutoff:3.500A) Processing helix chain 'C' and resid 676 through 681 removed outlier: 3.620A pdb=" N TYR C 680 " --> pdb=" O GLU C 676 " (cutoff:3.500A) Processing helix chain 'C' and resid 752 through 763 removed outlier: 3.554A pdb=" N ILE C 761 " --> pdb=" O LEU C 757 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N PHE C 762 " --> pdb=" O LEU C 758 " (cutoff:3.500A) Processing helix chain 'C' and resid 855 through 859 removed outlier: 3.938A pdb=" N GLY C 858 " --> pdb=" O ASN C 855 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL C 859 " --> pdb=" O PRO C 856 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 855 through 859' Processing helix chain 'C' and resid 865 through 881 removed outlier: 3.623A pdb=" N ALA C 876 " --> pdb=" O LEU C 872 " (cutoff:3.500A) Processing helix chain 'C' and resid 898 through 910 removed outlier: 3.533A pdb=" N VAL C 902 " --> pdb=" O SER C 898 " (cutoff:3.500A) Processing helix chain 'C' and resid 988 through 998 removed outlier: 3.661A pdb=" N ALA C 994 " --> pdb=" O MET C 990 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU C 995 " --> pdb=" O GLU C 991 " (cutoff:3.500A) Processing helix chain 'C' and resid 1000 through 1010 removed outlier: 3.638A pdb=" N LEU C1004 " --> pdb=" O ALA C1000 " (cutoff:3.500A) Processing helix chain 'C' and resid 1016 through 1028 removed outlier: 3.583A pdb=" N ILE C1025 " --> pdb=" O ALA C1021 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL C1026 " --> pdb=" O LEU C1022 " (cutoff:3.500A) Processing helix chain 'C' and resid 1037 through 1049 removed outlier: 3.822A pdb=" N LYS C1041 " --> pdb=" O PRO C1037 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 27 removed outlier: 3.545A pdb=" N TRP D 25 " --> pdb=" O ARG D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 59 through 64 Processing helix chain 'D' and resid 95 through 99 removed outlier: 3.818A pdb=" N VAL D 98 " --> pdb=" O GLU D 95 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ARG D 99 " --> pdb=" O SER D 96 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 95 through 99' Processing helix chain 'D' and resid 114 through 119 Processing helix chain 'D' and resid 123 through 129 removed outlier: 3.546A pdb=" N LEU D 128 " --> pdb=" O TYR D 124 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU D 129 " --> pdb=" O LEU D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 140 removed outlier: 3.515A pdb=" N ILE D 139 " --> pdb=" O ASP D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 173 removed outlier: 3.854A pdb=" N VAL D 168 " --> pdb=" O GLU D 164 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLU D 169 " --> pdb=" O ASP D 165 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE D 170 " --> pdb=" O GLN D 166 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASP D 172 " --> pdb=" O VAL D 168 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLN D 173 " --> pdb=" O GLU D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 199 removed outlier: 3.587A pdb=" N VAL D 193 " --> pdb=" O GLY D 189 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 215 removed outlier: 3.591A pdb=" N LYS D 208 " --> pdb=" O GLU D 204 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU D 211 " --> pdb=" O GLU D 207 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLU D 212 " --> pdb=" O LYS D 208 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU D 214 " --> pdb=" O ARG D 210 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA D 215 " --> pdb=" O GLU D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 217 through 219 No H-bonds generated for 'chain 'D' and resid 217 through 219' Processing helix chain 'D' and resid 220 through 237 removed outlier: 3.662A pdb=" N LEU D 224 " --> pdb=" O LYS D 220 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL D 230 " --> pdb=" O LYS D 226 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE D 234 " --> pdb=" O VAL D 230 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE D 235 " --> pdb=" O ILE D 231 " (cutoff:3.500A) Processing helix chain 'D' and resid 240 through 243 Processing helix chain 'D' and resid 253 through 257 Processing helix chain 'D' and resid 270 through 290 removed outlier: 3.954A pdb=" N ASP D 274 " --> pdb=" O SER D 270 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL D 279 " --> pdb=" O LEU D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 295 through 315 removed outlier: 3.615A pdb=" N ASN D 301 " --> pdb=" O ILE D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 349 removed outlier: 3.632A pdb=" N LEU D 349 " --> pdb=" O PHE D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 376 through 384 removed outlier: 4.077A pdb=" N GLU D 382 " --> pdb=" O GLU D 378 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 395 Processing helix chain 'D' and resid 400 through 409 removed outlier: 3.554A pdb=" N LEU D 407 " --> pdb=" O ALA D 403 " (cutoff:3.500A) Processing helix chain 'D' and resid 412 through 423 removed outlier: 4.042A pdb=" N TRP D 416 " --> pdb=" O ASP D 412 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER D 417 " --> pdb=" O PRO D 413 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU D 421 " --> pdb=" O SER D 417 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE D 423 " --> pdb=" O LEU D 419 " (cutoff:3.500A) Processing helix chain 'D' and resid 437 through 439 No H-bonds generated for 'chain 'D' and resid 437 through 439' Processing helix chain 'D' and resid 460 through 465 Processing helix chain 'D' and resid 480 through 490 Processing helix chain 'D' and resid 492 through 496 removed outlier: 3.524A pdb=" N ASN D 496 " --> pdb=" O ALA D 493 " (cutoff:3.500A) Processing helix chain 'D' and resid 511 through 521 removed outlier: 3.852A pdb=" N LEU D 515 " --> pdb=" O GLN D 511 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY D 516 " --> pdb=" O ASP D 512 " (cutoff:3.500A) Processing helix chain 'D' and resid 537 through 546 removed outlier: 4.015A pdb=" N ALA D 541 " --> pdb=" O GLY D 537 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASP D 546 " --> pdb=" O LEU D 542 " (cutoff:3.500A) Processing helix chain 'D' and resid 610 through 625 removed outlier: 3.611A pdb=" N ILE D 620 " --> pdb=" O TYR D 616 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA D 621 " --> pdb=" O ASN D 617 " (cutoff:3.500A) Processing helix chain 'E' and resid 12 through 21 removed outlier: 3.652A pdb=" N GLU E 18 " --> pdb=" O TYR E 14 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 44 removed outlier: 3.573A pdb=" N ARG E 32 " --> pdb=" O ASN E 28 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LYS E 38 " --> pdb=" O ALA E 34 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N GLU E 39 " --> pdb=" O LYS E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 54 through 66 removed outlier: 4.043A pdb=" N ILE E 60 " --> pdb=" O ALA E 56 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU E 66 " --> pdb=" O GLU E 62 " (cutoff:3.500A) Processing helix chain 'F' and resid 71 through 82 Processing helix chain 'F' and resid 89 through 112 removed outlier: 3.800A pdb=" N GLN F 97 " --> pdb=" O GLU F 93 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU F 103 " --> pdb=" O ALA F 99 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG F 108 " --> pdb=" O LEU F 104 " (cutoff:3.500A) Processing helix chain 'F' and resid 174 through 197 removed outlier: 3.646A pdb=" N VAL F 194 " --> pdb=" O LYS F 190 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN F 195 " --> pdb=" O ASP F 191 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASN F 197 " --> pdb=" O MET F 193 " (cutoff:3.500A) Processing helix chain 'F' and resid 198 through 206 removed outlier: 3.572A pdb=" N VAL F 202 " --> pdb=" O LEU F 198 " (cutoff:3.500A) Processing helix chain 'F' and resid 214 through 232 removed outlier: 3.649A pdb=" N LEU F 218 " --> pdb=" O SER F 214 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ILE F 219 " --> pdb=" O PHE F 215 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLN F 220 " --> pdb=" O GLN F 216 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY F 225 " --> pdb=" O GLU F 221 " (cutoff:3.500A) Processing helix chain 'F' and resid 240 through 260 removed outlier: 3.673A pdb=" N TYR F 244 " --> pdb=" O LYS F 240 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N THR F 246 " --> pdb=" O SER F 242 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N TRP F 247 " --> pdb=" O THR F 243 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N TRP F 248 " --> pdb=" O TYR F 244 " (cutoff:3.500A) Processing helix chain 'F' and resid 267 through 288 removed outlier: 3.600A pdb=" N TYR F 271 " --> pdb=" O PRO F 267 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU F 272 " --> pdb=" O VAL F 268 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLN F 286 " --> pdb=" O LYS F 282 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU F 287 " --> pdb=" O LEU F 283 " (cutoff:3.500A) Processing helix chain 'F' and resid 294 through 301 removed outlier: 3.592A pdb=" N ALA F 298 " --> pdb=" O GLU F 294 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS F 300 " --> pdb=" O GLU F 296 " (cutoff:3.500A) Processing helix chain 'F' and resid 304 through 315 removed outlier: 3.788A pdb=" N LEU F 308 " --> pdb=" O THR F 304 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ARG F 309 " --> pdb=" O ILE F 305 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N PHE F 310 " --> pdb=" O GLU F 306 " (cutoff:3.500A) Processing helix chain 'F' and resid 343 through 358 removed outlier: 3.559A pdb=" N GLU F 347 " --> pdb=" O THR F 343 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER F 349 " --> pdb=" O GLU F 345 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASN F 351 " --> pdb=" O GLU F 347 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG F 354 " --> pdb=" O LYS F 350 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLU F 355 " --> pdb=" O ASN F 351 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASP F 356 " --> pdb=" O LEU F 352 " (cutoff:3.500A) Processing helix chain 'F' and resid 358 through 363 removed outlier: 3.967A pdb=" N THR F 363 " --> pdb=" O ASN F 359 " (cutoff:3.500A) Processing helix chain 'F' and resid 365 through 377 removed outlier: 3.562A pdb=" N VAL F 371 " --> pdb=" O ARG F 367 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU F 372 " --> pdb=" O GLU F 368 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU F 374 " --> pdb=" O ASP F 370 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N TYR F 376 " --> pdb=" O LEU F 372 " (cutoff:3.500A) Processing helix chain 'F' and resid 385 through 393 removed outlier: 3.823A pdb=" N ILE F 389 " --> pdb=" O THR F 385 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ILE F 392 " --> pdb=" O GLU F 388 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE F 393 " --> pdb=" O ILE F 389 " (cutoff:3.500A) Processing helix chain 'F' and resid 399 through 413 removed outlier: 3.598A pdb=" N LEU F 411 " --> pdb=" O ALA F 407 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ARG F 412 " --> pdb=" O LEU F 408 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N HIS F 413 " --> pdb=" O ARG F 409 " (cutoff:3.500A) Processing helix chain 'Z' and resid 9 through 24 removed outlier: 3.603A pdb=" N LYS Z 15 " --> pdb=" O GLY Z 11 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU Z 16 " --> pdb=" O ARG Z 12 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG Z 22 " --> pdb=" O ALA Z 18 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG Z 23 " --> pdb=" O LEU Z 19 " (cutoff:3.500A) Processing helix chain 'Z' and resid 26 through 46 removed outlier: 3.526A pdb=" N LYS Z 37 " --> pdb=" O ALA Z 33 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLU Z 38 " --> pdb=" O ASP Z 34 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N THR Z 45 " --> pdb=" O PHE Z 41 " (cutoff:3.500A) Processing helix chain 'Z' and resid 61 through 81 removed outlier: 3.712A pdb=" N ALA Z 68 " --> pdb=" O GLN Z 64 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS Z 71 " --> pdb=" O GLU Z 67 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU Z 72 " --> pdb=" O ALA Z 68 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR Z 76 " --> pdb=" O GLU Z 72 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ARG Z 79 " --> pdb=" O THR Z 75 " (cutoff:3.500A) Processing helix chain 'Z' and resid 86 through 116 removed outlier: 3.536A pdb=" N ASP Z 96 " --> pdb=" O GLN Z 92 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU Z 104 " --> pdb=" O GLY Z 100 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL Z 110 " --> pdb=" O LYS Z 106 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ARG Z 114 " --> pdb=" O VAL Z 110 " (cutoff:3.500A) Processing helix chain 'Z' and resid 120 through 128 removed outlier: 3.695A pdb=" N MET Z 125 " --> pdb=" O SER Z 121 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA Z 126 " --> pdb=" O VAL Z 122 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER Z 128 " --> pdb=" O MET Z 124 " (cutoff:3.500A) Processing helix chain 'Z' and resid 133 through 142 removed outlier: 4.130A pdb=" N GLN Z 139 " --> pdb=" O SER Z 135 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU Z 140 " --> pdb=" O GLN Z 136 " (cutoff:3.500A) Processing helix chain 'Z' and resid 168 through 204 removed outlier: 3.616A pdb=" N VAL Z 173 " --> pdb=" O VAL Z 169 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE Z 174 " --> pdb=" O THR Z 170 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER Z 175 " --> pdb=" O GLU Z 171 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N TYR Z 177 " --> pdb=" O VAL Z 173 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLY Z 178 " --> pdb=" O ILE Z 174 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR Z 186 " --> pdb=" O GLY Z 182 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA Z 187 " --> pdb=" O LEU Z 183 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU Z 188 " --> pdb=" O VAL Z 184 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA Z 191 " --> pdb=" O ALA Z 187 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR Z 195 " --> pdb=" O ALA Z 191 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER Z 204 " --> pdb=" O LEU Z 200 " (cutoff:3.500A) Processing helix chain 'Z' and resid 234 through 239 removed outlier: 3.721A pdb=" N ARG Z 238 " --> pdb=" O SER Z 234 " (cutoff:3.500A) Processing helix chain 'Z' and resid 267 through 272 Processing helix chain 'Z' and resid 282 through 286 Processing helix chain 'Z' and resid 293 through 298 removed outlier: 3.649A pdb=" N GLY Z 298 " --> pdb=" O GLN Z 294 " (cutoff:3.500A) Processing helix chain 'Z' and resid 312 through 323 removed outlier: 4.023A pdb=" N ILE Z 316 " --> pdb=" O ALA Z 312 " (cutoff:3.500A) Processing helix chain 'Z' and resid 324 through 328 removed outlier: 3.890A pdb=" N LEU Z 328 " --> pdb=" O GLY Z 325 " (cutoff:3.500A) Processing helix chain 'Z' and resid 682 through 687 removed outlier: 3.943A pdb=" N VAL Z 686 " --> pdb=" O ASP Z 682 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LYS Z 687 " --> pdb=" O PRO Z 683 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 682 through 687' Processing helix chain 'Z' and resid 885 through 887 No H-bonds generated for 'chain 'Z' and resid 885 through 887' Processing helix chain 'Z' and resid 981 through 991 removed outlier: 3.642A pdb=" N ARG Z 985 " --> pdb=" O GLN Z 981 " (cutoff:3.500A) Processing helix chain 'Z' and resid 1062 through 1071 removed outlier: 3.875A pdb=" N ASP Z1066 " --> pdb=" O HIS Z1062 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL Z1067 " --> pdb=" O GLU Z1063 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE Z1068 " --> pdb=" O ILE Z1064 " (cutoff:3.500A) Processing helix chain 'Z' and resid 1077 through 1104 removed outlier: 3.561A pdb=" N ALA Z1088 " --> pdb=" O ARG Z1084 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLN Z1104 " --> pdb=" O VAL Z1100 " (cutoff:3.500A) Processing helix chain 'Z' and resid 1109 through 1121 removed outlier: 3.936A pdb=" N ILE Z1113 " --> pdb=" O SER Z1109 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N VAL Z1115 " --> pdb=" O LYS Z1111 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ILE Z1116 " --> pdb=" O HIS Z1112 " (cutoff:3.500A) Processing helix chain 'Z' and resid 1142 through 1153 Processing helix chain 'Z' and resid 1179 through 1184 Processing helix chain 'Z' and resid 1187 through 1199 removed outlier: 3.620A pdb=" N THR Z1193 " --> pdb=" O THR Z1189 " (cutoff:3.500A) Processing helix chain 'Z' and resid 1209 through 1214 Processing helix chain 'Z' and resid 1219 through 1223 removed outlier: 3.613A pdb=" N GLY Z1222 " --> pdb=" O ALA Z1219 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N PHE Z1223 " --> pdb=" O GLY Z1220 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 1219 through 1223' Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 13 removed outlier: 3.621A pdb=" N GLU A 26 " --> pdb=" O GLN A 5 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N LYS A 22 " --> pdb=" O VAL A 9 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N SER A 11 " --> pdb=" O TYR A 20 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N TYR A 20 " --> pdb=" O SER A 11 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN A 19 " --> pdb=" O THR A 204 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR A 183 " --> pdb=" O ILE A 199 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS A 179 " --> pdb=" O TRP A 203 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 49 through 53 Processing sheet with id=AA3, first strand: chain 'A' and resid 49 through 53 removed outlier: 3.821A pdb=" N GLY A 147 " --> pdb=" O PHE A 174 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 55 through 56 Processing sheet with id=AA5, first strand: chain 'A' and resid 87 through 89 removed outlier: 3.680A pdb=" N LYS A 88 " --> pdb=" O GLU A 119 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLU A 119 " --> pdb=" O LYS A 88 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 101 through 102 Processing sheet with id=AA7, first strand: chain 'B' and resid 5 through 13 removed outlier: 3.603A pdb=" N GLU B 7 " --> pdb=" O SER B 24 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N LYS B 22 " --> pdb=" O VAL B 9 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N SER B 11 " --> pdb=" O TYR B 20 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N TYR B 20 " --> pdb=" O SER B 11 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N GLN B 19 " --> pdb=" O THR B 200 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ASP B 192 " --> pdb=" O PRO B 27 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 95 through 99 removed outlier: 3.916A pdb=" N GLN B 95 " --> pdb=" O VAL B 142 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL B 142 " --> pdb=" O GLN B 95 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N GLU B 139 " --> pdb=" O ILE B 56 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N ILE B 56 " --> pdb=" O GLU B 139 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N ARG B 141 " --> pdb=" O THR B 54 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N THR B 54 " --> pdb=" O ARG B 141 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 87 through 88 removed outlier: 3.906A pdb=" N LYS B 88 " --> pdb=" O GLU B 119 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLU B 119 " --> pdb=" O LYS B 88 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 147 through 149 removed outlier: 4.331A pdb=" N GLY B 147 " --> pdb=" O PHE B 170 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N SER B 168 " --> pdb=" O ARG B 149 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 38 through 39 removed outlier: 3.774A pdb=" N HIS C 48 " --> pdb=" O ARG C 82 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG C 82 " --> pdb=" O HIS C 48 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N VAL C 75 " --> pdb=" O ASP C 100 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N ASP C 100 " --> pdb=" O VAL C 75 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N MET C 77 " --> pdb=" O ILE C 98 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL C 79 " --> pdb=" O VAL C 96 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 110 through 112 Processing sheet with id=AB4, first strand: chain 'C' and resid 305 through 308 removed outlier: 3.638A pdb=" N ASN C 121 " --> pdb=" O ARG C 383 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 128 through 134 removed outlier: 3.510A pdb=" N THR C 142 " --> pdb=" O GLU C 134 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 156 through 160 removed outlier: 3.930A pdb=" N LEU C 164 " --> pdb=" O ASP C 160 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 434 through 435 Processing sheet with id=AB8, first strand: chain 'C' and resid 445 through 447 Processing sheet with id=AB9, first strand: chain 'C' and resid 490 through 493 Processing sheet with id=AC1, first strand: chain 'C' and resid 572 through 573 removed outlier: 6.691A pdb=" N ILE C 572 " --> pdb=" O LEU C 639 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 579 through 583 removed outlier: 6.134A pdb=" N VAL C 580 " --> pdb=" O GLN C 591 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N GLN C 591 " --> pdb=" O VAL C 580 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL C 590 " --> pdb=" O ILE C 605 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 671 through 675 removed outlier: 7.208A pdb=" N ILE C 672 " --> pdb=" O ARG C 834 " (cutoff:3.500A) removed outlier: 8.214A pdb=" N LEU C 836 " --> pdb=" O ILE C 672 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ILE C 674 " --> pdb=" O LEU C 836 " (cutoff:3.500A) removed outlier: 9.716A pdb=" N ILE C 852 " --> pdb=" O ASN C 655 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N LEU C 657 " --> pdb=" O ILE C 852 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N LEU C 854 " --> pdb=" O LEU C 657 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N ALA C 659 " --> pdb=" O LEU C 854 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 702 through 703 removed outlier: 3.720A pdb=" N THR C 699 " --> pdb=" O GLY C 702 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N MET C 804 " --> pdb=" O ALA C 696 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N GLN C 698 " --> pdb=" O ALA C 802 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ALA C 802 " --> pdb=" O GLN C 698 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N TYR C 809 " --> pdb=" O VAL C 785 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 702 through 703 removed outlier: 3.720A pdb=" N THR C 699 " --> pdb=" O GLY C 702 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N MET C 804 " --> pdb=" O ALA C 696 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N GLN C 698 " --> pdb=" O ALA C 802 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ALA C 802 " --> pdb=" O GLN C 698 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 738 through 740 removed outlier: 6.729A pdb=" N LEU C 774 " --> pdb=" O LEU C 739 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 743 through 745 Processing sheet with id=AC8, first strand: chain 'C' and resid 961 through 963 removed outlier: 3.550A pdb=" N CYS D 373 " --> pdb=" O GLU D 445 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 961 through 963 Processing sheet with id=AD1, first strand: chain 'C' and resid 986 through 987 Processing sheet with id=AD2, first strand: chain 'C' and resid 1052 through 1057 removed outlier: 3.730A pdb=" N TYR D 11 " --> pdb=" O HIS C1057 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 105 through 113 removed outlier: 10.626A pdb=" N LEU D 108 " --> pdb=" O PRO D 250 " (cutoff:3.500A) removed outlier: 10.847A pdb=" N ALA D 110 " --> pdb=" O VAL D 248 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N VAL D 248 " --> pdb=" O ALA D 110 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 161 through 162 removed outlier: 6.192A pdb=" N GLU D 185 " --> pdb=" O LEU D 148 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 260 through 261 removed outlier: 3.546A pdb=" N VAL D 260 " --> pdb=" O ALA D 268 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N PHE D 267 " --> pdb=" O ILE F 319 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 533 through 535 Processing sheet with id=AD7, first strand: chain 'D' and resid 565 through 567 removed outlier: 6.828A pdb=" N VAL D 566 " --> pdb=" O ASN Z 5 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'Z' and resid 220 through 222 Processing sheet with id=AD9, first strand: chain 'Z' and resid 225 through 226 removed outlier: 7.129A pdb=" N MET Z 225 " --> pdb=" O LYS Z 232 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'Z' and resid 355 through 356 removed outlier: 4.200A pdb=" N ILE Z 384 " --> pdb=" O LYS Z 356 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'Z' and resid 363 through 367 removed outlier: 3.838A pdb=" N SER Z 403 " --> pdb=" O VAL Z 377 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N LEU Z 404 " --> pdb=" O GLU Z 421 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLU Z 421 " --> pdb=" O LEU Z 404 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'Z' and resid 433 through 439 removed outlier: 7.414A pdb=" N ALA Z 434 " --> pdb=" O VAL Z 970 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N VAL Z 970 " --> pdb=" O ALA Z 434 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N LYS Z 436 " --> pdb=" O LEU Z 968 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N LEU Z 968 " --> pdb=" O LYS Z 436 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N VAL Z 438 " --> pdb=" O LEU Z 966 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'Z' and resid 446 through 449 removed outlier: 3.645A pdb=" N ILE Z 475 " --> pdb=" O ARG Z 942 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'Z' and resid 446 through 449 removed outlier: 3.645A pdb=" N ILE Z 475 " --> pdb=" O ARG Z 942 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'Z' and resid 479 through 482 removed outlier: 3.980A pdb=" N LEU Z 882 " --> pdb=" O ARG Z 869 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG Z 869 " --> pdb=" O LEU Z 882 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU Z 884 " --> pdb=" O THR Z 867 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR Z 867 " --> pdb=" O GLU Z 884 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLY Z 866 " --> pdb=" O VAL Z 497 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'Z' and resid 487 through 489 removed outlier: 3.622A pdb=" N GLU Z 488 " --> pdb=" O GLU Z 505 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ALA Z 504 " --> pdb=" O ILE Z 860 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N THR Z 858 " --> pdb=" O THR Z 506 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LEU Z 508 " --> pdb=" O ALA Z 856 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ALA Z 856 " --> pdb=" O LEU Z 508 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ALA Z 836 " --> pdb=" O GLN Z 861 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'Z' and resid 487 through 489 removed outlier: 3.622A pdb=" N GLU Z 488 " --> pdb=" O GLU Z 505 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ALA Z 504 " --> pdb=" O ILE Z 860 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N THR Z 858 " --> pdb=" O THR Z 506 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LEU Z 508 " --> pdb=" O ALA Z 856 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ALA Z 856 " --> pdb=" O LEU Z 508 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'Z' and resid 515 through 516 removed outlier: 3.568A pdb=" N ILE Z 526 " --> pdb=" O GLU Z 820 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N ILE Z 818 " --> pdb=" O THR Z 528 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU Z 803 " --> pdb=" O GLN Z 815 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N VAL Z 817 " --> pdb=" O ILE Z 801 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'Z' and resid 538 through 539 removed outlier: 4.525A pdb=" N ALA Z 576 " --> pdb=" O LEU Z 782 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N THR Z 780 " --> pdb=" O LEU Z 578 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ARG Z 760 " --> pdb=" O SER Z 779 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'Z' and resid 589 through 594 removed outlier: 3.714A pdb=" N ARG Z 592 " --> pdb=" O LEU Z 616 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA Z 594 " --> pdb=" O THR Z 614 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N THR Z 614 " --> pdb=" O ALA Z 594 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'Z' and resid 646 through 647 Processing sheet with id=AF4, first strand: chain 'Z' and resid 656 through 662 removed outlier: 4.169A pdb=" N GLU Z 669 " --> pdb=" O VAL Z 661 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'Z' and resid 676 through 677 Processing sheet with id=AF6, first strand: chain 'Z' and resid 1139 through 1141 901 hydrogen bonds defined for protein. 2514 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 77 hydrogen bonds 154 hydrogen bond angles 0 basepair planarities 31 basepair parallelities 79 stacking parallelities Total time for adding SS restraints: 14.68 Time building geometry restraints manager: 12.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 8900 1.33 - 1.45: 4337 1.45 - 1.57: 16596 1.57 - 1.69: 192 1.69 - 1.81: 141 Bond restraints: 30166 Sorted by residual: bond pdb=" C3' DG 1 48 " pdb=" O3' DG 1 48 " ideal model delta sigma weight residual 1.422 1.489 -0.067 3.00e-02 1.11e+03 4.93e+00 bond pdb=" C GLU Z 323 " pdb=" N PRO Z 324 " ideal model delta sigma weight residual 1.334 1.381 -0.047 2.34e-02 1.83e+03 3.98e+00 bond pdb=" N THR B 108 " pdb=" CA THR B 108 " ideal model delta sigma weight residual 1.460 1.486 -0.026 1.54e-02 4.22e+03 2.87e+00 bond pdb=" C3' DG 2 17 " pdb=" O3' DG 2 17 " ideal model delta sigma weight residual 1.422 1.472 -0.050 3.00e-02 1.11e+03 2.76e+00 bond pdb=" C3' DG 1 34 " pdb=" O3' DG 1 34 " ideal model delta sigma weight residual 1.422 1.470 -0.048 3.00e-02 1.11e+03 2.61e+00 ... (remaining 30161 not shown) Histogram of bond angle deviations from ideal: 99.58 - 106.48: 1374 106.48 - 113.37: 16428 113.37 - 120.26: 11085 120.26 - 127.16: 12014 127.16 - 134.05: 420 Bond angle restraints: 41321 Sorted by residual: angle pdb=" C ARG Z 826 " pdb=" N ASP Z 827 " pdb=" CA ASP Z 827 " ideal model delta sigma weight residual 121.70 129.49 -7.79 1.80e+00 3.09e-01 1.87e+01 angle pdb=" C VAL B 107 " pdb=" N THR B 108 " pdb=" CA THR B 108 " ideal model delta sigma weight residual 122.46 128.34 -5.88 1.41e+00 5.03e-01 1.74e+01 angle pdb=" C ARG C 792 " pdb=" N GLU C 793 " pdb=" CA GLU C 793 " ideal model delta sigma weight residual 121.54 128.97 -7.43 1.91e+00 2.74e-01 1.51e+01 angle pdb=" C GLY D 74 " pdb=" N LYS D 75 " pdb=" CA LYS D 75 " ideal model delta sigma weight residual 121.54 128.28 -6.74 1.91e+00 2.74e-01 1.24e+01 angle pdb=" N ASP Z 827 " pdb=" CA ASP Z 827 " pdb=" C ASP Z 827 " ideal model delta sigma weight residual 111.00 120.37 -9.37 2.80e+00 1.28e-01 1.12e+01 ... (remaining 41316 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.69: 17504 35.69 - 71.38: 554 71.38 - 107.07: 28 107.07 - 142.76: 1 142.76 - 178.45: 2 Dihedral angle restraints: 18089 sinusoidal: 7695 harmonic: 10394 Sorted by residual: dihedral pdb=" CA ALA A 131 " pdb=" C ALA A 131 " pdb=" N GLU A 132 " pdb=" CA GLU A 132 " ideal model delta harmonic sigma weight residual 180.00 157.97 22.03 0 5.00e+00 4.00e-02 1.94e+01 dihedral pdb=" C4' DG 1 48 " pdb=" C3' DG 1 48 " pdb=" O3' DG 1 48 " pdb=" P DC 1 49 " ideal model delta sinusoidal sigma weight residual -140.00 38.45 -178.45 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DG 2 17 " pdb=" C3' DG 2 17 " pdb=" O3' DG 2 17 " pdb=" P DG 2 18 " ideal model delta sinusoidal sigma weight residual 220.00 76.99 143.01 1 3.50e+01 8.16e-04 1.41e+01 ... (remaining 18086 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 3894 0.054 - 0.108: 725 0.108 - 0.162: 155 0.162 - 0.216: 13 0.216 - 0.270: 1 Chirality restraints: 4788 Sorted by residual: chirality pdb=" CB VAL C1059 " pdb=" CA VAL C1059 " pdb=" CG1 VAL C1059 " pdb=" CG2 VAL C1059 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.82e+00 chirality pdb=" CB ILE D 370 " pdb=" CA ILE D 370 " pdb=" CG1 ILE D 370 " pdb=" CG2 ILE D 370 " both_signs ideal model delta sigma weight residual False 2.64 2.85 -0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CB ILE C 816 " pdb=" CA ILE C 816 " pdb=" CG1 ILE C 816 " pdb=" CG2 ILE C 816 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.65e-01 ... (remaining 4785 not shown) Planarity restraints: 5056 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE D 252 " 0.048 5.00e-02 4.00e+02 7.27e-02 8.46e+00 pdb=" N PRO D 253 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO D 253 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO D 253 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN C 373 " -0.040 5.00e-02 4.00e+02 6.00e-02 5.77e+00 pdb=" N PRO C 374 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO C 374 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO C 374 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 634 " 0.039 5.00e-02 4.00e+02 5.93e-02 5.63e+00 pdb=" N PRO C 635 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO C 635 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO C 635 " 0.033 5.00e-02 4.00e+02 ... (remaining 5053 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 1162 2.72 - 3.27: 25112 3.27 - 3.81: 44965 3.81 - 4.36: 57058 4.36 - 4.90: 95737 Nonbonded interactions: 224034 Sorted by model distance: nonbonded pdb=" O3' A 3 15 " pdb="MG MG D2001 " model vdw 2.178 2.170 nonbonded pdb=" OD1 ASP D 471 " pdb="MG MG D2001 " model vdw 2.192 2.170 nonbonded pdb=" OG SER Z 542 " pdb=" O GLN Z 548 " model vdw 2.306 2.440 nonbonded pdb=" OD2 ASP F 356 " pdb=" OH TYR F 423 " model vdw 2.326 2.440 nonbonded pdb=" O GLN D 528 " pdb=" OG SER D 554 " model vdw 2.326 2.440 ... (remaining 224029 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 3 and (name N or name CA or name C or name O or name CB ) \ ) or resid 4 through 100 or resid 106 or (resid 107 and (name N or name CA or na \ me C or name O or name CB )) or resid 108 through 112 or (resid 113 and (name N \ or name CA or name C or name O or name CB )) or resid 114 or resid 119 through 1 \ 31 or resid 136 through 152 or resid 166 through 186 or (resid 187 through 188 a \ nd (name N or name CA or name C or name O or name CB )) or resid 193 through 230 \ )) selection = (chain 'B' and (resid 3 through 13 or (resid 14 through 18 and (name N or name C \ A or name C or name O or name CB )) or resid 19 through 28 or (resid 29 through \ 30 and (name N or name CA or name C or name O or name CB )) or resid 31 through \ 97 or (resid 98 and (name N or name CA or name C or name O or name CB )) or resi \ d 99 through 148 or (resid 149 and (name N or name CA or name C or name O or nam \ e CB )) or resid 150 through 151 or (resid 152 and (name N or name CA or name C \ or name O or name CB )) or (resid 162 and (name N or name CA or name C or name O \ or name CB )) or resid 163 through 184 or resid 189 through 225 or (resid 226 a \ nd (name N or name CA or name C or name O or name CB )))) } 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=0.30 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.320 Construct map_model_manager: 0.020 Extract box with map and model: 7.350 Check model and map are aligned: 0.390 Set scattering table: 0.260 Process input model: 93.380 Find NCS groups from input model: 1.120 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 107.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 30166 Z= 0.166 Angle : 0.584 9.370 41321 Z= 0.332 Chirality : 0.045 0.270 4788 Planarity : 0.005 0.073 5056 Dihedral : 15.630 178.452 11389 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 0.11 % Allowed : 5.52 % Favored : 94.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.06 (0.10), residues: 3562 helix: -4.98 (0.04), residues: 1050 sheet: -1.84 (0.21), residues: 482 loop : -2.89 (0.11), residues: 2030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 203 HIS 0.003 0.001 HIS C 593 PHE 0.020 0.001 PHE B 65 TYR 0.016 0.001 TYR C 680 ARG 0.002 0.000 ARG D 438 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7124 Ramachandran restraints generated. 3562 Oldfield, 0 Emsley, 3562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7124 Ramachandran restraints generated. 3562 Oldfield, 0 Emsley, 3562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 3103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 532 time to evaluate : 3.388 Fit side-chains REVERT: A 195 LYS cc_start: 0.7368 (mttm) cc_final: 0.6859 (mtmt) REVERT: B 124 ASN cc_start: 0.6841 (p0) cc_final: 0.6627 (p0) REVERT: C 35 PHE cc_start: 0.7529 (t80) cc_final: 0.6892 (t80) REVERT: C 65 GLU cc_start: 0.5965 (tt0) cc_final: 0.5754 (tt0) REVERT: C 168 ARG cc_start: 0.7089 (ttm-80) cc_final: 0.6875 (ttm170) REVERT: C 550 ARG cc_start: 0.7459 (tpt170) cc_final: 0.7195 (tpp-160) REVERT: C 664 GLU cc_start: 0.6780 (mm-30) cc_final: 0.6540 (mm-30) REVERT: C 771 ASP cc_start: 0.6873 (t70) cc_final: 0.6575 (p0) REVERT: C 852 ILE cc_start: 0.8572 (mt) cc_final: 0.8330 (mt) REVERT: D 465 ASN cc_start: 0.8397 (t0) cc_final: 0.8178 (t0) REVERT: D 603 ILE cc_start: 0.8649 (mm) cc_final: 0.8313 (mt) REVERT: E 58 ARG cc_start: 0.8034 (ttp80) cc_final: 0.7724 (ttm170) REVERT: Z 112 ASN cc_start: 0.7540 (t0) cc_final: 0.7258 (t0) REVERT: Z 153 GLU cc_start: 0.7159 (mm-30) cc_final: 0.6935 (mm-30) REVERT: Z 367 ARG cc_start: 0.6984 (OUTLIER) cc_final: 0.6695 (ttt90) REVERT: Z 482 ASN cc_start: 0.7329 (p0) cc_final: 0.6949 (p0) REVERT: Z 537 GLN cc_start: 0.3665 (mm110) cc_final: 0.3448 (mp-120) REVERT: Z 539 LYS cc_start: 0.6704 (mtpp) cc_final: 0.6275 (mmmt) REVERT: Z 665 ASP cc_start: 0.6084 (t0) cc_final: 0.5804 (t0) REVERT: Z 762 PHE cc_start: 0.6842 (m-80) cc_final: 0.6430 (m-80) REVERT: Z 1152 MET cc_start: 0.6320 (ttm) cc_final: 0.5827 (mtp) REVERT: Z 1171 LYS cc_start: 0.8614 (tttt) cc_final: 0.7955 (tttt) REVERT: Z 1175 ASN cc_start: 0.7593 (m-40) cc_final: 0.7379 (m110) REVERT: Z 1180 ILE cc_start: 0.8446 (mt) cc_final: 0.8199 (mt) REVERT: Z 1187 GLU cc_start: 0.6928 (mt-10) cc_final: 0.6715 (mt-10) outliers start: 3 outliers final: 0 residues processed: 535 average time/residue: 0.5135 time to fit residues: 399.5043 Evaluate side-chains 366 residues out of total 3103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 365 time to evaluate : 3.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 367 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 310 optimal weight: 20.0000 chunk 278 optimal weight: 30.0000 chunk 154 optimal weight: 5.9990 chunk 95 optimal weight: 4.9990 chunk 188 optimal weight: 3.9990 chunk 149 optimal weight: 2.9990 chunk 288 optimal weight: 0.5980 chunk 111 optimal weight: 0.4980 chunk 175 optimal weight: 5.9990 chunk 214 optimal weight: 5.9990 chunk 334 optimal weight: 6.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN B 38 ASN C 17 HIS C 58 GLN C 113 ASN C 189 ASN C 277 GLN C 371 GLN C 577 HIS C 712 ASN C 724 HIS D 114 HIS D 166 GLN ** D 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 240 GLN D 283 ASN D 367 ASN D 528 GLN D 553 HIS F 110 ASN F 197 ASN F 402 GLN Z 139 GLN Z 662 GLN Z 664 ASN Z 711 GLN Z 781 GLN ** Z1098 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z1102 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.2377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 30166 Z= 0.404 Angle : 0.632 12.598 41321 Z= 0.332 Chirality : 0.046 0.191 4788 Planarity : 0.006 0.054 5056 Dihedral : 15.439 172.910 5022 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 1.71 % Allowed : 12.85 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.52 (0.12), residues: 3562 helix: -2.69 (0.11), residues: 1107 sheet: -1.13 (0.22), residues: 528 loop : -2.50 (0.12), residues: 1927 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 203 HIS 0.008 0.002 HIS C 577 PHE 0.020 0.002 PHE C 368 TYR 0.028 0.002 TYR C 680 ARG 0.024 0.001 ARG B 57 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7124 Ramachandran restraints generated. 3562 Oldfield, 0 Emsley, 3562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7124 Ramachandran restraints generated. 3562 Oldfield, 0 Emsley, 3562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 3103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 375 time to evaluate : 3.328 Fit side-chains REVERT: A 138 MET cc_start: 0.8540 (ptm) cc_final: 0.8134 (ptm) REVERT: B 74 ASP cc_start: 0.7412 (t0) cc_final: 0.7050 (t0) REVERT: B 124 ASN cc_start: 0.7241 (p0) cc_final: 0.6933 (p0) REVERT: C 21 HIS cc_start: 0.8078 (t70) cc_final: 0.7784 (t-90) REVERT: C 25 GLU cc_start: 0.7651 (pt0) cc_final: 0.7330 (pt0) REVERT: C 100 ASP cc_start: 0.7219 (t0) cc_final: 0.6643 (p0) REVERT: C 438 TYR cc_start: 0.8643 (m-10) cc_final: 0.8439 (m-80) REVERT: D 119 LYS cc_start: 0.8864 (tptt) cc_final: 0.8614 (tptp) REVERT: D 332 LYS cc_start: 0.8406 (tptt) cc_final: 0.8153 (mmmm) REVERT: D 603 ILE cc_start: 0.8723 (mm) cc_final: 0.8448 (mt) REVERT: F 110 ASN cc_start: 0.5398 (OUTLIER) cc_final: 0.4690 (p0) REVERT: F 367 ARG cc_start: 0.6784 (ttt180) cc_final: 0.6107 (tpm170) REVERT: Z 153 GLU cc_start: 0.7244 (mm-30) cc_final: 0.7021 (mm-30) REVERT: Z 537 GLN cc_start: 0.4189 (mm110) cc_final: 0.3639 (mp10) REVERT: Z 539 LYS cc_start: 0.6650 (mtpp) cc_final: 0.6116 (mmmt) REVERT: Z 665 ASP cc_start: 0.6315 (t0) cc_final: 0.5891 (t0) REVERT: Z 762 PHE cc_start: 0.7266 (m-80) cc_final: 0.6802 (m-80) REVERT: Z 1114 GLU cc_start: 0.7915 (pt0) cc_final: 0.7595 (mt-10) REVERT: Z 1147 GLN cc_start: 0.7794 (mm-40) cc_final: 0.7562 (mt0) REVERT: Z 1171 LYS cc_start: 0.8597 (tttt) cc_final: 0.8374 (tttt) outliers start: 48 outliers final: 26 residues processed: 404 average time/residue: 0.4511 time to fit residues: 281.1264 Evaluate side-chains 355 residues out of total 3103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 328 time to evaluate : 3.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 62 ASN Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 403 ASP Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 486 ILE Chi-restraints excluded: chain C residue 605 ILE Chi-restraints excluded: chain C residue 626 LEU Chi-restraints excluded: chain C residue 710 ILE Chi-restraints excluded: chain D residue 274 ASP Chi-restraints excluded: chain D residue 585 VAL Chi-restraints excluded: chain F residue 110 ASN Chi-restraints excluded: chain F residue 308 LEU Chi-restraints excluded: chain Z residue 264 ASP Chi-restraints excluded: chain Z residue 282 SER Chi-restraints excluded: chain Z residue 473 VAL Chi-restraints excluded: chain Z residue 528 THR Chi-restraints excluded: chain Z residue 629 ILE Chi-restraints excluded: chain Z residue 652 CYS Chi-restraints excluded: chain Z residue 783 VAL Chi-restraints excluded: chain Z residue 891 VAL Chi-restraints excluded: chain Z residue 951 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 185 optimal weight: 0.7980 chunk 103 optimal weight: 3.9990 chunk 278 optimal weight: 0.0670 chunk 227 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 334 optimal weight: 0.3980 chunk 361 optimal weight: 3.9990 chunk 298 optimal weight: 9.9990 chunk 331 optimal weight: 7.9990 chunk 114 optimal weight: 0.8980 chunk 268 optimal weight: 0.7980 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 85 ASN C 113 ASN C 121 ASN C 577 HIS C 654 GLN C 655 ASN D 201 GLN D 608 GLN Z 664 ASN ** Z 781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z1098 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 30166 Z= 0.144 Angle : 0.463 10.808 41321 Z= 0.245 Chirality : 0.041 0.160 4788 Planarity : 0.004 0.048 5056 Dihedral : 15.262 177.823 5018 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.53 % Allowed : 14.95 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.43 (0.13), residues: 3562 helix: -1.09 (0.14), residues: 1108 sheet: -0.81 (0.22), residues: 518 loop : -2.21 (0.12), residues: 1936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 25 HIS 0.007 0.001 HIS C 577 PHE 0.008 0.001 PHE C 157 TYR 0.013 0.001 TYR C 680 ARG 0.006 0.000 ARG C 82 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7124 Ramachandran restraints generated. 3562 Oldfield, 0 Emsley, 3562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7124 Ramachandran restraints generated. 3562 Oldfield, 0 Emsley, 3562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 3103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 356 time to evaluate : 3.252 Fit side-chains REVERT: A 93 GLN cc_start: 0.7748 (mm-40) cc_final: 0.7006 (mt0) REVERT: A 138 MET cc_start: 0.8389 (ptm) cc_final: 0.7968 (ptm) REVERT: B 74 ASP cc_start: 0.7316 (t0) cc_final: 0.6999 (t0) REVERT: B 124 ASN cc_start: 0.7138 (p0) cc_final: 0.6863 (p0) REVERT: C 25 GLU cc_start: 0.7661 (pt0) cc_final: 0.7443 (pt0) REVERT: C 100 ASP cc_start: 0.7130 (t0) cc_final: 0.6631 (p0) REVERT: D 119 LYS cc_start: 0.8787 (tptt) cc_final: 0.8549 (tptp) REVERT: D 332 LYS cc_start: 0.8364 (tptt) cc_final: 0.8147 (mmmm) REVERT: D 603 ILE cc_start: 0.8688 (mm) cc_final: 0.8440 (mt) REVERT: F 367 ARG cc_start: 0.6615 (ttt180) cc_final: 0.6043 (tpm170) REVERT: Z 153 GLU cc_start: 0.7238 (mm-30) cc_final: 0.7004 (mm-30) REVERT: Z 537 GLN cc_start: 0.4144 (mm110) cc_final: 0.3583 (mp10) REVERT: Z 539 LYS cc_start: 0.6705 (mtpp) cc_final: 0.6201 (mmmt) REVERT: Z 665 ASP cc_start: 0.6439 (t0) cc_final: 0.6085 (t0) REVERT: Z 762 PHE cc_start: 0.7185 (m-80) cc_final: 0.6708 (m-80) REVERT: Z 1020 ILE cc_start: 0.4393 (OUTLIER) cc_final: 0.4150 (pt) outliers start: 43 outliers final: 24 residues processed: 385 average time/residue: 0.4480 time to fit residues: 266.0732 Evaluate side-chains 354 residues out of total 3103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 329 time to evaluate : 3.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ASN Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 90 TYR Chi-restraints excluded: chain B residue 6 ILE Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 486 ILE Chi-restraints excluded: chain C residue 497 GLU Chi-restraints excluded: chain C residue 626 LEU Chi-restraints excluded: chain C residue 852 ILE Chi-restraints excluded: chain D residue 585 VAL Chi-restraints excluded: chain F residue 308 LEU Chi-restraints excluded: chain Z residue 112 ASN Chi-restraints excluded: chain Z residue 151 GLN Chi-restraints excluded: chain Z residue 237 ASP Chi-restraints excluded: chain Z residue 247 ASP Chi-restraints excluded: chain Z residue 264 ASP Chi-restraints excluded: chain Z residue 528 THR Chi-restraints excluded: chain Z residue 629 ILE Chi-restraints excluded: chain Z residue 891 VAL Chi-restraints excluded: chain Z residue 951 VAL Chi-restraints excluded: chain Z residue 1010 VAL Chi-restraints excluded: chain Z residue 1020 ILE Chi-restraints excluded: chain Z residue 1132 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 330 optimal weight: 0.0270 chunk 251 optimal weight: 2.9990 chunk 173 optimal weight: 0.9990 chunk 37 optimal weight: 7.9990 chunk 159 optimal weight: 1.9990 chunk 224 optimal weight: 3.9990 chunk 335 optimal weight: 8.9990 chunk 355 optimal weight: 4.9990 chunk 175 optimal weight: 5.9990 chunk 318 optimal weight: 6.9990 chunk 95 optimal weight: 5.9990 overall best weight: 2.0046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 ASN C 113 ASN C 577 HIS C 593 HIS C 724 HIS ** Z 781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 815 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.2988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 30166 Z= 0.312 Angle : 0.551 15.250 41321 Z= 0.287 Chirality : 0.045 0.163 4788 Planarity : 0.004 0.045 5056 Dihedral : 15.430 173.456 5018 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 2.06 % Allowed : 16.41 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.13), residues: 3562 helix: -0.54 (0.15), residues: 1126 sheet: -0.65 (0.22), residues: 514 loop : -2.09 (0.12), residues: 1922 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 203 HIS 0.009 0.001 HIS C 577 PHE 0.013 0.002 PHE C 157 TYR 0.025 0.002 TYR Z 6 ARG 0.007 0.001 ARG C 330 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7124 Ramachandran restraints generated. 3562 Oldfield, 0 Emsley, 3562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7124 Ramachandran restraints generated. 3562 Oldfield, 0 Emsley, 3562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 3103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 345 time to evaluate : 3.515 Fit side-chains REVERT: A 93 GLN cc_start: 0.7914 (mm-40) cc_final: 0.7229 (mt0) REVERT: B 74 ASP cc_start: 0.7460 (t0) cc_final: 0.7140 (t0) REVERT: C 21 HIS cc_start: 0.7903 (t70) cc_final: 0.7602 (t-90) REVERT: C 25 GLU cc_start: 0.7782 (pt0) cc_final: 0.7408 (pt0) REVERT: C 100 ASP cc_start: 0.7191 (t0) cc_final: 0.6677 (p0) REVERT: D 119 LYS cc_start: 0.8908 (tptt) cc_final: 0.8700 (tptp) REVERT: D 332 LYS cc_start: 0.8335 (tptt) cc_final: 0.8127 (mmmm) REVERT: E 15 ARG cc_start: 0.8463 (OUTLIER) cc_final: 0.8126 (mtt-85) REVERT: Z 153 GLU cc_start: 0.7297 (mm-30) cc_final: 0.7068 (mm-30) REVERT: Z 537 GLN cc_start: 0.4323 (mm110) cc_final: 0.3765 (mp10) REVERT: Z 539 LYS cc_start: 0.6783 (mtpp) cc_final: 0.6267 (mmmt) REVERT: Z 762 PHE cc_start: 0.7103 (m-80) cc_final: 0.6736 (m-80) outliers start: 58 outliers final: 45 residues processed: 385 average time/residue: 0.4551 time to fit residues: 271.8634 Evaluate side-chains 368 residues out of total 3103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 322 time to evaluate : 3.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 62 ASN Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 201 ASP Chi-restraints excluded: chain B residue 6 ILE Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 486 ILE Chi-restraints excluded: chain C residue 577 HIS Chi-restraints excluded: chain C residue 626 LEU Chi-restraints excluded: chain C residue 710 ILE Chi-restraints excluded: chain C residue 953 VAL Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 585 VAL Chi-restraints excluded: chain E residue 15 ARG Chi-restraints excluded: chain F residue 80 ILE Chi-restraints excluded: chain F residue 297 ILE Chi-restraints excluded: chain F residue 308 LEU Chi-restraints excluded: chain Z residue 2 THR Chi-restraints excluded: chain Z residue 151 GLN Chi-restraints excluded: chain Z residue 237 ASP Chi-restraints excluded: chain Z residue 247 ASP Chi-restraints excluded: chain Z residue 264 ASP Chi-restraints excluded: chain Z residue 293 CYS Chi-restraints excluded: chain Z residue 473 VAL Chi-restraints excluded: chain Z residue 482 ASN Chi-restraints excluded: chain Z residue 528 THR Chi-restraints excluded: chain Z residue 629 ILE Chi-restraints excluded: chain Z residue 644 THR Chi-restraints excluded: chain Z residue 652 CYS Chi-restraints excluded: chain Z residue 660 VAL Chi-restraints excluded: chain Z residue 728 VAL Chi-restraints excluded: chain Z residue 783 VAL Chi-restraints excluded: chain Z residue 891 VAL Chi-restraints excluded: chain Z residue 951 VAL Chi-restraints excluded: chain Z residue 1010 VAL Chi-restraints excluded: chain Z residue 1020 ILE Chi-restraints excluded: chain Z residue 1054 LEU Chi-restraints excluded: chain Z residue 1128 ASP Chi-restraints excluded: chain Z residue 1132 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 296 optimal weight: 0.0270 chunk 201 optimal weight: 4.9990 chunk 5 optimal weight: 0.1980 chunk 264 optimal weight: 7.9990 chunk 146 optimal weight: 0.9980 chunk 303 optimal weight: 5.9990 chunk 245 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 181 optimal weight: 0.8980 chunk 319 optimal weight: 30.0000 chunk 89 optimal weight: 0.9980 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 113 ASN C 577 HIS ** D 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 402 GLN ** Z 781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 30166 Z= 0.147 Angle : 0.465 12.926 41321 Z= 0.244 Chirality : 0.041 0.212 4788 Planarity : 0.003 0.046 5056 Dihedral : 15.300 176.138 5018 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.81 % Allowed : 17.05 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.13), residues: 3562 helix: 0.03 (0.16), residues: 1122 sheet: -0.46 (0.23), residues: 517 loop : -1.92 (0.13), residues: 1923 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 203 HIS 0.012 0.001 HIS C 577 PHE 0.008 0.001 PHE Z1179 TYR 0.017 0.001 TYR C 61 ARG 0.009 0.000 ARG C 68 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7124 Ramachandran restraints generated. 3562 Oldfield, 0 Emsley, 3562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7124 Ramachandran restraints generated. 3562 Oldfield, 0 Emsley, 3562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 3103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 341 time to evaluate : 3.342 Fit side-chains REVERT: A 93 GLN cc_start: 0.7866 (mm-40) cc_final: 0.7240 (mt0) REVERT: B 5 GLN cc_start: 0.7005 (OUTLIER) cc_final: 0.6642 (pm20) REVERT: B 74 ASP cc_start: 0.7390 (t0) cc_final: 0.7047 (t0) REVERT: C 100 ASP cc_start: 0.7155 (t0) cc_final: 0.6685 (p0) REVERT: D 119 LYS cc_start: 0.8817 (tptt) cc_final: 0.8612 (tptp) REVERT: D 332 LYS cc_start: 0.8288 (tptt) cc_final: 0.8084 (mmmm) REVERT: Z 14 LYS cc_start: 0.7961 (ttmm) cc_final: 0.7752 (tttt) REVERT: Z 153 GLU cc_start: 0.7265 (mm-30) cc_final: 0.7029 (mm-30) REVERT: Z 537 GLN cc_start: 0.4046 (mm110) cc_final: 0.3788 (mp10) REVERT: Z 539 LYS cc_start: 0.6783 (mtpp) cc_final: 0.6213 (mmmt) REVERT: Z 665 ASP cc_start: 0.6516 (t0) cc_final: 0.6276 (t0) REVERT: Z 762 PHE cc_start: 0.7174 (m-80) cc_final: 0.6742 (m-80) REVERT: Z 816 LEU cc_start: 0.6677 (mm) cc_final: 0.5912 (tp) outliers start: 51 outliers final: 38 residues processed: 376 average time/residue: 0.4487 time to fit residues: 261.6505 Evaluate side-chains 365 residues out of total 3103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 326 time to evaluate : 3.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ASN Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 90 TYR Chi-restraints excluded: chain A residue 201 ASP Chi-restraints excluded: chain B residue 5 GLN Chi-restraints excluded: chain B residue 6 ILE Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 403 ASP Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 486 ILE Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain C residue 626 LEU Chi-restraints excluded: chain C residue 950 LEU Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 428 VAL Chi-restraints excluded: chain D residue 585 VAL Chi-restraints excluded: chain F residue 217 ASP Chi-restraints excluded: chain F residue 297 ILE Chi-restraints excluded: chain F residue 308 LEU Chi-restraints excluded: chain Z residue 237 ASP Chi-restraints excluded: chain Z residue 247 ASP Chi-restraints excluded: chain Z residue 264 ASP Chi-restraints excluded: chain Z residue 282 SER Chi-restraints excluded: chain Z residue 293 CYS Chi-restraints excluded: chain Z residue 473 VAL Chi-restraints excluded: chain Z residue 482 ASN Chi-restraints excluded: chain Z residue 528 THR Chi-restraints excluded: chain Z residue 629 ILE Chi-restraints excluded: chain Z residue 660 VAL Chi-restraints excluded: chain Z residue 891 VAL Chi-restraints excluded: chain Z residue 951 VAL Chi-restraints excluded: chain Z residue 1010 VAL Chi-restraints excluded: chain Z residue 1054 LEU Chi-restraints excluded: chain Z residue 1128 ASP Chi-restraints excluded: chain Z residue 1132 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 119 optimal weight: 0.9980 chunk 320 optimal weight: 10.0000 chunk 70 optimal weight: 4.9990 chunk 208 optimal weight: 0.9980 chunk 87 optimal weight: 4.9990 chunk 356 optimal weight: 2.9990 chunk 295 optimal weight: 10.0000 chunk 164 optimal weight: 0.9990 chunk 29 optimal weight: 7.9990 chunk 117 optimal weight: 1.9990 chunk 186 optimal weight: 3.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 ASN C 113 ASN C 577 HIS C 772 ASN ** Z 781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.3239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 30166 Z= 0.259 Angle : 0.519 14.994 41321 Z= 0.270 Chirality : 0.043 0.175 4788 Planarity : 0.004 0.045 5056 Dihedral : 15.368 173.905 5018 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 2.53 % Allowed : 17.15 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.13), residues: 3562 helix: 0.23 (0.16), residues: 1125 sheet: -0.47 (0.22), residues: 538 loop : -1.88 (0.13), residues: 1899 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 203 HIS 0.005 0.001 HIS A 63 PHE 0.010 0.001 PHE Z1179 TYR 0.021 0.001 TYR Z 6 ARG 0.005 0.000 ARG C 68 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7124 Ramachandran restraints generated. 3562 Oldfield, 0 Emsley, 3562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7124 Ramachandran restraints generated. 3562 Oldfield, 0 Emsley, 3562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 3103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 341 time to evaluate : 3.319 Fit side-chains REVERT: A 93 GLN cc_start: 0.7816 (mm-40) cc_final: 0.7202 (mt0) REVERT: A 195 LYS cc_start: 0.7645 (OUTLIER) cc_final: 0.7276 (mttm) REVERT: B 5 GLN cc_start: 0.7083 (OUTLIER) cc_final: 0.6712 (pm20) REVERT: B 74 ASP cc_start: 0.7481 (t0) cc_final: 0.7131 (t0) REVERT: C 25 GLU cc_start: 0.7755 (pt0) cc_final: 0.7522 (pt0) REVERT: C 100 ASP cc_start: 0.7176 (t0) cc_final: 0.6724 (p0) REVERT: C 772 ASN cc_start: 0.8759 (OUTLIER) cc_final: 0.8111 (m110) REVERT: C 1016 GLN cc_start: 0.7782 (tp40) cc_final: 0.7437 (tt0) REVERT: D 119 LYS cc_start: 0.8897 (tptt) cc_final: 0.8682 (tptp) REVERT: E 15 ARG cc_start: 0.8468 (OUTLIER) cc_final: 0.8155 (mtt-85) REVERT: Z 14 LYS cc_start: 0.7965 (ttmm) cc_final: 0.7665 (tttt) REVERT: Z 153 GLU cc_start: 0.7278 (mm-30) cc_final: 0.7054 (mm-30) REVERT: Z 537 GLN cc_start: 0.4254 (mm110) cc_final: 0.3931 (mp10) REVERT: Z 539 LYS cc_start: 0.6838 (mtpp) cc_final: 0.6228 (mmmt) REVERT: Z 665 ASP cc_start: 0.6606 (t0) cc_final: 0.6364 (t0) REVERT: Z 762 PHE cc_start: 0.7242 (m-80) cc_final: 0.6698 (m-80) outliers start: 71 outliers final: 56 residues processed: 389 average time/residue: 0.4488 time to fit residues: 271.5764 Evaluate side-chains 386 residues out of total 3103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 326 time to evaluate : 3.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 62 ASN Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 201 ASP Chi-restraints excluded: chain B residue 5 GLN Chi-restraints excluded: chain B residue 6 ILE Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 486 ILE Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain C residue 626 LEU Chi-restraints excluded: chain C residue 656 ILE Chi-restraints excluded: chain C residue 772 ASN Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain C residue 944 VAL Chi-restraints excluded: chain C residue 950 LEU Chi-restraints excluded: chain C residue 953 VAL Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 513 MET Chi-restraints excluded: chain D residue 585 VAL Chi-restraints excluded: chain E residue 15 ARG Chi-restraints excluded: chain E residue 45 PHE Chi-restraints excluded: chain F residue 80 ILE Chi-restraints excluded: chain F residue 297 ILE Chi-restraints excluded: chain F residue 308 LEU Chi-restraints excluded: chain Z residue 2 THR Chi-restraints excluded: chain Z residue 85 ILE Chi-restraints excluded: chain Z residue 151 GLN Chi-restraints excluded: chain Z residue 237 ASP Chi-restraints excluded: chain Z residue 247 ASP Chi-restraints excluded: chain Z residue 264 ASP Chi-restraints excluded: chain Z residue 282 SER Chi-restraints excluded: chain Z residue 293 CYS Chi-restraints excluded: chain Z residue 355 VAL Chi-restraints excluded: chain Z residue 473 VAL Chi-restraints excluded: chain Z residue 482 ASN Chi-restraints excluded: chain Z residue 497 VAL Chi-restraints excluded: chain Z residue 516 VAL Chi-restraints excluded: chain Z residue 528 THR Chi-restraints excluded: chain Z residue 629 ILE Chi-restraints excluded: chain Z residue 660 VAL Chi-restraints excluded: chain Z residue 783 VAL Chi-restraints excluded: chain Z residue 891 VAL Chi-restraints excluded: chain Z residue 951 VAL Chi-restraints excluded: chain Z residue 1010 VAL Chi-restraints excluded: chain Z residue 1020 ILE Chi-restraints excluded: chain Z residue 1054 LEU Chi-restraints excluded: chain Z residue 1128 ASP Chi-restraints excluded: chain Z residue 1132 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 343 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 202 optimal weight: 4.9990 chunk 260 optimal weight: 0.4980 chunk 201 optimal weight: 2.9990 chunk 299 optimal weight: 8.9990 chunk 198 optimal weight: 3.9990 chunk 354 optimal weight: 4.9990 chunk 221 optimal weight: 3.9990 chunk 216 optimal weight: 9.9990 chunk 163 optimal weight: 1.9990 overall best weight: 2.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 113 ASN C 577 HIS C 655 ASN F 402 GLN ** Z 781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.3629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 30166 Z= 0.393 Angle : 0.609 17.142 41321 Z= 0.317 Chirality : 0.047 0.223 4788 Planarity : 0.005 0.079 5056 Dihedral : 15.682 173.467 5018 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 3.13 % Allowed : 17.08 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.13), residues: 3562 helix: 0.09 (0.15), residues: 1126 sheet: -0.44 (0.23), residues: 506 loop : -1.96 (0.13), residues: 1930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 203 HIS 0.009 0.001 HIS C 577 PHE 0.016 0.002 PHE Z 677 TYR 0.029 0.002 TYR Z 6 ARG 0.007 0.001 ARG C 770 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7124 Ramachandran restraints generated. 3562 Oldfield, 0 Emsley, 3562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7124 Ramachandran restraints generated. 3562 Oldfield, 0 Emsley, 3562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 3103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 340 time to evaluate : 3.239 Fit side-chains REVERT: A 93 GLN cc_start: 0.7826 (mm-40) cc_final: 0.7166 (mt0) REVERT: A 195 LYS cc_start: 0.7758 (OUTLIER) cc_final: 0.7406 (mttm) REVERT: B 5 GLN cc_start: 0.7210 (OUTLIER) cc_final: 0.6767 (pm20) REVERT: B 73 GLU cc_start: 0.7102 (pm20) cc_final: 0.6858 (pm20) REVERT: B 74 ASP cc_start: 0.7567 (t0) cc_final: 0.7237 (t0) REVERT: C 21 HIS cc_start: 0.8038 (t70) cc_final: 0.7788 (t-90) REVERT: C 25 GLU cc_start: 0.7821 (pt0) cc_final: 0.7507 (pt0) REVERT: C 100 ASP cc_start: 0.7405 (t0) cc_final: 0.7029 (p0) REVERT: C 350 LYS cc_start: 0.8360 (tttp) cc_final: 0.8023 (mtpp) REVERT: C 1016 GLN cc_start: 0.7823 (tp40) cc_final: 0.7608 (tt0) REVERT: D 119 LYS cc_start: 0.8924 (tptt) cc_final: 0.8581 (mmmt) REVERT: D 529 LYS cc_start: 0.8051 (OUTLIER) cc_final: 0.7677 (tttp) REVERT: F 92 ILE cc_start: 0.8497 (OUTLIER) cc_final: 0.8120 (mm) REVERT: Z 14 LYS cc_start: 0.8000 (ttmm) cc_final: 0.7644 (tttt) REVERT: Z 539 LYS cc_start: 0.6818 (mtpp) cc_final: 0.6202 (mmmt) REVERT: Z 762 PHE cc_start: 0.7339 (m-80) cc_final: 0.6567 (m-80) REVERT: Z 1197 ILE cc_start: 0.9285 (OUTLIER) cc_final: 0.9012 (mm) outliers start: 88 outliers final: 62 residues processed: 405 average time/residue: 0.4330 time to fit residues: 274.1454 Evaluate side-chains 389 residues out of total 3103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 322 time to evaluate : 3.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 62 ASN Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 201 ASP Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain B residue 5 GLN Chi-restraints excluded: chain B residue 6 ILE Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 55 LYS Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 486 ILE Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain C residue 710 ILE Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain C residue 882 VAL Chi-restraints excluded: chain C residue 944 VAL Chi-restraints excluded: chain C residue 950 LEU Chi-restraints excluded: chain C residue 953 VAL Chi-restraints excluded: chain C residue 969 SER Chi-restraints excluded: chain C residue 1064 ASP Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 513 MET Chi-restraints excluded: chain D residue 529 LYS Chi-restraints excluded: chain D residue 585 VAL Chi-restraints excluded: chain E residue 15 ARG Chi-restraints excluded: chain F residue 80 ILE Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain F residue 297 ILE Chi-restraints excluded: chain F residue 308 LEU Chi-restraints excluded: chain F residue 402 GLN Chi-restraints excluded: chain Z residue 2 THR Chi-restraints excluded: chain Z residue 85 ILE Chi-restraints excluded: chain Z residue 237 ASP Chi-restraints excluded: chain Z residue 264 ASP Chi-restraints excluded: chain Z residue 282 SER Chi-restraints excluded: chain Z residue 293 CYS Chi-restraints excluded: chain Z residue 300 SER Chi-restraints excluded: chain Z residue 355 VAL Chi-restraints excluded: chain Z residue 473 VAL Chi-restraints excluded: chain Z residue 482 ASN Chi-restraints excluded: chain Z residue 516 VAL Chi-restraints excluded: chain Z residue 528 THR Chi-restraints excluded: chain Z residue 610 THR Chi-restraints excluded: chain Z residue 629 ILE Chi-restraints excluded: chain Z residue 644 THR Chi-restraints excluded: chain Z residue 660 VAL Chi-restraints excluded: chain Z residue 728 VAL Chi-restraints excluded: chain Z residue 783 VAL Chi-restraints excluded: chain Z residue 891 VAL Chi-restraints excluded: chain Z residue 951 VAL Chi-restraints excluded: chain Z residue 1010 VAL Chi-restraints excluded: chain Z residue 1020 ILE Chi-restraints excluded: chain Z residue 1054 LEU Chi-restraints excluded: chain Z residue 1128 ASP Chi-restraints excluded: chain Z residue 1132 THR Chi-restraints excluded: chain Z residue 1197 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 219 optimal weight: 2.9990 chunk 141 optimal weight: 3.9990 chunk 211 optimal weight: 6.9990 chunk 106 optimal weight: 0.8980 chunk 69 optimal weight: 0.0370 chunk 68 optimal weight: 2.9990 chunk 225 optimal weight: 0.9980 chunk 241 optimal weight: 8.9990 chunk 175 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 278 optimal weight: 30.0000 overall best weight: 1.5862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 113 ASN C 577 HIS C 772 ASN ** Z 781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.3673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 30166 Z= 0.255 Angle : 0.537 16.353 41321 Z= 0.280 Chirality : 0.044 0.214 4788 Planarity : 0.004 0.043 5056 Dihedral : 15.542 174.332 5018 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 2.56 % Allowed : 17.97 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.14), residues: 3562 helix: 0.34 (0.16), residues: 1125 sheet: -0.48 (0.23), residues: 525 loop : -1.87 (0.13), residues: 1912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 203 HIS 0.012 0.001 HIS C 577 PHE 0.011 0.001 PHE Z1179 TYR 0.019 0.001 TYR C 680 ARG 0.007 0.000 ARG F 401 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7124 Ramachandran restraints generated. 3562 Oldfield, 0 Emsley, 3562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7124 Ramachandran restraints generated. 3562 Oldfield, 0 Emsley, 3562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 3103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 335 time to evaluate : 3.253 Fit side-chains REVERT: A 93 GLN cc_start: 0.7784 (mm-40) cc_final: 0.7149 (mt0) REVERT: A 195 LYS cc_start: 0.7738 (OUTLIER) cc_final: 0.7366 (mttm) REVERT: B 5 GLN cc_start: 0.7158 (OUTLIER) cc_final: 0.6722 (pm20) REVERT: B 74 ASP cc_start: 0.7535 (t0) cc_final: 0.7171 (t0) REVERT: C 25 GLU cc_start: 0.7754 (pt0) cc_final: 0.7508 (pt0) REVERT: C 100 ASP cc_start: 0.7333 (t0) cc_final: 0.7026 (p0) REVERT: C 350 LYS cc_start: 0.8283 (tttp) cc_final: 0.7956 (mtpp) REVERT: D 119 LYS cc_start: 0.8905 (tptt) cc_final: 0.8596 (tptm) REVERT: E 15 ARG cc_start: 0.8480 (OUTLIER) cc_final: 0.8170 (mtt-85) REVERT: Z 14 LYS cc_start: 0.7964 (ttmm) cc_final: 0.7610 (tttt) REVERT: Z 539 LYS cc_start: 0.6792 (mtpp) cc_final: 0.6206 (mmmt) REVERT: Z 762 PHE cc_start: 0.7213 (m-80) cc_final: 0.6451 (m-80) REVERT: Z 816 LEU cc_start: 0.6642 (mm) cc_final: 0.6107 (tp) REVERT: Z 1197 ILE cc_start: 0.9259 (OUTLIER) cc_final: 0.8978 (mm) outliers start: 72 outliers final: 60 residues processed: 385 average time/residue: 0.4282 time to fit residues: 258.6167 Evaluate side-chains 393 residues out of total 3103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 329 time to evaluate : 3.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 62 ASN Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 201 ASP Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain B residue 5 GLN Chi-restraints excluded: chain B residue 6 ILE Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 486 ILE Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain C residue 626 LEU Chi-restraints excluded: chain C residue 710 ILE Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain C residue 944 VAL Chi-restraints excluded: chain C residue 950 LEU Chi-restraints excluded: chain C residue 953 VAL Chi-restraints excluded: chain C residue 969 SER Chi-restraints excluded: chain C residue 1064 ASP Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 513 MET Chi-restraints excluded: chain D residue 585 VAL Chi-restraints excluded: chain E residue 15 ARG Chi-restraints excluded: chain F residue 80 ILE Chi-restraints excluded: chain F residue 297 ILE Chi-restraints excluded: chain F residue 308 LEU Chi-restraints excluded: chain Z residue 2 THR Chi-restraints excluded: chain Z residue 85 ILE Chi-restraints excluded: chain Z residue 151 GLN Chi-restraints excluded: chain Z residue 237 ASP Chi-restraints excluded: chain Z residue 264 ASP Chi-restraints excluded: chain Z residue 282 SER Chi-restraints excluded: chain Z residue 293 CYS Chi-restraints excluded: chain Z residue 300 SER Chi-restraints excluded: chain Z residue 458 ASP Chi-restraints excluded: chain Z residue 473 VAL Chi-restraints excluded: chain Z residue 482 ASN Chi-restraints excluded: chain Z residue 516 VAL Chi-restraints excluded: chain Z residue 528 THR Chi-restraints excluded: chain Z residue 610 THR Chi-restraints excluded: chain Z residue 629 ILE Chi-restraints excluded: chain Z residue 644 THR Chi-restraints excluded: chain Z residue 660 VAL Chi-restraints excluded: chain Z residue 728 VAL Chi-restraints excluded: chain Z residue 783 VAL Chi-restraints excluded: chain Z residue 891 VAL Chi-restraints excluded: chain Z residue 951 VAL Chi-restraints excluded: chain Z residue 1010 VAL Chi-restraints excluded: chain Z residue 1020 ILE Chi-restraints excluded: chain Z residue 1054 LEU Chi-restraints excluded: chain Z residue 1128 ASP Chi-restraints excluded: chain Z residue 1132 THR Chi-restraints excluded: chain Z residue 1197 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 322 optimal weight: 9.9990 chunk 339 optimal weight: 8.9990 chunk 310 optimal weight: 5.9990 chunk 330 optimal weight: 0.9980 chunk 198 optimal weight: 0.9990 chunk 143 optimal weight: 1.9990 chunk 259 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 chunk 298 optimal weight: 9.9990 chunk 312 optimal weight: 5.9990 chunk 329 optimal weight: 9.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 ASN C 113 ASN C 577 HIS F 402 GLN ** Z 781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 815 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.3796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 30166 Z= 0.306 Angle : 0.562 17.319 41321 Z= 0.292 Chirality : 0.044 0.218 4788 Planarity : 0.004 0.048 5056 Dihedral : 15.559 173.843 5018 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 2.88 % Allowed : 17.83 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.14), residues: 3562 helix: 0.37 (0.16), residues: 1126 sheet: -0.40 (0.23), residues: 504 loop : -1.88 (0.13), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 72 HIS 0.012 0.001 HIS C 577 PHE 0.012 0.001 PHE Z1179 TYR 0.021 0.001 TYR Z 6 ARG 0.006 0.000 ARG A 144 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7124 Ramachandran restraints generated. 3562 Oldfield, 0 Emsley, 3562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7124 Ramachandran restraints generated. 3562 Oldfield, 0 Emsley, 3562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 3103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 339 time to evaluate : 3.144 Fit side-chains REVERT: A 93 GLN cc_start: 0.7740 (mm-40) cc_final: 0.7060 (mt0) REVERT: A 195 LYS cc_start: 0.7736 (OUTLIER) cc_final: 0.7327 (mttm) REVERT: B 5 GLN cc_start: 0.7184 (OUTLIER) cc_final: 0.6748 (pm20) REVERT: B 74 ASP cc_start: 0.7480 (t0) cc_final: 0.7175 (t0) REVERT: C 25 GLU cc_start: 0.7755 (pt0) cc_final: 0.7465 (pt0) REVERT: C 350 LYS cc_start: 0.8304 (tttp) cc_final: 0.7972 (mtpp) REVERT: D 119 LYS cc_start: 0.8889 (tptt) cc_final: 0.8591 (tptm) REVERT: E 15 ARG cc_start: 0.8512 (OUTLIER) cc_final: 0.8178 (mtt-85) REVERT: F 92 ILE cc_start: 0.8416 (OUTLIER) cc_final: 0.8004 (mm) REVERT: F 383 MET cc_start: 0.6327 (tmm) cc_final: 0.6032 (tmm) REVERT: Z 14 LYS cc_start: 0.7969 (ttmm) cc_final: 0.7609 (tttt) REVERT: Z 539 LYS cc_start: 0.6847 (mtpp) cc_final: 0.6260 (mmmt) REVERT: Z 549 TYR cc_start: 0.7043 (m-80) cc_final: 0.6834 (m-10) REVERT: Z 762 PHE cc_start: 0.7258 (m-80) cc_final: 0.6439 (m-80) REVERT: Z 816 LEU cc_start: 0.6877 (mm) cc_final: 0.6316 (tp) REVERT: Z 1131 ASP cc_start: 0.2816 (OUTLIER) cc_final: 0.2399 (p0) REVERT: Z 1161 ARG cc_start: 0.6943 (mtt-85) cc_final: 0.6575 (mmp80) REVERT: Z 1197 ILE cc_start: 0.9267 (OUTLIER) cc_final: 0.8984 (mm) outliers start: 81 outliers final: 66 residues processed: 394 average time/residue: 0.4372 time to fit residues: 269.5930 Evaluate side-chains 404 residues out of total 3103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 332 time to evaluate : 3.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 62 ASN Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 201 ASP Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain B residue 5 GLN Chi-restraints excluded: chain B residue 6 ILE Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 55 LYS Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 370 ASP Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 403 ASP Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 486 ILE Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain C residue 882 VAL Chi-restraints excluded: chain C residue 944 VAL Chi-restraints excluded: chain C residue 950 LEU Chi-restraints excluded: chain C residue 953 VAL Chi-restraints excluded: chain C residue 969 SER Chi-restraints excluded: chain C residue 1064 ASP Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 428 VAL Chi-restraints excluded: chain D residue 513 MET Chi-restraints excluded: chain D residue 585 VAL Chi-restraints excluded: chain E residue 15 ARG Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain F residue 183 LEU Chi-restraints excluded: chain F residue 297 ILE Chi-restraints excluded: chain F residue 308 LEU Chi-restraints excluded: chain F residue 402 GLN Chi-restraints excluded: chain Z residue 2 THR Chi-restraints excluded: chain Z residue 85 ILE Chi-restraints excluded: chain Z residue 237 ASP Chi-restraints excluded: chain Z residue 264 ASP Chi-restraints excluded: chain Z residue 282 SER Chi-restraints excluded: chain Z residue 293 CYS Chi-restraints excluded: chain Z residue 300 SER Chi-restraints excluded: chain Z residue 355 VAL Chi-restraints excluded: chain Z residue 458 ASP Chi-restraints excluded: chain Z residue 473 VAL Chi-restraints excluded: chain Z residue 482 ASN Chi-restraints excluded: chain Z residue 516 VAL Chi-restraints excluded: chain Z residue 528 THR Chi-restraints excluded: chain Z residue 610 THR Chi-restraints excluded: chain Z residue 629 ILE Chi-restraints excluded: chain Z residue 644 THR Chi-restraints excluded: chain Z residue 660 VAL Chi-restraints excluded: chain Z residue 728 VAL Chi-restraints excluded: chain Z residue 783 VAL Chi-restraints excluded: chain Z residue 815 GLN Chi-restraints excluded: chain Z residue 891 VAL Chi-restraints excluded: chain Z residue 951 VAL Chi-restraints excluded: chain Z residue 1010 VAL Chi-restraints excluded: chain Z residue 1020 ILE Chi-restraints excluded: chain Z residue 1041 MET Chi-restraints excluded: chain Z residue 1054 LEU Chi-restraints excluded: chain Z residue 1128 ASP Chi-restraints excluded: chain Z residue 1131 ASP Chi-restraints excluded: chain Z residue 1132 THR Chi-restraints excluded: chain Z residue 1197 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 217 optimal weight: 8.9990 chunk 349 optimal weight: 4.9990 chunk 213 optimal weight: 3.9990 chunk 165 optimal weight: 0.0170 chunk 242 optimal weight: 3.9990 chunk 366 optimal weight: 5.9990 chunk 337 optimal weight: 8.9990 chunk 291 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 225 optimal weight: 0.9980 chunk 179 optimal weight: 2.9990 overall best weight: 1.6022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 113 ASN C 577 HIS ** Z 781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 815 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.3822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 30166 Z= 0.258 Angle : 0.545 16.492 41321 Z= 0.283 Chirality : 0.044 0.246 4788 Planarity : 0.004 0.042 5056 Dihedral : 15.527 174.236 5018 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 2.78 % Allowed : 18.08 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.14), residues: 3562 helix: 0.47 (0.16), residues: 1125 sheet: -0.43 (0.23), residues: 511 loop : -1.84 (0.13), residues: 1926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 72 HIS 0.011 0.001 HIS C 577 PHE 0.011 0.001 PHE Z1179 TYR 0.020 0.001 TYR C 680 ARG 0.007 0.000 ARG A 144 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7124 Ramachandran restraints generated. 3562 Oldfield, 0 Emsley, 3562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7124 Ramachandran restraints generated. 3562 Oldfield, 0 Emsley, 3562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 3103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 337 time to evaluate : 3.022 Fit side-chains REVERT: A 93 GLN cc_start: 0.7754 (mm-40) cc_final: 0.7058 (mt0) REVERT: A 195 LYS cc_start: 0.7702 (OUTLIER) cc_final: 0.7269 (mttm) REVERT: B 5 GLN cc_start: 0.7184 (OUTLIER) cc_final: 0.6745 (pm20) REVERT: B 74 ASP cc_start: 0.7481 (t0) cc_final: 0.7131 (t0) REVERT: C 25 GLU cc_start: 0.7704 (pt0) cc_final: 0.7457 (pt0) REVERT: C 350 LYS cc_start: 0.8278 (tttp) cc_final: 0.7949 (mtpp) REVERT: D 119 LYS cc_start: 0.8887 (tptt) cc_final: 0.8596 (tptm) REVERT: E 15 ARG cc_start: 0.8494 (OUTLIER) cc_final: 0.8182 (mtt-85) REVERT: F 92 ILE cc_start: 0.8324 (OUTLIER) cc_final: 0.7984 (mm) REVERT: F 347 GLU cc_start: 0.7306 (mt-10) cc_final: 0.6896 (mt-10) REVERT: F 383 MET cc_start: 0.6290 (tmm) cc_final: 0.6045 (tmm) REVERT: Z 14 LYS cc_start: 0.7959 (ttmm) cc_final: 0.7598 (tttt) REVERT: Z 539 LYS cc_start: 0.6837 (mtpp) cc_final: 0.6252 (mmmt) REVERT: Z 762 PHE cc_start: 0.7265 (m-80) cc_final: 0.6429 (m-80) REVERT: Z 1131 ASP cc_start: 0.2892 (OUTLIER) cc_final: 0.2488 (p0) REVERT: Z 1161 ARG cc_start: 0.7060 (mtt-85) cc_final: 0.6656 (mmp80) REVERT: Z 1197 ILE cc_start: 0.9251 (OUTLIER) cc_final: 0.8976 (mm) outliers start: 78 outliers final: 67 residues processed: 390 average time/residue: 0.4526 time to fit residues: 275.3688 Evaluate side-chains 403 residues out of total 3103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 330 time to evaluate : 3.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 62 ASN Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 201 ASP Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain B residue 5 GLN Chi-restraints excluded: chain B residue 6 ILE Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 55 LYS Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 370 ASP Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 403 ASP Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 486 ILE Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain C residue 626 LEU Chi-restraints excluded: chain C residue 710 ILE Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain C residue 882 VAL Chi-restraints excluded: chain C residue 944 VAL Chi-restraints excluded: chain C residue 950 LEU Chi-restraints excluded: chain C residue 953 VAL Chi-restraints excluded: chain C residue 969 SER Chi-restraints excluded: chain C residue 1064 ASP Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 428 VAL Chi-restraints excluded: chain D residue 513 MET Chi-restraints excluded: chain D residue 585 VAL Chi-restraints excluded: chain E residue 15 ARG Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain F residue 183 LEU Chi-restraints excluded: chain F residue 297 ILE Chi-restraints excluded: chain F residue 308 LEU Chi-restraints excluded: chain Z residue 2 THR Chi-restraints excluded: chain Z residue 85 ILE Chi-restraints excluded: chain Z residue 151 GLN Chi-restraints excluded: chain Z residue 237 ASP Chi-restraints excluded: chain Z residue 247 ASP Chi-restraints excluded: chain Z residue 264 ASP Chi-restraints excluded: chain Z residue 282 SER Chi-restraints excluded: chain Z residue 293 CYS Chi-restraints excluded: chain Z residue 300 SER Chi-restraints excluded: chain Z residue 458 ASP Chi-restraints excluded: chain Z residue 473 VAL Chi-restraints excluded: chain Z residue 482 ASN Chi-restraints excluded: chain Z residue 516 VAL Chi-restraints excluded: chain Z residue 528 THR Chi-restraints excluded: chain Z residue 610 THR Chi-restraints excluded: chain Z residue 629 ILE Chi-restraints excluded: chain Z residue 644 THR Chi-restraints excluded: chain Z residue 660 VAL Chi-restraints excluded: chain Z residue 728 VAL Chi-restraints excluded: chain Z residue 815 GLN Chi-restraints excluded: chain Z residue 891 VAL Chi-restraints excluded: chain Z residue 951 VAL Chi-restraints excluded: chain Z residue 1010 VAL Chi-restraints excluded: chain Z residue 1020 ILE Chi-restraints excluded: chain Z residue 1054 LEU Chi-restraints excluded: chain Z residue 1128 ASP Chi-restraints excluded: chain Z residue 1131 ASP Chi-restraints excluded: chain Z residue 1132 THR Chi-restraints excluded: chain Z residue 1197 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 231 optimal weight: 0.9980 chunk 310 optimal weight: 1.9990 chunk 89 optimal weight: 4.9990 chunk 269 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 81 optimal weight: 0.4980 chunk 292 optimal weight: 20.0000 chunk 122 optimal weight: 0.9980 chunk 300 optimal weight: 6.9990 chunk 37 optimal weight: 9.9990 chunk 53 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 113 ASN C 577 HIS C 920 ASN C 923 HIS F 402 GLN ** Z 781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 815 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.164269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.132127 restraints weight = 36736.043| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 1.64 r_work: 0.3222 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3023 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3023 r_free = 0.3023 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3023 r_free = 0.3023 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3023 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.3829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 30166 Z= 0.200 Angle : 0.519 15.569 41321 Z= 0.271 Chirality : 0.043 0.235 4788 Planarity : 0.004 0.042 5056 Dihedral : 15.444 174.939 5018 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 2.60 % Allowed : 18.33 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.14), residues: 3562 helix: 0.62 (0.16), residues: 1130 sheet: -0.45 (0.23), residues: 544 loop : -1.76 (0.13), residues: 1888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 72 HIS 0.011 0.001 HIS C 577 PHE 0.010 0.001 PHE Z1179 TYR 0.016 0.001 TYR C 680 ARG 0.007 0.000 ARG D 80 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6687.02 seconds wall clock time: 121 minutes 16.53 seconds (7276.53 seconds total)