Starting phenix.real_space_refine (version: 1.21rc1) on Thu Aug 24 13:12:54 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qg2_4545/08_2023/6qg2_4545_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qg2_4545/08_2023/6qg2_4545.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qg2_4545/08_2023/6qg2_4545.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qg2_4545/08_2023/6qg2_4545.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qg2_4545/08_2023/6qg2_4545_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qg2_4545/08_2023/6qg2_4545_updated.pdb" } resolution = 4.55 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= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 177 5.16 5 C 24589 2.51 5 N 6619 2.21 5 O 7277 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 28": "OE1" <-> "OE2" Residue "A ARG 104": "NH1" <-> "NH2" Residue "A GLU 297": "OE1" <-> "OE2" Residue "B GLU 28": "OE1" <-> "OE2" Residue "B ARG 104": "NH1" <-> "NH2" Residue "B GLU 297": "OE1" <-> "OE2" Residue "C GLU 65": "OE1" <-> "OE2" Residue "C ARG 90": "NH1" <-> "NH2" Residue "C GLU 98": "OE1" <-> "OE2" Residue "C GLU 100": "OE1" <-> "OE2" Residue "C GLU 164": "OE1" <-> "OE2" Residue "C GLU 170": "OE1" <-> "OE2" Residue "C GLU 239": "OE1" <-> "OE2" Residue "C ARG 289": "NH1" <-> "NH2" Residue "C TYR 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 65": "OE1" <-> "OE2" Residue "D ARG 90": "NH1" <-> "NH2" Residue "D GLU 98": "OE1" <-> "OE2" Residue "D GLU 100": "OE1" <-> "OE2" Residue "D GLU 164": "OE1" <-> "OE2" Residue "D GLU 170": "OE1" <-> "OE2" Residue "D GLU 239": "OE1" <-> "OE2" Residue "D ARG 289": "NH1" <-> "NH2" Residue "D GLU 344": "OE1" <-> "OE2" Residue "E PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 262": "OE1" <-> "OE2" Residue "G GLU 436": "OE1" <-> "OE2" Residue "G GLU 525": "OE1" <-> "OE2" Residue "G GLU 538": "OE1" <-> "OE2" Residue "H GLU 262": "OE1" <-> "OE2" Residue "H GLU 436": "OE1" <-> "OE2" Residue "H GLU 508": "OE1" <-> "OE2" Residue "H GLU 538": "OE1" <-> "OE2" Residue "H GLU 583": "OE1" <-> "OE2" Residue "I ARG 113": "NH1" <-> "NH2" Residue "I GLU 216": "OE1" <-> "OE2" Residue "I GLU 358": "OE1" <-> "OE2" Residue "I GLU 370": "OE1" <-> "OE2" Residue "J GLU 91": "OE1" <-> "OE2" Residue "J ARG 113": "NH1" <-> "NH2" Residue "J GLU 216": "OE1" <-> "OE2" Residue "J GLU 358": "OE1" <-> "OE2" Residue "J GLU 370": "OE1" <-> "OE2" Residue "K GLU 10": "OE1" <-> "OE2" Residue "K GLU 29": "OE1" <-> "OE2" Residue "K GLU 43": "OE1" <-> "OE2" Residue "K ARG 54": "NH1" <-> "NH2" Residue "K ARG 64": "NH1" <-> "NH2" Residue "K ARG 88": "NH1" <-> "NH2" Residue "K GLU 93": "OE1" <-> "OE2" Residue "K GLU 100": "OE1" <-> "OE2" Residue "K GLU 125": "OE1" <-> "OE2" Residue "K GLU 152": "OE1" <-> "OE2" Residue "K GLU 159": "OE1" <-> "OE2" Residue "K GLU 168": "OE1" <-> "OE2" Residue "K GLU 209": "OE1" <-> "OE2" Residue "L GLU 10": "OE1" <-> "OE2" Residue "L GLU 29": "OE1" <-> "OE2" Residue "L TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 43": "OE1" <-> "OE2" Residue "L ARG 54": "NH1" <-> "NH2" Residue "L ARG 64": "NH1" <-> "NH2" Residue "L ARG 88": "NH1" <-> "NH2" Residue "L GLU 93": "OE1" <-> "OE2" Residue "L GLU 100": "OE1" <-> "OE2" Residue "L GLU 125": "OE1" <-> "OE2" Residue "L GLU 152": "OE1" <-> "OE2" Residue "L GLU 159": "OE1" <-> "OE2" Residue "L GLU 168": "OE1" <-> "OE2" Residue "L GLU 209": "OE1" <-> "OE2" Residue "M GLU 231": "OE1" <-> "OE2" Residue "M PHE 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 383": "OE1" <-> "OE2" Residue "M GLU 494": "OE1" <-> "OE2" Residue "M GLU 506": "OE1" <-> "OE2" Residue "N TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 383": "OE1" <-> "OE2" Residue "N GLU 494": "OE1" <-> "OE2" Residue "N GLU 506": "OE1" <-> "OE2" Residue "P GLU 232": "OE1" <-> "OE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 38664 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2351 Classifications: {'peptide': 302} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 12, 'TRANS': 289} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 2351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2351 Classifications: {'peptide': 302} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 12, 'TRANS': 289} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 14 Chain: "C" Number of atoms: 2665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2665 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 16, 'TRANS': 328} Chain breaks: 2 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 2, 'GLN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 30 Chain: "D" Number of atoms: 2665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2665 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 16, 'TRANS': 328} Chain breaks: 2 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 2, 'GLN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 30 Chain: "E" Number of atoms: 2164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2164 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 16, 'TRANS': 250} Chain breaks: 6 Chain: "F" Number of atoms: 2967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2967 Classifications: {'peptide': 375} Link IDs: {'PTRANS': 20, 'TRANS': 354} Chain breaks: 8 Chain: "G" Number of atoms: 2744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 355, 2744 Classifications: {'peptide': 355} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 12, 'TRANS': 342} Chain breaks: 2 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "H" Number of atoms: 2744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 355, 2744 Classifications: {'peptide': 355} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 12, 'TRANS': 342} Chain breaks: 2 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "I" Number of atoms: 3406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3406 Classifications: {'peptide': 431} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 15, 'TRANS': 415} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "J" Number of atoms: 3406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3406 Classifications: {'peptide': 431} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 15, 'TRANS': 415} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "K" Number of atoms: 1967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1967 Classifications: {'peptide': 246} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 6, 'TRANS': 239} Chain breaks: 3 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "L" Number of atoms: 1967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1967 Classifications: {'peptide': 246} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 6, 'TRANS': 239} Chain breaks: 3 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "M" Number of atoms: 3044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 3044 Classifications: {'peptide': 408} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 20, 'TRANS': 387} Chain breaks: 4 Unresolved non-hydrogen bonds: 97 Unresolved non-hydrogen angles: 119 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 50 Chain: "O" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 143 Classifications: {'peptide': 17} Link IDs: {'PTRANS': 1, 'TRANS': 15} Chain: "N" Number of atoms: 3044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 3044 Classifications: {'peptide': 408} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 20, 'TRANS': 387} Chain breaks: 4 Unresolved non-hydrogen bonds: 97 Unresolved non-hydrogen angles: 119 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 50 Chain: "P" Number of atoms: 1036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1036 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain breaks: 3 Residues with excluded nonbonded symmetry interactions: 108 residue: pdb=" N GLN F 414 " occ=0.00 ... (7 atoms not shown) pdb=" NE2 GLN F 414 " occ=0.00 residue: pdb=" N THR F 415 " occ=0.00 ... (5 atoms not shown) pdb=" CG2 THR F 415 " occ=0.00 residue: pdb=" N MET F 416 " occ=0.00 ... (6 atoms not shown) pdb=" CE MET F 416 " occ=0.00 residue: pdb=" N PHE F 417 " occ=0.00 ... (9 atoms not shown) pdb=" CZ PHE F 417 " occ=0.00 residue: pdb=" N THR F 418 " occ=0.00 ... (5 atoms not shown) pdb=" CG2 THR F 418 " occ=0.00 residue: pdb=" N LYS F 419 " occ=0.00 ... (7 atoms not shown) pdb=" NZ LYS F 419 " occ=0.00 residue: pdb=" N ASN F 420 " occ=0.00 ... (6 atoms not shown) pdb=" ND2 ASN F 420 " occ=0.00 residue: pdb=" N ILE F 421 " occ=0.00 ... (6 atoms not shown) pdb=" CD1 ILE F 421 " occ=0.00 residue: pdb=" N GLN F 422 " occ=0.00 ... (7 atoms not shown) pdb=" NE2 GLN F 422 " occ=0.00 residue: pdb=" N ILE F 423 " occ=0.00 ... (6 atoms not shown) pdb=" CD1 ILE F 423 " occ=0.00 residue: pdb=" N GLN F 424 " occ=0.00 ... (7 atoms not shown) pdb=" NE2 GLN F 424 " occ=0.00 residue: pdb=" N ALA F 426 " occ=0.00 ... (3 atoms not shown) pdb=" CB ALA F 426 " occ=0.00 ... (remaining 96 not shown) Time building chain proxies: 18.03, per 1000 atoms: 0.47 Number of scatterers: 38664 At special positions: 0 Unit cell: (276.04, 164.82, 135.34, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 177 16.00 P 2 15.00 O 7277 8.00 N 6619 7.00 C 24589 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: 13.49 Conformation dependent library (CDL) restraints added in 5.7 seconds 9682 Ramachandran restraints generated. 4841 Oldfield, 0 Emsley, 4841 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9398 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 124 helices and 52 sheets defined 27.4% alpha, 11.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.77 Creating SS restraints... Processing helix chain 'A' and resid 6 through 12 Processing helix chain 'A' and resid 22 through 36 removed outlier: 3.629A pdb=" N ILE A 27 " --> pdb=" O ILE A 24 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ILE A 36 " --> pdb=" O LEU A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 59 Processing helix chain 'A' and resid 65 through 80 Processing helix chain 'A' and resid 87 through 96 Processing helix chain 'A' and resid 99 through 114 Processing helix chain 'A' and resid 133 through 145 Processing helix chain 'A' and resid 161 through 170 Processing helix chain 'A' and resid 214 through 223 Processing helix chain 'A' and resid 294 through 302 Processing helix chain 'B' and resid 7 through 12 Processing helix chain 'B' and resid 22 through 34 Processing helix chain 'B' and resid 42 through 59 removed outlier: 4.386A pdb=" N ASN B 47 " --> pdb=" O ALA B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 83 removed outlier: 3.777A pdb=" N LEU B 81 " --> pdb=" O VAL B 77 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N HIS B 82 " --> pdb=" O LEU B 78 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N LEU B 83 " --> pdb=" O ARG B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 96 removed outlier: 3.675A pdb=" N LYS B 91 " --> pdb=" O TRP B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 115 removed outlier: 3.820A pdb=" N LYS B 106 " --> pdb=" O VAL B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 145 Processing helix chain 'B' and resid 162 through 172 removed outlier: 3.764A pdb=" N LYS B 172 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 186 removed outlier: 3.921A pdb=" N ALA B 186 " --> pdb=" O ALA B 183 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 183 through 186' Processing helix chain 'B' and resid 214 through 223 Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'C' and resid 22 through 31 Processing helix chain 'C' and resid 37 through 54 Processing helix chain 'C' and resid 61 through 77 Processing helix chain 'C' and resid 83 through 107 removed outlier: 3.633A pdb=" N GLU C 98 " --> pdb=" O VAL C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 166 Processing helix chain 'C' and resid 194 through 205 removed outlier: 3.572A pdb=" N LYS C 198 " --> pdb=" O LYS C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 219 through 235 removed outlier: 3.644A pdb=" N THR C 223 " --> pdb=" O PHE C 219 " (cutoff:3.500A) removed outlier: 8.362A pdb=" N LYS C 224 " --> pdb=" O PRO C 220 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ASN C 225 " --> pdb=" O ASN C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 254 removed outlier: 3.693A pdb=" N MET C 252 " --> pdb=" O PHE C 249 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N SER C 253 " --> pdb=" O ALA C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 288 Processing helix chain 'C' and resid 318 through 320 No H-bonds generated for 'chain 'C' and resid 318 through 320' Processing helix chain 'C' and resid 361 through 368 Processing helix chain 'D' and resid 23 through 31 Processing helix chain 'D' and resid 37 through 54 removed outlier: 3.582A pdb=" N ALA D 54 " --> pdb=" O ARG D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 77 Processing helix chain 'D' and resid 83 through 107 removed outlier: 3.730A pdb=" N GLU D 98 " --> pdb=" O VAL D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 166 Processing helix chain 'D' and resid 176 through 178 No H-bonds generated for 'chain 'D' and resid 176 through 178' Processing helix chain 'D' and resid 194 through 205 Processing helix chain 'D' and resid 222 through 236 Processing helix chain 'D' and resid 279 through 288 Processing helix chain 'D' and resid 309 through 312 No H-bonds generated for 'chain 'D' and resid 309 through 312' Processing helix chain 'D' and resid 327 through 329 No H-bonds generated for 'chain 'D' and resid 327 through 329' Processing helix chain 'D' and resid 358 through 366 removed outlier: 3.576A pdb=" N ILE D 361 " --> pdb=" O PRO D 358 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N TYR D 362 " --> pdb=" O SER D 359 " (cutoff:3.500A) Processing helix chain 'E' and resid 76 through 86 removed outlier: 4.061A pdb=" N VAL E 80 " --> pdb=" O MET E 76 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 109 Processing helix chain 'E' and resid 153 through 158 Processing helix chain 'E' and resid 181 through 189 Processing helix chain 'E' and resid 287 through 290 No H-bonds generated for 'chain 'E' and resid 287 through 290' Processing helix chain 'E' and resid 404 through 411 Processing helix chain 'F' and resid 76 through 87 removed outlier: 4.022A pdb=" N TYR F 79 " --> pdb=" O MET F 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 103 through 109 Processing helix chain 'F' and resid 153 through 158 Processing helix chain 'F' and resid 182 through 190 Processing helix chain 'F' and resid 258 through 261 No H-bonds generated for 'chain 'F' and resid 258 through 261' Processing helix chain 'F' and resid 287 through 290 No H-bonds generated for 'chain 'F' and resid 287 through 290' Processing helix chain 'F' and resid 406 through 411 Processing helix chain 'G' and resid 272 through 282 Processing helix chain 'G' and resid 290 through 306 removed outlier: 4.266A pdb=" N ILE G 294 " --> pdb=" O ILE G 290 " (cutoff:3.500A) Processing helix chain 'G' and resid 319 through 333 Processing helix chain 'G' and resid 338 through 353 Processing helix chain 'G' and resid 363 through 378 removed outlier: 3.612A pdb=" N GLU G 369 " --> pdb=" O LYS G 365 " (cutoff:3.500A) Processing helix chain 'G' and resid 380 through 393 Processing helix chain 'G' and resid 407 through 417 Processing helix chain 'G' and resid 437 through 445 Processing helix chain 'G' and resid 460 through 462 No H-bonds generated for 'chain 'G' and resid 460 through 462' Processing helix chain 'G' and resid 490 through 498 Processing helix chain 'G' and resid 529 through 531 No H-bonds generated for 'chain 'G' and resid 529 through 531' Processing helix chain 'G' and resid 583 through 585 No H-bonds generated for 'chain 'G' and resid 583 through 585' Processing helix chain 'H' and resid 272 through 283 removed outlier: 3.779A pdb=" N HIS H 283 " --> pdb=" O SER H 279 " (cutoff:3.500A) Processing helix chain 'H' and resid 290 through 306 Processing helix chain 'H' and resid 319 through 333 Processing helix chain 'H' and resid 338 through 353 Processing helix chain 'H' and resid 360 through 378 removed outlier: 3.637A pdb=" N GLU H 369 " --> pdb=" O LYS H 365 " (cutoff:3.500A) Processing helix chain 'H' and resid 380 through 393 Processing helix chain 'H' and resid 407 through 418 Processing helix chain 'H' and resid 436 through 447 Processing helix chain 'H' and resid 460 through 463 No H-bonds generated for 'chain 'H' and resid 460 through 463' Processing helix chain 'H' and resid 487 through 498 removed outlier: 4.065A pdb=" N ALA H 490 " --> pdb=" O ALA H 487 " (cutoff:3.500A) Processing helix chain 'I' and resid 49 through 51 No H-bonds generated for 'chain 'I' and resid 49 through 51' Processing helix chain 'I' and resid 59 through 70 removed outlier: 3.562A pdb=" N THR I 63 " --> pdb=" O LEU I 59 " (cutoff:3.500A) Processing helix chain 'I' and resid 83 through 92 Processing helix chain 'I' and resid 115 through 125 Processing helix chain 'I' and resid 145 through 158 Processing helix chain 'I' and resid 215 through 221 removed outlier: 5.779A pdb=" N ASP I 219 " --> pdb=" O GLU I 216 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ASN I 220 " --> pdb=" O LEU I 217 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N VAL I 221 " --> pdb=" O LEU I 218 " (cutoff:3.500A) Processing helix chain 'I' and resid 241 through 248 Processing helix chain 'I' and resid 259 through 265 Processing helix chain 'I' and resid 289 through 299 Processing helix chain 'J' and resid 60 through 70 Processing helix chain 'J' and resid 83 through 92 Processing helix chain 'J' and resid 116 through 125 Processing helix chain 'J' and resid 146 through 158 Processing helix chain 'J' and resid 242 through 248 Processing helix chain 'J' and resid 259 through 264 Processing helix chain 'J' and resid 288 through 299 Processing helix chain 'K' and resid 95 through 111 Processing helix chain 'K' and resid 114 through 118 Processing helix chain 'K' and resid 123 through 137 Proline residue: K 133 - end of helix removed outlier: 4.407A pdb=" N ARG K 136 " --> pdb=" O TRP K 132 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N LYS K 137 " --> pdb=" O PRO K 133 " (cutoff:3.500A) Processing helix chain 'K' and resid 141 through 150 Processing helix chain 'K' and resid 163 through 173 Processing helix chain 'K' and resid 198 through 207 Processing helix chain 'K' and resid 241 through 255 removed outlier: 5.374A pdb=" N SER K 246 " --> pdb=" O GLU K 242 " (cutoff:3.500A) Processing helix chain 'L' and resid 92 through 119 removed outlier: 4.206A pdb=" N ILE L 96 " --> pdb=" O SER L 92 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LYS L 97 " --> pdb=" O GLU L 93 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N CYS L 115 " --> pdb=" O ILE L 111 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ALA L 116 " --> pdb=" O LEU L 112 " (cutoff:3.500A) Processing helix chain 'L' and resid 123 through 134 removed outlier: 4.251A pdb=" N TRP L 132 " --> pdb=" O LYS L 128 " (cutoff:3.500A) Proline residue: L 133 - end of helix Processing helix chain 'L' and resid 142 through 150 Processing helix chain 'L' and resid 155 through 157 No H-bonds generated for 'chain 'L' and resid 155 through 157' Processing helix chain 'L' and resid 164 through 173 Processing helix chain 'L' and resid 198 through 207 Processing helix chain 'L' and resid 241 through 256 removed outlier: 3.941A pdb=" N SER L 246 " --> pdb=" O GLU L 242 " (cutoff:3.500A) Processing helix chain 'M' and resid 114 through 120 Processing helix chain 'M' and resid 202 through 210 removed outlier: 3.667A pdb=" N VAL M 210 " --> pdb=" O SER M 206 " (cutoff:3.500A) Processing helix chain 'M' and resid 227 through 238 Processing helix chain 'M' and resid 258 through 269 Processing helix chain 'M' and resid 291 through 301 Processing helix chain 'O' and resid 132 through 140 Processing helix chain 'N' and resid 114 through 120 Processing helix chain 'N' and resid 202 through 210 removed outlier: 3.557A pdb=" N VAL N 210 " --> pdb=" O SER N 206 " (cutoff:3.500A) Processing helix chain 'N' and resid 227 through 238 Processing helix chain 'N' and resid 258 through 269 Processing helix chain 'N' and resid 292 through 300 Processing helix chain 'P' and resid 132 through 140 Processing helix chain 'P' and resid 177 through 183 Processing helix chain 'P' and resid 188 through 198 Processing helix chain 'P' and resid 219 through 230 Processing sheet with id= A, first strand: chain 'A' and resid 193 through 196 removed outlier: 4.049A pdb=" N HIS A 129 " --> pdb=" O PHE A 195 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N THR A 154 " --> pdb=" O VAL A 128 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N THR A 177 " --> pdb=" O CYS A 151 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N VAL A 153 " --> pdb=" O THR A 177 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 207 through 209 removed outlier: 3.764A pdb=" N ILE A 207 " --> pdb=" O THR A 275 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N THR A 275 " --> pdb=" O ILE A 207 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 227 through 230 removed outlier: 8.431A pdb=" N VAL A 229 " --> pdb=" O THR A 281 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N LEU A 283 " --> pdb=" O VAL A 229 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 149 through 152 removed outlier: 7.485A pdb=" N ASP B 124 " --> pdb=" O ARG B 150 " (cutoff:3.500A) removed outlier: 8.456A pdb=" N VAL B 152 " --> pdb=" O ASP B 124 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N ILE B 126 " --> pdb=" O VAL B 152 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N LYS B 193 " --> pdb=" O LEU B 127 " (cutoff:3.500A) removed outlier: 8.162A pdb=" N HIS B 129 " --> pdb=" O LYS B 193 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N PHE B 195 " --> pdb=" O HIS B 129 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N ALA B 282 " --> pdb=" O VAL B 229 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 153 through 155 Processing sheet with id= F, first strand: chain 'C' and resid 292 through 295 removed outlier: 6.329A pdb=" N VAL C 258 " --> pdb=" O PHE C 293 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N VAL C 295 " --> pdb=" O VAL C 258 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ILE C 260 " --> pdb=" O VAL C 295 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS C 257 " --> pdb=" O ILE C 185 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE C 259 " --> pdb=" O LEU C 187 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N THR C 212 " --> pdb=" O LEU C 186 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N THR C 188 " --> pdb=" O THR C 212 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N LEU C 214 " --> pdb=" O THR C 188 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 339 through 341 removed outlier: 4.262A pdb=" N ASP C 339 " --> pdb=" O SER C 273 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL C 341 " --> pdb=" O THR C 271 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N THR C 271 " --> pdb=" O VAL C 341 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 184 through 187 removed outlier: 3.697A pdb=" N THR D 212 " --> pdb=" O GLU D 184 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 257 through 260 removed outlier: 8.350A pdb=" N ILE D 260 " --> pdb=" O PRO D 291 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N PHE D 293 " --> pdb=" O ILE D 260 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'E' and resid 134 through 136 removed outlier: 6.063A pdb=" N ASP E 166 " --> pdb=" O GLN E 4 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N PHE E 6 " --> pdb=" O ASP E 166 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N VAL E 168 " --> pdb=" O PHE E 6 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N PHE E 8 " --> pdb=" O VAL E 168 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N LEU E 170 " --> pdb=" O PHE E 8 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 194 through 199 removed outlier: 3.638A pdb=" N PHE E 392 " --> pdb=" O THR E 198 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 223 through 225 removed outlier: 3.821A pdb=" N PHE E 223 " --> pdb=" O SER E 269 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'F' and resid 134 through 136 removed outlier: 3.668A pdb=" N HIS F 134 " --> pdb=" O ILE F 92 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ALA F 5 " --> pdb=" O SER F 93 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N VAL F 95 " --> pdb=" O ALA F 5 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N VAL F 7 " --> pdb=" O VAL F 95 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TYR F 278 " --> pdb=" O ILE F 169 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'F' and resid 195 through 198 removed outlier: 6.191A pdb=" N ASN F 388 " --> pdb=" O ALA F 196 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N THR F 198 " --> pdb=" O ASN F 388 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N THR F 390 " --> pdb=" O THR F 198 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'F' and resid 223 through 225 removed outlier: 4.186A pdb=" N PHE F 223 " --> pdb=" O SER F 269 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'F' and resid 444 through 447 removed outlier: 6.670A pdb=" N CYS F 461 " --> pdb=" O ASN F 445 " (cutoff:3.500A) removed outlier: 8.258A pdb=" N LYS F 447 " --> pdb=" O CYS F 461 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N VAL F 463 " --> pdb=" O LYS F 447 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'F' and resid 472 through 475 removed outlier: 6.487A pdb=" N ALA F 489 " --> pdb=" O HIS F 473 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N GLY F 475 " --> pdb=" O ALA F 489 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N ILE F 491 " --> pdb=" O GLY F 475 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'F' and resid 479 through 481 removed outlier: 3.733A pdb=" N LEU F 497 " --> pdb=" O ILE F 479 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'G' and resid 400 through 403 Processing sheet with id= T, first strand: chain 'G' and resid 470 through 473 removed outlier: 3.779A pdb=" N CYS G 506 " --> pdb=" O LEU G 472 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N GLY G 573 " --> pdb=" O VAL G 505 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASN G 574 " --> pdb=" O GLY G 581 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLY G 581 " --> pdb=" O ASN G 574 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE G 576 " --> pdb=" O LYS G 579 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'G' and resid 483 through 485 removed outlier: 3.731A pdb=" N LEU G 483 " --> pdb=" O ALA G 566 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'H' and resid 398 through 403 removed outlier: 3.972A pdb=" N LYS H 425 " --> pdb=" O THR H 398 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'H' and resid 483 through 486 Processing sheet with id= X, first strand: chain 'H' and resid 503 through 506 removed outlier: 3.524A pdb=" N LYS H 572 " --> pdb=" O VAL H 503 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N VAL H 505 " --> pdb=" O LYS H 572 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ASN H 574 " --> pdb=" O VAL H 505 " (cutoff:3.500A) No H-bonds generated for sheet with id= X Processing sheet with id= Y, first strand: chain 'I' and resid 74 through 77 removed outlier: 5.984A pdb=" N ILE I 133 " --> pdb=" O VAL I 30 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N LEU I 32 " --> pdb=" O ILE I 133 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N VAL I 135 " --> pdb=" O LEU I 32 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'I' and resid 165 through 169 removed outlier: 6.912A pdb=" N TYR I 274 " --> pdb=" O MET I 166 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N LEU I 168 " --> pdb=" O TYR I 274 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N TYR I 276 " --> pdb=" O LEU I 168 " (cutoff:3.500A) No H-bonds generated for sheet with id= Z Processing sheet with id= AA, first strand: chain 'I' and resid 318 through 321 removed outlier: 3.631A pdb=" N ILE I 325 " --> pdb=" O GLU I 321 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'I' and resid 331 through 333 removed outlier: 6.250A pdb=" N THR I 349 " --> pdb=" O VAL I 332 " (cutoff:3.500A) No H-bonds generated for sheet with id= AB Processing sheet with id= AC, first strand: chain 'I' and resid 356 through 358 removed outlier: 3.681A pdb=" N ILE I 391 " --> pdb=" O ARG I 373 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'J' and resid 235 through 238 removed outlier: 7.587A pdb=" N GLN J 28 " --> pdb=" O ILE J 133 " (cutoff:3.500A) removed outlier: 9.099A pdb=" N VAL J 135 " --> pdb=" O GLN J 28 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N VAL J 30 " --> pdb=" O VAL J 135 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N ALA J 29 " --> pdb=" O HIS J 73 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N VAL J 75 " --> pdb=" O ALA J 29 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N VAL J 31 " --> pdb=" O VAL J 75 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N LEU J 77 " --> pdb=" O VAL J 31 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N LYS J 103 " --> pdb=" O VAL J 75 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N LEU J 77 " --> pdb=" O LYS J 103 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N THR J 105 " --> pdb=" O LEU J 77 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N CYS J 79 " --> pdb=" O THR J 105 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N ILE J 107 " --> pdb=" O CYS J 79 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'J' and resid 165 through 168 removed outlier: 7.097A pdb=" N TYR J 274 " --> pdb=" O MET J 166 " (cutoff:3.500A) removed outlier: 8.461A pdb=" N LEU J 168 " --> pdb=" O TYR J 274 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N TYR J 276 " --> pdb=" O LEU J 168 " (cutoff:3.500A) No H-bonds generated for sheet with id= AE Processing sheet with id= AF, first strand: chain 'J' and resid 185 through 187 Processing sheet with id= AG, first strand: chain 'J' and resid 318 through 321 removed outlier: 3.667A pdb=" N LYS J 327 " --> pdb=" O SER J 319 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ILE J 325 " --> pdb=" O GLU J 321 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N THR J 343 " --> pdb=" O TYR J 326 " (cutoff:3.500A) removed outlier: 8.940A pdb=" N GLU J 328 " --> pdb=" O THR J 343 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N ILE J 345 " --> pdb=" O GLU J 328 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'J' and resid 373 through 375 removed outlier: 6.504A pdb=" N VAL J 406 " --> pdb=" O ILE J 390 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N ASP J 392 " --> pdb=" O VAL J 406 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N LEU J 408 " --> pdb=" O ASP J 392 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N MET J 424 " --> pdb=" O ARG J 407 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'K' and resid 19 through 23 removed outlier: 6.705A pdb=" N ASP K 84 " --> pdb=" O LEU K 74 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N VAL K 76 " --> pdb=" O TYR K 82 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N TYR K 82 " --> pdb=" O VAL K 76 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'K' and resid 31 through 35 Processing sheet with id= AK, first strand: chain 'K' and resid 261 through 263 removed outlier: 4.055A pdb=" N VAL K 261 " --> pdb=" O SER K 191 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N SER K 191 " --> pdb=" O VAL K 261 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU K 230 " --> pdb=" O ALA K 186 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL K 188 " --> pdb=" O TYR K 228 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL K 229 " --> pdb=" O LYS K 221 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LYS K 219 " --> pdb=" O THR K 231 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'L' and resid 19 through 23 Processing sheet with id= AM, first strand: chain 'L' and resid 31 through 34 Processing sheet with id= AN, first strand: chain 'L' and resid 261 through 264 removed outlier: 4.299A pdb=" N VAL L 261 " --> pdb=" O SER L 191 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N SER L 191 " --> pdb=" O VAL L 261 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU L 230 " --> pdb=" O ALA L 186 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N VAL L 188 " --> pdb=" O TYR L 228 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N TYR L 228 " --> pdb=" O VAL L 188 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL L 229 " --> pdb=" O LYS L 221 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS L 221 " --> pdb=" O VAL L 229 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N THR L 231 " --> pdb=" O LYS L 219 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LYS L 219 " --> pdb=" O THR L 231 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'M' and resid 280 through 282 removed outlier: 8.641A pdb=" N VAL M 281 " --> pdb=" O VAL M 244 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ILE M 246 " --> pdb=" O VAL M 281 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ALA M 214 " --> pdb=" O ILE M 245 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N LEU M 247 " --> pdb=" O ALA M 214 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N LEU M 216 " --> pdb=" O LEU M 247 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N THR M 100 " --> pdb=" O VAL M 186 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N HIS M 188 " --> pdb=" O THR M 100 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ASN M 102 " --> pdb=" O HIS M 188 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N SER M 190 " --> pdb=" O ASN M 102 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N GLY M 104 " --> pdb=" O SER M 190 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N VAL M 192 " --> pdb=" O GLY M 104 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N ILE M 106 " --> pdb=" O VAL M 192 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N VAL M 186 " --> pdb=" O ILE M 147 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N ILE M 147 " --> pdb=" O VAL M 186 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N HIS M 188 " --> pdb=" O ALA M 145 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N ALA M 145 " --> pdb=" O HIS M 188 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N SER M 190 " --> pdb=" O ALA M 143 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ALA M 143 " --> pdb=" O SER M 190 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N VAL M 192 " --> pdb=" O GLY M 141 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N GLY M 141 " --> pdb=" O VAL M 192 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'M' and resid 373 through 376 removed outlier: 3.921A pdb=" N ILE M 373 " --> pdb=" O ILE M 355 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ASN M 344 " --> pdb=" O ARG M 314 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N ILE M 316 " --> pdb=" O ILE M 342 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N ILE M 342 " --> pdb=" O ILE M 316 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLY M 394 " --> pdb=" O ILE M 342 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'M' and resid 319 through 321 Processing sheet with id= AR, first strand: chain 'M' and resid 425 through 427 removed outlier: 4.054A pdb=" N ASN M 425 " --> pdb=" O THR M 493 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ALA M 491 " --> pdb=" O TYR M 427 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'M' and resid 482 through 486 removed outlier: 7.423A pdb=" N LEU M 501 " --> pdb=" O ILE M 512 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N TRP M 514 " --> pdb=" O ILE M 499 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N ILE M 499 " --> pdb=" O TRP M 514 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N ARG M 504 " --> pdb=" O VAL M 461 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N VAL M 461 " --> pdb=" O ARG M 504 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N THR M 471 " --> pdb=" O VAL M 464 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ILE M 466 " --> pdb=" O THR M 469 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR M 469 " --> pdb=" O ILE M 466 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N ARG M 484 " --> pdb=" O VAL M 476 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'N' and resid 103 through 106 removed outlier: 6.629A pdb=" N ALA N 213 " --> pdb=" O GLY N 104 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N ILE N 106 " --> pdb=" O ALA N 213 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N LEU N 215 " --> pdb=" O ILE N 106 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'N' and resid 314 through 317 removed outlier: 4.134A pdb=" N ASN N 344 " --> pdb=" O ARG N 314 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N ILE N 316 " --> pdb=" O ILE N 342 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N ILE N 342 " --> pdb=" O ILE N 316 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N SER N 379 " --> pdb=" O GLY N 399 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'N' and resid 373 through 376 Processing sheet with id= AW, first strand: chain 'N' and resid 425 through 427 removed outlier: 3.505A pdb=" N ASN N 425 " --> pdb=" O THR N 493 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N THR N 493 " --> pdb=" O ASN N 425 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TYR N 427 " --> pdb=" O ALA N 491 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ALA N 491 " --> pdb=" O TYR N 427 " (cutoff:3.500A) No H-bonds generated for sheet with id= AW Processing sheet with id= AX, first strand: chain 'N' and resid 513 through 516 removed outlier: 3.813A pdb=" N TRP N 514 " --> pdb=" O PHE N 435 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE N 466 " --> pdb=" O THR N 469 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N THR N 471 " --> pdb=" O VAL N 464 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASN N 465 " --> pdb=" O ALA N 500 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'N' and resid 140 through 149 removed outlier: 3.851A pdb=" N ALA N 143 " --> pdb=" O PHE N 191 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N LYS N 149 " --> pdb=" O LEU N 185 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N LEU N 185 " --> pdb=" O LYS N 149 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'P' and resid 171 through 174 removed outlier: 4.142A pdb=" N PHE P 174 " --> pdb=" O LEU P 211 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU P 211 " --> pdb=" O PHE P 174 " (cutoff:3.500A) 1069 hydrogen bonds defined for protein. 3033 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 12.53 Time building geometry restraints manager: 14.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 12514 1.34 - 1.48: 8591 1.48 - 1.61: 17936 1.61 - 1.75: 1 1.75 - 1.88: 262 Bond restraints: 39304 Sorted by residual: bond pdb=" CA VAL J 242 " pdb=" CB VAL J 242 " ideal model delta sigma weight residual 1.537 1.564 -0.028 5.00e-03 4.00e+04 3.03e+01 bond pdb=" CA GLY M 141 " pdb=" C GLY M 141 " ideal model delta sigma weight residual 1.518 1.557 -0.038 7.30e-03 1.88e+04 2.75e+01 bond pdb=" O1P SEP L 52 " pdb=" P SEP L 52 " ideal model delta sigma weight residual 1.610 1.509 0.101 2.00e-02 2.50e+03 2.55e+01 bond pdb=" O2P SEP L 52 " pdb=" P SEP L 52 " ideal model delta sigma weight residual 1.610 1.511 0.099 2.00e-02 2.50e+03 2.47e+01 bond pdb=" O3P SEP K 52 " pdb=" P SEP K 52 " ideal model delta sigma weight residual 1.610 1.511 0.099 2.00e-02 2.50e+03 2.46e+01 ... (remaining 39299 not shown) Histogram of bond angle deviations from ideal: 100.37 - 107.12: 1011 107.12 - 113.88: 21348 113.88 - 120.63: 15082 120.63 - 127.39: 15488 127.39 - 134.14: 248 Bond angle restraints: 53177 Sorted by residual: angle pdb=" C SER N 489 " pdb=" N PRO N 490 " pdb=" CA PRO N 490 " ideal model delta sigma weight residual 119.84 129.20 -9.36 1.25e+00 6.40e-01 5.61e+01 angle pdb=" N PHE B 149 " pdb=" CA PHE B 149 " pdb=" C PHE B 149 " ideal model delta sigma weight residual 108.45 117.78 -9.33 1.26e+00 6.30e-01 5.48e+01 angle pdb=" C LEU I 97 " pdb=" N PRO I 98 " pdb=" CA PRO I 98 " ideal model delta sigma weight residual 119.84 128.84 -9.00 1.25e+00 6.40e-01 5.18e+01 angle pdb=" N LYS M 300 " pdb=" CA LYS M 300 " pdb=" C LYS M 300 " ideal model delta sigma weight residual 110.97 118.75 -7.78 1.09e+00 8.42e-01 5.09e+01 angle pdb=" N VAL A 211 " pdb=" CA VAL A 211 " pdb=" C VAL A 211 " ideal model delta sigma weight residual 110.62 117.78 -7.16 1.02e+00 9.61e-01 4.92e+01 ... (remaining 53172 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 20199 17.67 - 35.34: 2824 35.34 - 53.01: 631 53.01 - 70.68: 338 70.68 - 88.35: 42 Dihedral angle restraints: 24034 sinusoidal: 9591 harmonic: 14443 Sorted by residual: dihedral pdb=" C ILE K 150 " pdb=" N ILE K 150 " pdb=" CA ILE K 150 " pdb=" CB ILE K 150 " ideal model delta harmonic sigma weight residual -122.00 -136.70 14.70 0 2.50e+00 1.60e-01 3.46e+01 dihedral pdb=" C ILE L 150 " pdb=" N ILE L 150 " pdb=" CA ILE L 150 " pdb=" CB ILE L 150 " ideal model delta harmonic sigma weight residual -122.00 -136.25 14.25 0 2.50e+00 1.60e-01 3.25e+01 dihedral pdb=" N ILE K 150 " pdb=" C ILE K 150 " pdb=" CA ILE K 150 " pdb=" CB ILE K 150 " ideal model delta harmonic sigma weight residual 123.40 137.37 -13.97 0 2.50e+00 1.60e-01 3.12e+01 ... (remaining 24031 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 4908 0.099 - 0.198: 1028 0.198 - 0.297: 242 0.297 - 0.396: 42 0.396 - 0.495: 17 Chirality restraints: 6237 Sorted by residual: chirality pdb=" CA LEU J 202 " pdb=" N LEU J 202 " pdb=" C LEU J 202 " pdb=" CB LEU J 202 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 6.12e+00 chirality pdb=" CA ARG M 356 " pdb=" N ARG M 356 " pdb=" C ARG M 356 " pdb=" CB ARG M 356 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.66e+00 chirality pdb=" CA ASN C 275 " pdb=" N ASN C 275 " pdb=" C ASN C 275 " pdb=" CB ASN C 275 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.51e+00 ... (remaining 6234 not shown) Planarity restraints: 6785 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS M 139 " 0.016 2.00e-02 2.50e+03 3.21e-02 1.03e+01 pdb=" C LYS M 139 " -0.056 2.00e-02 2.50e+03 pdb=" O LYS M 139 " 0.020 2.00e-02 2.50e+03 pdb=" N LEU M 140 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR I 304 " -0.051 5.00e-02 4.00e+02 7.65e-02 9.37e+00 pdb=" N PRO I 305 " 0.132 5.00e-02 4.00e+02 pdb=" CA PRO I 305 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO I 305 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 157 " -0.045 5.00e-02 4.00e+02 6.76e-02 7.32e+00 pdb=" N PRO A 158 " 0.117 5.00e-02 4.00e+02 pdb=" CA PRO A 158 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 158 " -0.038 5.00e-02 4.00e+02 ... (remaining 6782 not shown) Histogram of nonbonded interaction distances: 1.24 - 1.97: 5 1.97 - 2.70: 261 2.70 - 3.43: 51220 3.43 - 4.17: 80706 4.17 - 4.90: 137805 Nonbonded interactions: 269997 Sorted by model distance: nonbonded pdb=" OG SER F 413 " pdb=" OE1 GLN F 414 " model vdw 1.236 2.440 nonbonded pdb=" OG SER F 413 " pdb=" CD GLN F 414 " model vdw 1.543 3.270 nonbonded pdb=" OD2 ASP B 17 " pdb=" NH1 ARG B 133 " model vdw 1.700 2.520 nonbonded pdb=" OG SER F 413 " pdb=" NE2 GLN F 414 " model vdw 1.775 2.520 nonbonded pdb=" ND2 ASN M 144 " pdb=" OE2 GLU M 383 " model vdw 1.777 2.520 ... (remaining 269992 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' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' } 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=0.00 max=1.00 mean=0.98 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 8.550 Check model and map are aligned: 0.520 Set scattering table: 0.310 Process input model: 88.270 Find NCS groups from input model: 2.410 Set up NCS constraints: 0.260 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 104.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3816 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 : 0.009 0.101 39304 Z= 0.566 Angle : 1.437 13.515 53177 Z= 0.943 Chirality : 0.090 0.495 6237 Planarity : 0.005 0.077 6785 Dihedral : 18.646 88.352 14636 Min Nonbonded Distance : 1.236 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 3.41 % Allowed : 13.22 % Favored : 83.37 % Rotamer Outliers : 7.64 % Cbeta Deviations : 0.74 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.11), residues: 4841 helix: 1.61 (0.12), residues: 1454 sheet: -0.47 (0.23), residues: 519 loop : -3.19 (0.10), residues: 2868 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9682 Ramachandran restraints generated. 4841 Oldfield, 0 Emsley, 4841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9682 Ramachandran restraints generated. 4841 Oldfield, 0 Emsley, 4841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 908 residues out of total 4398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 326 poor density : 582 time to evaluate : 4.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 326 outliers final: 48 residues processed: 853 average time/residue: 0.5243 time to fit residues: 722.2527 Evaluate side-chains 369 residues out of total 4398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 321 time to evaluate : 4.687 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 48 outliers final: 1 residues processed: 48 average time/residue: 0.4209 time to fit residues: 41.4585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 412 optimal weight: 0.0040 chunk 369 optimal weight: 1.9990 chunk 205 optimal weight: 0.9990 chunk 126 optimal weight: 0.9990 chunk 249 optimal weight: 10.0000 chunk 197 optimal weight: 0.6980 chunk 382 optimal weight: 0.9980 chunk 148 optimal weight: 0.7980 chunk 232 optimal weight: 9.9990 chunk 284 optimal weight: 1.9990 chunk 443 optimal weight: 0.9980 overall best weight: 0.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 HIS ** A 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 163 ASN ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 ASN B 80 ASN ** B 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 152 GLN C 156 GLN C 237 ASN D 19 ASN D 58 ASN D 78 HIS ** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 336 GLN D 345 ASN D 375 HIS E 133 HIS ** E 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 258 HIS F 156 GLN F 186 GLN ** F 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 258 HIS ** G 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 446 ASN G 500 ASN G 539 ASN H 271 HIS ** H 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 446 ASN H 517 GLN H 546 ASN I 335 GLN I 371 ASN I 460 GLN J 28 GLN J 56 ASN J 73 HIS J 87 ASN J 92 ASN J 96 ASN J 212 GLN J 241 HIS ** J 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 365 ASN J 423 ASN K 41 ASN K 140 HIS M 221 ASN M 232 HIS M 262 HIS M 324 ASN M 344 ASN M 465 ASN N 98 GLN ** N 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 465 ASN ** P 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3800 moved from start: 0.3367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 39304 Z= 0.218 Angle : 0.738 10.904 53177 Z= 0.379 Chirality : 0.048 0.255 6237 Planarity : 0.005 0.066 6785 Dihedral : 6.052 48.314 5276 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 1.14 % Allowed : 10.60 % Favored : 88.27 % Rotamer Outliers : 0.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.24 (0.12), residues: 4841 helix: 2.73 (0.15), residues: 1452 sheet: -0.64 (0.19), residues: 679 loop : -3.14 (0.10), residues: 2710 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9682 Ramachandran restraints generated. 4841 Oldfield, 0 Emsley, 4841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9682 Ramachandran restraints generated. 4841 Oldfield, 0 Emsley, 4841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 4398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 428 time to evaluate : 4.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 3 residues processed: 440 average time/residue: 0.5199 time to fit residues: 376.8353 Evaluate side-chains 288 residues out of total 4398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 285 time to evaluate : 5.187 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.3341 time to fit residues: 8.8465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 246 optimal weight: 3.9990 chunk 137 optimal weight: 20.0000 chunk 368 optimal weight: 1.9990 chunk 301 optimal weight: 5.9990 chunk 122 optimal weight: 20.0000 chunk 443 optimal weight: 0.0970 chunk 479 optimal weight: 50.0000 chunk 395 optimal weight: 40.0000 chunk 440 optimal weight: 50.0000 chunk 151 optimal weight: 0.0010 chunk 356 optimal weight: 7.9990 overall best weight: 2.4190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 ASN ** A 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 80 ASN ** B 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 61 ASN C 66 GLN C 72 ASN ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 33 GLN D 72 ASN ** D 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 GLN ** D 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 298 GLN G 271 HIS ** G 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 389 ASN H 416 ASN ** H 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 530 ASN ** J 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 68 ASN ** M 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 197 HIS ** P 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3938 moved from start: 0.4049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 39304 Z= 0.200 Angle : 0.669 9.854 53177 Z= 0.340 Chirality : 0.046 0.271 6237 Planarity : 0.005 0.121 6785 Dihedral : 5.682 36.895 5276 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.93 % Allowed : 11.82 % Favored : 87.25 % Rotamer Outliers : 0.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.12), residues: 4841 helix: 2.19 (0.14), residues: 1446 sheet: -0.59 (0.19), residues: 660 loop : -3.06 (0.10), residues: 2735 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9682 Ramachandran restraints generated. 4841 Oldfield, 0 Emsley, 4841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9682 Ramachandran restraints generated. 4841 Oldfield, 0 Emsley, 4841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 4398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 381 time to evaluate : 4.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 383 average time/residue: 0.5032 time to fit residues: 318.5757 Evaluate side-chains 264 residues out of total 4398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 263 time to evaluate : 4.838 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.4291 time to fit residues: 7.3050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 438 optimal weight: 40.0000 chunk 333 optimal weight: 0.9990 chunk 230 optimal weight: 6.9990 chunk 49 optimal weight: 2.9990 chunk 211 optimal weight: 0.9980 chunk 298 optimal weight: 6.9990 chunk 445 optimal weight: 50.0000 chunk 471 optimal weight: 6.9990 chunk 232 optimal weight: 8.9990 chunk 422 optimal weight: 50.0000 chunk 127 optimal weight: 4.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 388 ASN G 280 HIS ** G 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 530 ASN I 417 ASN J 87 ASN ** J 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 228 ASN J 393 HIS K 5 HIS M 98 GLN ** M 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 450 GLN N 286 GLN N 465 ASN ** P 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4047 moved from start: 0.4560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 39304 Z= 0.208 Angle : 0.657 10.296 53177 Z= 0.334 Chirality : 0.046 0.269 6237 Planarity : 0.005 0.074 6785 Dihedral : 5.638 34.579 5276 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 15.51 Ramachandran Plot: Outliers : 0.87 % Allowed : 10.66 % Favored : 88.47 % Rotamer Outliers : 0.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.49 % 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: -1.59 (0.12), residues: 4841 helix: 1.70 (0.14), residues: 1470 sheet: -0.64 (0.20), residues: 619 loop : -2.93 (0.10), residues: 2752 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9682 Ramachandran restraints generated. 4841 Oldfield, 0 Emsley, 4841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9682 Ramachandran restraints generated. 4841 Oldfield, 0 Emsley, 4841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 4398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 353 time to evaluate : 4.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 355 average time/residue: 0.5041 time to fit residues: 302.7021 Evaluate side-chains 256 residues out of total 4398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 256 time to evaluate : 4.181 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.7275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 392 optimal weight: 10.0000 chunk 267 optimal weight: 7.9990 chunk 6 optimal weight: 20.0000 chunk 351 optimal weight: 20.0000 chunk 194 optimal weight: 7.9990 chunk 402 optimal weight: 40.0000 chunk 326 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 240 optimal weight: 1.9990 chunk 423 optimal weight: 40.0000 chunk 119 optimal weight: 8.9990 overall best weight: 7.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 ASN ** B 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 221 HIS C 33 GLN ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 319 GLN ** C 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 19 ASN ** D 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 181 HIS ** D 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 352 ASN ** E 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 156 GLN F 219 GLN F 220 GLN ** F 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 280 HIS G 384 GLN ** G 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 475 HIS ** G 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 530 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 539 ASN ** I 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 335 GLN ** I 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 409 ASN I 417 ASN ** J 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 388 ASN K 68 ASN K 109 HIS ** L 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 249 ASN N 243 HIS ** N 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4401 moved from start: 0.5740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.093 39304 Z= 0.360 Angle : 0.847 13.365 53177 Z= 0.437 Chirality : 0.051 0.260 6237 Planarity : 0.006 0.075 6785 Dihedral : 6.552 36.880 5276 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 27.46 Ramachandran Plot: Outliers : 0.87 % Allowed : 13.26 % Favored : 85.87 % Rotamer Outliers : 0.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.49 % Twisted General : 0.04 % 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: -2.51 (0.11), residues: 4841 helix: 0.30 (0.13), residues: 1456 sheet: -1.21 (0.20), residues: 604 loop : -3.05 (0.10), residues: 2781 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9682 Ramachandran restraints generated. 4841 Oldfield, 0 Emsley, 4841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9682 Ramachandran restraints generated. 4841 Oldfield, 0 Emsley, 4841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 4398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 317 time to evaluate : 4.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 321 average time/residue: 0.5187 time to fit residues: 281.5432 Evaluate side-chains 238 residues out of total 4398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 238 time to evaluate : 4.874 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 9.5984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 158 optimal weight: 8.9990 chunk 424 optimal weight: 8.9990 chunk 93 optimal weight: 3.9990 chunk 276 optimal weight: 0.5980 chunk 116 optimal weight: 6.9990 chunk 472 optimal weight: 0.4980 chunk 391 optimal weight: 0.8980 chunk 218 optimal weight: 7.9990 chunk 39 optimal weight: 8.9990 chunk 156 optimal weight: 0.2980 chunk 247 optimal weight: 5.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 ASN ** B 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 HIS B 277 GLN ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 181 HIS D 183 HIS ** D 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 220 GLN ** F 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 280 HIS ** G 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 280 HIS H 530 ASN I 73 HIS J 87 ASN ** J 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 156 HIS J 212 GLN K 5 HIS ** L 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4150 moved from start: 0.5701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.058 39304 Z= 0.183 Angle : 0.668 12.544 53177 Z= 0.334 Chirality : 0.046 0.267 6237 Planarity : 0.004 0.067 6785 Dihedral : 5.746 36.314 5276 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 16.54 Ramachandran Plot: Outliers : 0.83 % Allowed : 9.30 % Favored : 89.88 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.49 % 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: -2.01 (0.12), residues: 4841 helix: 0.91 (0.13), residues: 1465 sheet: -0.97 (0.20), residues: 635 loop : -2.88 (0.11), residues: 2741 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9682 Ramachandran restraints generated. 4841 Oldfield, 0 Emsley, 4841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9682 Ramachandran restraints generated. 4841 Oldfield, 0 Emsley, 4841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 4398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 342 time to evaluate : 4.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 342 average time/residue: 0.4712 time to fit residues: 276.5191 Evaluate side-chains 250 residues out of total 4398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 250 time to evaluate : 4.908 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.6717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 455 optimal weight: 0.4980 chunk 53 optimal weight: 0.1980 chunk 269 optimal weight: 6.9990 chunk 344 optimal weight: 5.9990 chunk 267 optimal weight: 0.9980 chunk 397 optimal weight: 0.0980 chunk 263 optimal weight: 0.9990 chunk 470 optimal weight: 9.9990 chunk 294 optimal weight: 7.9990 chunk 286 optimal weight: 20.0000 chunk 217 optimal weight: 6.9990 overall best weight: 0.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 375 HIS ** D 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 181 HIS D 183 HIS ** D 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 59 GLN G 280 HIS G 553 GLN ** H 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 475 HIS ** I 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 335 GLN ** J 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 25 GLN ** L 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 111 HIS ** N 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4078 moved from start: 0.5764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.046 39304 Z= 0.164 Angle : 0.625 10.649 53177 Z= 0.310 Chirality : 0.045 0.227 6237 Planarity : 0.004 0.075 6785 Dihedral : 5.334 40.623 5276 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.76 % Allowed : 10.16 % Favored : 89.07 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.12), residues: 4841 helix: 1.19 (0.14), residues: 1476 sheet: -1.00 (0.20), residues: 686 loop : -2.74 (0.11), residues: 2679 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9682 Ramachandran restraints generated. 4841 Oldfield, 0 Emsley, 4841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9682 Ramachandran restraints generated. 4841 Oldfield, 0 Emsley, 4841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 4398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 350 time to evaluate : 4.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 350 average time/residue: 0.4474 time to fit residues: 271.6298 Evaluate side-chains 253 residues out of total 4398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 253 time to evaluate : 4.590 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.3440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 290 optimal weight: 0.9990 chunk 187 optimal weight: 0.9990 chunk 280 optimal weight: 4.9990 chunk 141 optimal weight: 7.9990 chunk 92 optimal weight: 6.9990 chunk 91 optimal weight: 3.9990 chunk 299 optimal weight: 4.9990 chunk 320 optimal weight: 8.9990 chunk 232 optimal weight: 2.9990 chunk 43 optimal weight: 6.9990 chunk 369 optimal weight: 50.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 46 GLN ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 181 HIS D 183 HIS ** D 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 553 GLN ** H 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 530 ASN I 28 GLN I 365 ASN ** J 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4178 moved from start: 0.6018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 39304 Z= 0.187 Angle : 0.636 9.828 53177 Z= 0.319 Chirality : 0.045 0.220 6237 Planarity : 0.004 0.082 6785 Dihedral : 5.378 44.377 5276 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 16.74 Ramachandran Plot: Outliers : 0.76 % Allowed : 10.27 % Favored : 88.97 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.49 % 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: -1.80 (0.12), residues: 4841 helix: 1.06 (0.14), residues: 1481 sheet: -0.95 (0.20), residues: 684 loop : -2.75 (0.11), residues: 2676 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9682 Ramachandran restraints generated. 4841 Oldfield, 0 Emsley, 4841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9682 Ramachandran restraints generated. 4841 Oldfield, 0 Emsley, 4841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 4398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 319 time to evaluate : 4.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 319 average time/residue: 0.4566 time to fit residues: 253.9860 Evaluate side-chains 244 residues out of total 4398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 244 time to evaluate : 5.050 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.8225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 427 optimal weight: 10.0000 chunk 450 optimal weight: 0.3980 chunk 411 optimal weight: 30.0000 chunk 438 optimal weight: 4.9990 chunk 263 optimal weight: 0.3980 chunk 190 optimal weight: 0.0470 chunk 344 optimal weight: 5.9990 chunk 134 optimal weight: 7.9990 chunk 396 optimal weight: 30.0000 chunk 414 optimal weight: 2.9990 chunk 436 optimal weight: 40.0000 overall best weight: 1.7682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 277 GLN ** B 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 141 HIS ** B 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 181 HIS D 183 HIS ** D 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 475 HIS I 365 ASN ** J 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4137 moved from start: 0.6129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.073 39304 Z= 0.164 Angle : 0.618 9.853 53177 Z= 0.307 Chirality : 0.045 0.244 6237 Planarity : 0.004 0.082 6785 Dihedral : 5.254 46.034 5276 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 15.39 Ramachandran Plot: Outliers : 0.70 % Allowed : 10.10 % Favored : 89.20 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.49 % 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: -1.72 (0.12), residues: 4841 helix: 1.15 (0.14), residues: 1465 sheet: -0.93 (0.20), residues: 695 loop : -2.68 (0.11), residues: 2681 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9682 Ramachandran restraints generated. 4841 Oldfield, 0 Emsley, 4841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9682 Ramachandran restraints generated. 4841 Oldfield, 0 Emsley, 4841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 4398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 328 time to evaluate : 4.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 328 average time/residue: 0.4650 time to fit residues: 263.8530 Evaluate side-chains 254 residues out of total 4398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 254 time to evaluate : 5.012 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.3823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 287 optimal weight: 1.9990 chunk 463 optimal weight: 50.0000 chunk 282 optimal weight: 10.0000 chunk 219 optimal weight: 20.0000 chunk 322 optimal weight: 3.9990 chunk 486 optimal weight: 0.5980 chunk 447 optimal weight: 0.0370 chunk 387 optimal weight: 10.0000 chunk 40 optimal weight: 6.9990 chunk 299 optimal weight: 0.0060 chunk 237 optimal weight: 7.9990 overall best weight: 1.3278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 236 HIS D 10 HIS ** D 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 181 HIS D 183 HIS ** D 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 4 GLN F 298 GLN ** G 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 475 HIS ** J 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4107 moved from start: 0.6225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.042 39304 Z= 0.159 Angle : 0.610 9.519 53177 Z= 0.304 Chirality : 0.044 0.292 6237 Planarity : 0.004 0.080 6785 Dihedral : 5.165 47.002 5276 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.66 % Allowed : 10.06 % Favored : 89.28 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.49 % 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: -1.68 (0.12), residues: 4841 helix: 1.16 (0.14), residues: 1472 sheet: -0.90 (0.19), residues: 759 loop : -2.69 (0.12), residues: 2610 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9682 Ramachandran restraints generated. 4841 Oldfield, 0 Emsley, 4841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9682 Ramachandran restraints generated. 4841 Oldfield, 0 Emsley, 4841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 4398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 331 time to evaluate : 4.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 331 average time/residue: 0.4528 time to fit residues: 260.9345 Evaluate side-chains 255 residues out of total 4398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 255 time to evaluate : 4.433 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.0218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 307 optimal weight: 0.0060 chunk 412 optimal weight: 40.0000 chunk 118 optimal weight: 6.9990 chunk 356 optimal weight: 8.9990 chunk 57 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 387 optimal weight: 8.9990 chunk 162 optimal weight: 1.9990 chunk 398 optimal weight: 0.2980 chunk 49 optimal weight: 0.7980 chunk 71 optimal weight: 5.9990 overall best weight: 1.2200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 10 HIS ** C 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 181 HIS D 183 HIS ** D 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 4 GLN F 298 GLN ** H 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 475 HIS J 87 ASN ** J 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 109 HIS ** M 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5041 r_free = 0.5041 target = 0.119517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4588 r_free = 0.4588 target = 0.095287 restraints weight = 260648.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4639 r_free = 0.4639 target = 0.097041 restraints weight = 190899.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4681 r_free = 0.4681 target = 0.099099 restraints weight = 130755.796| |-----------------------------------------------------------------------------| r_work (final): 0.4564 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4564 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4564 r_free = 0.4564 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 803 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4564 r_free = 0.4564 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 803 | |-----------------------------------------------------------------------------| r_final: 0.4564 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5687 moved from start: 0.6311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.041 39304 Z= 0.157 Angle : 0.602 9.243 53177 Z= 0.299 Chirality : 0.044 0.411 6237 Planarity : 0.004 0.067 6785 Dihedral : 5.071 47.033 5276 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.62 % Allowed : 9.87 % Favored : 89.51 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.12), residues: 4841 helix: 1.21 (0.14), residues: 1471 sheet: -0.88 (0.19), residues: 755 loop : -2.65 (0.12), residues: 2615 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7419.89 seconds wall clock time: 137 minutes 53.69 seconds (8273.69 seconds total)