Starting phenix.real_space_refine on Sun Feb 18 04:16:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uja_26562/02_2024/7uja_26562.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uja_26562/02_2024/7uja_26562.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uja_26562/02_2024/7uja_26562.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uja_26562/02_2024/7uja_26562.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uja_26562/02_2024/7uja_26562.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uja_26562/02_2024/7uja_26562.pdb" } resolution = 3.7 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= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 114 5.16 5 C 13089 2.51 5 N 3471 2.21 5 O 4074 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 163": "OE1" <-> "OE2" Residue "A GLU 236": "OE1" <-> "OE2" Residue "A GLU 295": "OE1" <-> "OE2" Residue "A GLU 356": "OE1" <-> "OE2" Residue "B GLU 89": "OE1" <-> "OE2" Residue "C GLU 222": "OE1" <-> "OE2" Residue "C GLU 256": "OE1" <-> "OE2" Residue "D GLU 45": "OE1" <-> "OE2" Residue "F GLU 17": "OE1" <-> "OE2" Residue "G GLU 56": "OE1" <-> "OE2" Residue "G GLU 89": "OE1" <-> "OE2" Residue "I GLU 54": "OE1" <-> "OE2" Residue "I GLU 57": "OE1" <-> "OE2" Residue "K GLU 487": "OE1" <-> "OE2" Residue "L GLU 46": "OE1" <-> "OE2" Residue "L TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 57": "OE1" <-> "OE2" Residue "O GLU 17": "OE1" <-> "OE2" Residue "O GLU 82": "OE1" <-> "OE2" Residue "O PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 45": "OE1" <-> "OE2" Residue "H GLU 55": "OE1" <-> "OE2" Residue "M TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 31": "OE1" <-> "OE2" Residue "P GLU 82": "OE1" <-> "OE2" Residue "Q GLU 31": "OE1" <-> "OE2" Residue "R GLU 31": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 20748 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 2859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2859 Classifications: {'peptide': 372} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 359} Chain: "B" Number of atoms: 934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 934 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "C" Number of atoms: 2859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2859 Classifications: {'peptide': 372} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 359} Chain: "D" Number of atoms: 769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 769 Classifications: {'peptide': 99} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 91} Chain breaks: 1 Chain: "E" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 940 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "F" Number of atoms: 785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 785 Classifications: {'peptide': 105} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 97} Chain: "G" Number of atoms: 934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 934 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "I" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 940 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "J" Number of atoms: 785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 785 Classifications: {'peptide': 105} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 97} Chain: "K" Number of atoms: 2859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2859 Classifications: {'peptide': 372} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 359} Chain: "L" Number of atoms: 934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 934 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "N" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 940 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "O" Number of atoms: 785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 785 Classifications: {'peptide': 105} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 97} Chain: "H" Number of atoms: 769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 769 Classifications: {'peptide': 99} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 91} Chain breaks: 1 Chain: "M" Number of atoms: 769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 769 Classifications: {'peptide': 99} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 91} Chain breaks: 1 Chain: "P" Number of atoms: 615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 615 Classifications: {'peptide': 79} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "Q" Number of atoms: 615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 615 Classifications: {'peptide': 79} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "R" Number of atoms: 615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 615 Classifications: {'peptide': 79} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 10.20, per 1000 atoms: 0.49 Number of scatterers: 20748 At special positions: 0 Unit cell: (156.18, 150.7, 153.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 114 16.00 O 4074 8.00 N 3471 7.00 C 13089 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=31, symmetry=0 Simple disulfide: pdb=" SG CYS A 148 " - pdb=" SG CYS P 103 " distance=2.03 Simple disulfide: pdb=" SG CYS A 212 " - pdb=" SG CYS P 69 " distance=2.03 Simple disulfide: pdb=" SG CYS A 313 " - pdb=" SG CYS A 343 " distance=2.29 Simple disulfide: pdb=" SG CYS A 322 " - pdb=" SG CYS A 333 " distance=2.04 Simple disulfide: pdb=" SG CYS A 358 " - pdb=" SG CYS A 367 " distance=2.03 Simple disulfide: pdb=" SG CYS A 382 " - pdb=" SG CYS A 393 " distance=2.03 Simple disulfide: pdb=" SG CYS A 416 " - pdb=" SG CYS A 422 " distance=2.03 Simple disulfide: pdb=" SG CYS A 439 " - pdb=" SG CYS P 37 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 148 " - pdb=" SG CYS Q 103 " distance=2.03 Simple disulfide: pdb=" SG CYS C 212 " - pdb=" SG CYS Q 69 " distance=2.03 Simple disulfide: pdb=" SG CYS C 313 " - pdb=" SG CYS C 343 " distance=2.03 Simple disulfide: pdb=" SG CYS C 322 " - pdb=" SG CYS C 333 " distance=2.04 Simple disulfide: pdb=" SG CYS C 358 " - pdb=" SG CYS C 367 " distance=2.03 Simple disulfide: pdb=" SG CYS C 382 " - pdb=" SG CYS C 393 " distance=2.03 Simple disulfide: pdb=" SG CYS C 416 " - pdb=" SG CYS C 422 " distance=2.03 Simple disulfide: pdb=" SG CYS C 439 " - pdb=" SG CYS Q 37 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.10 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 89 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 89 " distance=2.03 Simple disulfide: pdb=" SG CYS K 148 " - pdb=" SG CYS R 103 " distance=2.03 Simple disulfide: pdb=" SG CYS K 212 " - pdb=" SG CYS R 69 " distance=2.03 Simple disulfide: pdb=" SG CYS K 313 " - pdb=" SG CYS K 343 " distance=2.04 Simple disulfide: pdb=" SG CYS K 322 " - pdb=" SG CYS K 333 " distance=2.04 Simple disulfide: pdb=" SG CYS K 358 " - pdb=" SG CYS K 367 " distance=2.04 Simple disulfide: pdb=" SG CYS K 382 " - pdb=" SG CYS K 393 " distance=2.03 Simple disulfide: pdb=" SG CYS K 416 " - pdb=" SG CYS K 422 " distance=2.03 Simple disulfide: pdb=" SG CYS K 439 " - pdb=" SG CYS R 37 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 96 " distance=2.03 Simple disulfide: pdb=" SG CYS O 23 " - pdb=" SG CYS O 89 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 601 " - " ASN A 500 " " NAG C 601 " - " ASN C 500 " " NAG K 601 " - " ASN K 500 " Time building additional restraints: 8.07 Conformation dependent library (CDL) restraints added in 3.7 seconds 5304 Ramachandran restraints generated. 2652 Oldfield, 0 Emsley, 2652 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4968 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 46 sheets defined 16.6% alpha, 26.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.43 Creating SS restraints... Processing helix chain 'A' and resid 151 through 156 Processing helix chain 'A' and resid 163 through 171 removed outlier: 3.536A pdb=" N ILE A 167 " --> pdb=" O GLU A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 200 removed outlier: 3.538A pdb=" N ILE A 199 " --> pdb=" O LEU A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 208 removed outlier: 3.627A pdb=" N VAL A 207 " --> pdb=" O LEU A 203 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ASN A 208 " --> pdb=" O LEU A 204 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 203 through 208' Processing helix chain 'A' and resid 216 through 238 removed outlier: 4.204A pdb=" N VAL A 220 " --> pdb=" O ASN A 216 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ARG A 229 " --> pdb=" O GLN A 225 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N LEU A 230 " --> pdb=" O LYS A 226 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N THR A 234 " --> pdb=" O LEU A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 262 removed outlier: 3.631A pdb=" N LEU A 258 " --> pdb=" O ASN A 254 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N SER A 259 " --> pdb=" O SER A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 276 Processing helix chain 'A' and resid 277 through 282 Processing helix chain 'A' and resid 379 through 385 removed outlier: 3.998A pdb=" N ASN A 383 " --> pdb=" O VAL A 379 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ILE A 384 " --> pdb=" O ASN A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 478 removed outlier: 3.744A pdb=" N PHE A 477 " --> pdb=" O ILE A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 506 removed outlier: 3.525A pdb=" N ILE A 506 " --> pdb=" O SER A 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 32 removed outlier: 3.532A pdb=" N HIS B 31 " --> pdb=" O SER B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 91 removed outlier: 4.045A pdb=" N THR B 91 " --> pdb=" O PRO B 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 142 removed outlier: 3.644A pdb=" N LEU C 141 " --> pdb=" O LEU C 138 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU C 142 " --> pdb=" O GLY C 139 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 138 through 142' Processing helix chain 'C' and resid 151 through 156 Processing helix chain 'C' and resid 163 through 171 removed outlier: 3.574A pdb=" N ILE C 167 " --> pdb=" O GLU C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 200 removed outlier: 3.565A pdb=" N ILE C 199 " --> pdb=" O LEU C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 208 removed outlier: 3.542A pdb=" N VAL C 207 " --> pdb=" O LEU C 203 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASN C 208 " --> pdb=" O LEU C 204 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 203 through 208' Processing helix chain 'C' and resid 216 through 227 removed outlier: 4.278A pdb=" N VAL C 220 " --> pdb=" O ASN C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 241 removed outlier: 3.570A pdb=" N LEU C 231 " --> pdb=" O ASN C 227 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR C 234 " --> pdb=" O LEU C 230 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N VAL C 239 " --> pdb=" O ARG C 235 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASN C 240 " --> pdb=" O GLU C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 262 removed outlier: 3.609A pdb=" N LEU C 258 " --> pdb=" O ASN C 254 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N SER C 259 " --> pdb=" O SER C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 276 Processing helix chain 'C' and resid 277 through 282 Processing helix chain 'C' and resid 368 through 372 removed outlier: 4.088A pdb=" N ASN C 371 " --> pdb=" O ASP C 368 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N SER C 372 " --> pdb=" O THR C 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 368 through 372' Processing helix chain 'C' and resid 379 through 385 removed outlier: 4.049A pdb=" N ASN C 383 " --> pdb=" O VAL C 379 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ILE C 384 " --> pdb=" O ASN C 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 474 through 478 removed outlier: 3.577A pdb=" N PHE C 477 " --> pdb=" O ILE C 474 " (cutoff:3.500A) Processing helix chain 'C' and resid 492 through 507 removed outlier: 3.678A pdb=" N ILE C 506 " --> pdb=" O SER C 502 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG C 507 " --> pdb=" O LEU C 503 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 32 removed outlier: 3.509A pdb=" N HIS G 31 " --> pdb=" O SER G 28 " (cutoff:3.500A) Processing helix chain 'G' and resid 87 through 91 removed outlier: 3.918A pdb=" N THR G 91 " --> pdb=" O PRO G 88 " (cutoff:3.500A) Processing helix chain 'I' and resid 62 through 65 Processing helix chain 'K' and resid 148 through 159 removed outlier: 4.196A pdb=" N ILE K 152 " --> pdb=" O CYS K 148 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA K 153 " --> pdb=" O ALA K 149 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N VAL K 154 " --> pdb=" O SER K 150 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL K 157 " --> pdb=" O ALA K 153 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU K 158 " --> pdb=" O VAL K 154 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N HIS K 159 " --> pdb=" O SER K 155 " (cutoff:3.500A) Processing helix chain 'K' and resid 163 through 171 removed outlier: 3.579A pdb=" N ILE K 167 " --> pdb=" O GLU K 163 " (cutoff:3.500A) Processing helix chain 'K' and resid 195 through 200 removed outlier: 3.588A pdb=" N ILE K 199 " --> pdb=" O LEU K 195 " (cutoff:3.500A) Processing helix chain 'K' and resid 203 through 208 removed outlier: 3.647A pdb=" N VAL K 207 " --> pdb=" O LEU K 203 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASN K 208 " --> pdb=" O LEU K 204 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 203 through 208' Processing helix chain 'K' and resid 216 through 241 removed outlier: 4.173A pdb=" N VAL K 220 " --> pdb=" O ASN K 216 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU K 222 " --> pdb=" O GLU K 218 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ARG K 229 " --> pdb=" O GLN K 225 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N LEU K 230 " --> pdb=" O LYS K 226 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LEU K 231 " --> pdb=" O ASN K 227 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N THR K 234 " --> pdb=" O LEU K 230 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N VAL K 239 " --> pdb=" O ARG K 235 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ASN K 240 " --> pdb=" O GLU K 236 " (cutoff:3.500A) Processing helix chain 'K' and resid 253 through 262 removed outlier: 3.546A pdb=" N LEU K 258 " --> pdb=" O ASN K 254 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N SER K 259 " --> pdb=" O SER K 255 " (cutoff:3.500A) Processing helix chain 'K' and resid 269 through 276 removed outlier: 3.566A pdb=" N SER K 276 " --> pdb=" O LYS K 272 " (cutoff:3.500A) Processing helix chain 'K' and resid 277 through 282 Processing helix chain 'K' and resid 376 through 378 No H-bonds generated for 'chain 'K' and resid 376 through 378' Processing helix chain 'K' and resid 379 through 385 removed outlier: 4.204A pdb=" N ASN K 383 " --> pdb=" O VAL K 379 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ILE K 384 " --> pdb=" O ASN K 380 " (cutoff:3.500A) Processing helix chain 'K' and resid 473 through 478 removed outlier: 3.913A pdb=" N ASN K 476 " --> pdb=" O PRO K 473 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N PHE K 477 " --> pdb=" O ILE K 474 " (cutoff:3.500A) Processing helix chain 'K' and resid 492 through 507 removed outlier: 3.524A pdb=" N ILE K 506 " --> pdb=" O SER K 502 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG K 507 " --> pdb=" O LEU K 503 " (cutoff:3.500A) Processing helix chain 'L' and resid 28 through 32 removed outlier: 3.559A pdb=" N HIS L 31 " --> pdb=" O SER L 28 " (cutoff:3.500A) Processing helix chain 'L' and resid 87 through 91 removed outlier: 3.753A pdb=" N THR L 91 " --> pdb=" O PRO L 88 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 65 Processing helix chain 'O' and resid 80 through 84 removed outlier: 4.135A pdb=" N PHE O 84 " --> pdb=" O PRO O 81 " (cutoff:3.500A) Processing helix chain 'P' and resid 73 through 95 removed outlier: 3.669A pdb=" N LYS P 77 " --> pdb=" O ASP P 73 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE P 79 " --> pdb=" O LYS P 75 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU P 95 " --> pdb=" O THR P 91 " (cutoff:3.500A) Processing helix chain 'Q' and resid 74 through 97 removed outlier: 3.674A pdb=" N LEU Q 95 " --> pdb=" O THR Q 91 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU Q 96 " --> pdb=" O GLU Q 92 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N MET Q 97 " --> pdb=" O LEU Q 93 " (cutoff:3.500A) Processing helix chain 'R' and resid 74 through 97 removed outlier: 3.505A pdb=" N ILE R 79 " --> pdb=" O LYS R 75 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU R 95 " --> pdb=" O THR R 91 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU R 96 " --> pdb=" O GLU R 92 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N MET R 97 " --> pdb=" O LEU R 93 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 177 through 180 removed outlier: 7.276A pdb=" N SER A 186 " --> pdb=" O THR P 54 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N VAL P 56 " --> pdb=" O SER A 186 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N LEU A 188 " --> pdb=" O VAL P 56 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N THR P 58 " --> pdb=" O LEU A 188 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N ILE A 190 " --> pdb=" O THR P 58 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLY P 51 " --> pdb=" O LEU A 305 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N ALA A 298 " --> pdb=" O SER A 290 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 213 through 214 removed outlier: 3.508A pdb=" N SER A 213 " --> pdb=" O LEU E 108 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 349 through 352 removed outlier: 3.771A pdb=" N GLY A 340 " --> pdb=" O LEU A 316 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER P 38 " --> pdb=" O TYR P 33 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N TYR P 33 " --> pdb=" O SER P 38 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU P 30 " --> pdb=" O LYS A 465 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 333 through 336 removed outlier: 3.604A pdb=" N CYS A 333 " --> pdb=" O SER A 398 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 406 through 407 removed outlier: 4.026A pdb=" N CYS A 416 " --> pdb=" O GLY A 438 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 430 through 434 removed outlier: 3.546A pdb=" N GLY A 430 " --> pdb=" O ASN A 426 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N ALA A 424 " --> pdb=" O ILE A 432 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N THR A 434 " --> pdb=" O CYS A 422 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N CYS A 422 " --> pdb=" O THR A 434 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 18 through 23 Processing sheet with id=AA8, first strand: chain 'B' and resid 58 through 59 removed outlier: 3.576A pdb=" N TRP B 36 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N VAL B 50 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N MET B 34 " --> pdb=" O VAL B 50 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 177 through 180 removed outlier: 7.235A pdb=" N SER C 186 " --> pdb=" O THR Q 54 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N VAL Q 56 " --> pdb=" O SER C 186 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N LEU C 188 " --> pdb=" O VAL Q 56 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N THR Q 58 " --> pdb=" O LEU C 188 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N ILE C 190 " --> pdb=" O THR Q 58 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLY Q 51 " --> pdb=" O LEU C 305 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N ALA C 298 " --> pdb=" O SER C 290 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 213 through 214 Processing sheet with id=AB2, first strand: chain 'C' and resid 349 through 352 removed outlier: 3.504A pdb=" N CYS C 343 " --> pdb=" O SER C 350 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLY C 340 " --> pdb=" O LEU C 316 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU C 316 " --> pdb=" O GLY C 340 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER Q 38 " --> pdb=" O TYR Q 33 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N TYR Q 33 " --> pdb=" O SER Q 38 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU Q 30 " --> pdb=" O LYS C 465 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 333 through 336 Processing sheet with id=AB4, first strand: chain 'C' and resid 406 through 407 removed outlier: 4.086A pdb=" N CYS C 416 " --> pdb=" O GLY C 438 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 430 through 434 removed outlier: 7.012A pdb=" N ALA C 424 " --> pdb=" O ILE C 432 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N THR C 434 " --> pdb=" O CYS C 422 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N CYS C 422 " --> pdb=" O THR C 434 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AB7, first strand: chain 'D' and resid 53 through 54 removed outlier: 7.076A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 3 through 6 removed outlier: 4.146A pdb=" N GLN E 3 " --> pdb=" O SER E 25 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N SER E 25 " --> pdb=" O GLN E 3 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL E 79 " --> pdb=" O CYS E 22 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE E 71 " --> pdb=" O TYR E 80 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU E 82 " --> pdb=" O THR E 69 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.879A pdb=" N GLU E 10 " --> pdb=" O LEU E 119 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ILE E 34 " --> pdb=" O GLY E 50 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N GLY E 50 " --> pdb=" O ILE E 34 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N TRP E 36 " --> pdb=" O MET E 48 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 4 through 7 Processing sheet with id=AC2, first strand: chain 'F' and resid 10 through 11 removed outlier: 3.565A pdb=" N THR F 103 " --> pdb=" O TYR F 87 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N LEU F 34 " --> pdb=" O PHE F 50 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N PHE F 50 " --> pdb=" O LEU F 34 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N TRP F 36 " --> pdb=" O LEU F 48 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 10 through 11 removed outlier: 3.565A pdb=" N THR F 103 " --> pdb=" O TYR F 87 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR F 98 " --> pdb=" O SER F 91 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 18 through 23 Processing sheet with id=AC5, first strand: chain 'G' and resid 45 through 51 removed outlier: 3.668A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N VAL G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N MET G 34 " --> pdb=" O VAL G 50 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 3 through 6 removed outlier: 3.924A pdb=" N GLN I 3 " --> pdb=" O SER I 25 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N SER I 25 " --> pdb=" O GLN I 3 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL I 79 " --> pdb=" O CYS I 22 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU I 82 " --> pdb=" O THR I 69 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N THR I 69 " --> pdb=" O GLU I 82 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 10 through 12 removed outlier: 4.010A pdb=" N GLU I 10 " --> pdb=" O LEU I 119 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ILE I 34 " --> pdb=" O GLY I 50 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N GLY I 50 " --> pdb=" O ILE I 34 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N TRP I 36 " --> pdb=" O MET I 48 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 107 through 108 Processing sheet with id=AC9, first strand: chain 'J' and resid 4 through 7 Processing sheet with id=AD1, first strand: chain 'J' and resid 10 through 11 removed outlier: 6.961A pdb=" N LEU J 34 " --> pdb=" O PHE J 50 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N PHE J 50 " --> pdb=" O LEU J 34 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N TRP J 36 " --> pdb=" O LEU J 48 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'J' and resid 10 through 11 Processing sheet with id=AD3, first strand: chain 'K' and resid 177 through 180 removed outlier: 7.120A pdb=" N SER K 186 " --> pdb=" O THR R 54 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N VAL R 56 " --> pdb=" O SER K 186 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N LEU K 188 " --> pdb=" O VAL R 56 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N THR R 58 " --> pdb=" O LEU K 188 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N ILE K 190 " --> pdb=" O THR R 58 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY R 51 " --> pdb=" O LEU K 305 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ALA K 298 " --> pdb=" O SER K 290 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'K' and resid 349 through 352 removed outlier: 3.506A pdb=" N CYS K 343 " --> pdb=" O SER K 350 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLY K 340 " --> pdb=" O LEU K 316 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU K 316 " --> pdb=" O GLY K 340 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N SER R 38 " --> pdb=" O TYR R 33 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N TYR R 33 " --> pdb=" O SER R 38 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU R 30 " --> pdb=" O LYS K 465 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'K' and resid 333 through 336 Processing sheet with id=AD6, first strand: chain 'K' and resid 406 through 407 Processing sheet with id=AD7, first strand: chain 'K' and resid 415 through 416 removed outlier: 4.210A pdb=" N CYS K 416 " --> pdb=" O GLY K 438 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'K' and resid 430 through 434 removed outlier: 3.624A pdb=" N ILE K 432 " --> pdb=" O ALA K 424 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ALA K 424 " --> pdb=" O ILE K 432 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N THR K 434 " --> pdb=" O CYS K 422 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N CYS K 422 " --> pdb=" O THR K 434 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'L' and resid 18 through 23 Processing sheet with id=AE1, first strand: chain 'L' and resid 58 through 59 removed outlier: 5.440A pdb=" N TRP L 47 " --> pdb=" O ARG L 38 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N ARG L 38 " --> pdb=" O TRP L 47 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ALA L 49 " --> pdb=" O TRP L 36 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'N' and resid 3 through 6 removed outlier: 4.132A pdb=" N GLN N 3 " --> pdb=" O SER N 25 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N SER N 25 " --> pdb=" O GLN N 3 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL N 79 " --> pdb=" O CYS N 22 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'N' and resid 10 through 12 removed outlier: 3.907A pdb=" N GLU N 10 " --> pdb=" O LEU N 119 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLY N 49 " --> pdb=" O TRP N 36 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'O' and resid 4 through 7 Processing sheet with id=AE5, first strand: chain 'O' and resid 10 through 11 removed outlier: 6.938A pdb=" N LEU O 34 " --> pdb=" O PHE O 50 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N PHE O 50 " --> pdb=" O LEU O 34 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N TRP O 36 " --> pdb=" O LEU O 48 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'O' and resid 10 through 11 Processing sheet with id=AE7, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AE8, first strand: chain 'H' and resid 53 through 54 removed outlier: 6.861A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N HIS H 49 " --> pdb=" O LEU H 33 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N LEU H 33 " --> pdb=" O HIS H 49 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'M' and resid 4 through 7 Processing sheet with id=AF1, first strand: chain 'M' and resid 53 through 54 removed outlier: 7.125A pdb=" N TRP M 35 " --> pdb=" O LEU M 47 " (cutoff:3.500A) 677 hydrogen bonds defined for protein. 1749 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: 7.53 Time building geometry restraints manager: 8.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 6692 1.35 - 1.47: 5065 1.47 - 1.59: 9213 1.59 - 1.72: 0 1.72 - 1.84: 156 Bond restraints: 21126 Sorted by residual: bond pdb=" CA GLN D 90 " pdb=" CB GLN D 90 " ideal model delta sigma weight residual 1.530 1.558 -0.028 1.55e-02 4.16e+03 3.32e+00 bond pdb=" C PRO M 95 " pdb=" N PRO M 96 " ideal model delta sigma weight residual 1.334 1.374 -0.040 2.34e-02 1.83e+03 2.94e+00 bond pdb=" C PRO D 95 " pdb=" N PRO D 96 " ideal model delta sigma weight residual 1.334 1.374 -0.040 2.34e-02 1.83e+03 2.94e+00 bond pdb=" C PRO H 95 " pdb=" N PRO H 96 " ideal model delta sigma weight residual 1.334 1.373 -0.039 2.34e-02 1.83e+03 2.75e+00 bond pdb=" C1 NAG K 601 " pdb=" O5 NAG K 601 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.48e+00 ... (remaining 21121 not shown) Histogram of bond angle deviations from ideal: 98.12 - 105.29: 327 105.29 - 112.47: 11052 112.47 - 119.64: 6704 119.64 - 126.81: 10329 126.81 - 133.99: 235 Bond angle restraints: 28647 Sorted by residual: angle pdb=" CA LEU E 29 " pdb=" CB LEU E 29 " pdb=" CG LEU E 29 " ideal model delta sigma weight residual 116.30 127.94 -11.64 3.50e+00 8.16e-02 1.11e+01 angle pdb=" CA GLN D 90 " pdb=" CB GLN D 90 " pdb=" CG GLN D 90 " ideal model delta sigma weight residual 114.10 120.67 -6.57 2.00e+00 2.50e-01 1.08e+01 angle pdb=" C THR I 76 " pdb=" N ASP I 77 " pdb=" CA ASP I 77 " ideal model delta sigma weight residual 121.54 127.65 -6.11 1.91e+00 2.74e-01 1.02e+01 angle pdb=" CA GLN H 90 " pdb=" CB GLN H 90 " pdb=" CG GLN H 90 " ideal model delta sigma weight residual 114.10 120.48 -6.38 2.00e+00 2.50e-01 1.02e+01 angle pdb=" CA CYS C 343 " pdb=" CB CYS C 343 " pdb=" SG CYS C 343 " ideal model delta sigma weight residual 114.40 121.20 -6.80 2.30e+00 1.89e-01 8.75e+00 ... (remaining 28642 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 11310 17.95 - 35.91: 1132 35.91 - 53.86: 268 53.86 - 71.82: 43 71.82 - 89.77: 18 Dihedral angle restraints: 12771 sinusoidal: 5010 harmonic: 7761 Sorted by residual: dihedral pdb=" CB CYS K 148 " pdb=" SG CYS K 148 " pdb=" SG CYS R 103 " pdb=" CB CYS R 103 " ideal model delta sinusoidal sigma weight residual 93.00 156.42 -63.42 1 1.00e+01 1.00e-02 5.30e+01 dihedral pdb=" CB CYS C 148 " pdb=" SG CYS C 148 " pdb=" SG CYS Q 103 " pdb=" CB CYS Q 103 " ideal model delta sinusoidal sigma weight residual 93.00 154.65 -61.65 1 1.00e+01 1.00e-02 5.04e+01 dihedral pdb=" CB CYS A 148 " pdb=" SG CYS A 148 " pdb=" SG CYS P 103 " pdb=" CB CYS P 103 " ideal model delta sinusoidal sigma weight residual 93.00 150.95 -57.95 1 1.00e+01 1.00e-02 4.51e+01 ... (remaining 12768 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 2103 0.031 - 0.062: 790 0.062 - 0.092: 234 0.092 - 0.123: 190 0.123 - 0.154: 13 Chirality restraints: 3330 Sorted by residual: chirality pdb=" CA ASN G 77 " pdb=" N ASN G 77 " pdb=" C ASN G 77 " pdb=" CB ASN G 77 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.93e-01 chirality pdb=" CA VAL L 48 " pdb=" N VAL L 48 " pdb=" C VAL L 48 " pdb=" CB VAL L 48 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.50e-01 chirality pdb=" CA ASP I 77 " pdb=" N ASP I 77 " pdb=" C ASP I 77 " pdb=" CB ASP I 77 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.21e-01 ... (remaining 3327 not shown) Planarity restraints: 3633 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG L 87 " -0.034 5.00e-02 4.00e+02 5.23e-02 4.38e+00 pdb=" N PRO L 88 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO L 88 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO L 88 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO H 95 " -0.032 5.00e-02 4.00e+02 4.89e-02 3.83e+00 pdb=" N PRO H 96 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO H 96 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO H 96 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO M 95 " -0.030 5.00e-02 4.00e+02 4.59e-02 3.38e+00 pdb=" N PRO M 96 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO M 96 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO M 96 " -0.026 5.00e-02 4.00e+02 ... (remaining 3630 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 306 2.67 - 3.23: 18828 3.23 - 3.79: 28870 3.79 - 4.34: 39089 4.34 - 4.90: 66770 Nonbonded interactions: 153863 Sorted by model distance: nonbonded pdb=" OD1 ASP J 106 " pdb=" N PHE J 107 " model vdw 2.114 2.520 nonbonded pdb=" O ILE I 110 " pdb=" OG SER K 211 " model vdw 2.197 2.440 nonbonded pdb=" OG1 THR K 311 " pdb=" OG SER R 46 " model vdw 2.199 2.440 nonbonded pdb=" OG1 THR A 311 " pdb=" OG SER P 46 " model vdw 2.208 2.440 nonbonded pdb=" OG SER A 211 " pdb=" O ILE E 110 " model vdw 2.212 2.440 ... (remaining 153858 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 'C' selection = chain 'K' } ncs_group { reference = chain 'B' selection = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'M' } ncs_group { reference = chain 'E' selection = chain 'I' selection = chain 'N' } ncs_group { reference = chain 'F' selection = chain 'J' selection = chain 'O' } ncs_group { reference = chain 'P' selection = chain 'Q' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 5.820 Check model and map are aligned: 0.300 Set scattering table: 0.180 Process input model: 54.530 Find NCS groups from input model: 1.330 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 21126 Z= 0.165 Angle : 0.583 11.638 28647 Z= 0.307 Chirality : 0.042 0.154 3330 Planarity : 0.004 0.055 3630 Dihedral : 15.085 89.770 7710 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 0.13 % Allowed : 16.84 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (0.16), residues: 2652 helix: -1.04 (0.26), residues: 366 sheet: -0.97 (0.19), residues: 816 loop : -2.00 (0.15), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 314 HIS 0.006 0.001 HIS M 37 PHE 0.015 0.001 PHE E 64 TYR 0.013 0.001 TYR E 113 ARG 0.014 0.001 ARG N 85 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5304 Ramachandran restraints generated. 2652 Oldfield, 0 Emsley, 2652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5304 Ramachandran restraints generated. 2652 Oldfield, 0 Emsley, 2652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 2349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 369 time to evaluate : 2.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 289 MET cc_start: 0.7301 (tpp) cc_final: 0.7020 (mmm) REVERT: G 83 MET cc_start: 0.6263 (mtm) cc_final: 0.5966 (mtm) REVERT: K 367 CYS cc_start: 0.6300 (m) cc_final: 0.5914 (m) outliers start: 3 outliers final: 2 residues processed: 370 average time/residue: 0.3014 time to fit residues: 174.4246 Evaluate side-chains 331 residues out of total 2349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 329 time to evaluate : 2.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain N residue 28 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 217 optimal weight: 7.9990 chunk 195 optimal weight: 7.9990 chunk 108 optimal weight: 0.5980 chunk 66 optimal weight: 0.5980 chunk 131 optimal weight: 1.9990 chunk 104 optimal weight: 0.0980 chunk 202 optimal weight: 10.0000 chunk 78 optimal weight: 9.9990 chunk 122 optimal weight: 0.9990 chunk 150 optimal weight: 0.8980 chunk 234 optimal weight: 7.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 183 ASN C 284 GLN F 38 GLN G 74 ASN J 38 GLN K 227 ASN K 284 GLN ** L 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 90 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.1089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 21126 Z= 0.153 Angle : 0.547 8.663 28647 Z= 0.285 Chirality : 0.042 0.152 3330 Planarity : 0.004 0.055 3630 Dihedral : 4.897 46.806 2946 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 3.84 % Allowed : 17.86 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.16), residues: 2652 helix: 0.14 (0.28), residues: 354 sheet: -0.80 (0.18), residues: 915 loop : -2.04 (0.15), residues: 1383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 314 HIS 0.005 0.001 HIS M 37 PHE 0.010 0.001 PHE G 68 TYR 0.017 0.001 TYR B 53 ARG 0.007 0.000 ARG N 85 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5304 Ramachandran restraints generated. 2652 Oldfield, 0 Emsley, 2652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5304 Ramachandran restraints generated. 2652 Oldfield, 0 Emsley, 2652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 2349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 352 time to evaluate : 2.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 505 PHE cc_start: 0.8138 (t80) cc_final: 0.7853 (t80) REVERT: C 396 MET cc_start: 0.7881 (ptm) cc_final: 0.7642 (ptp) REVERT: E 113 TYR cc_start: 0.7136 (m-10) cc_final: 0.6908 (m-10) REVERT: J 38 GLN cc_start: 0.8916 (OUTLIER) cc_final: 0.8695 (tm-30) REVERT: L 72 ARG cc_start: 0.8500 (ttt90) cc_final: 0.8264 (ttt90) REVERT: O 103 THR cc_start: 0.8383 (t) cc_final: 0.7979 (m) REVERT: H 90 GLN cc_start: 0.7872 (pp30) cc_final: 0.7645 (pp30) REVERT: M 90 GLN cc_start: 0.8252 (OUTLIER) cc_final: 0.8012 (pp30) outliers start: 90 outliers final: 52 residues processed: 407 average time/residue: 0.3016 time to fit residues: 194.3959 Evaluate side-chains 368 residues out of total 2349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 314 time to evaluate : 2.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain C residue 333 CYS Chi-restraints excluded: chain C residue 344 ASP Chi-restraints excluded: chain C residue 360 VAL Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 32 ASN Chi-restraints excluded: chain F residue 38 GLN Chi-restraints excluded: chain F residue 59 ILE Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 98 THR Chi-restraints excluded: chain F residue 106 ASP Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 34 ILE Chi-restraints excluded: chain I residue 71 ILE Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 10 THR Chi-restraints excluded: chain J residue 38 GLN Chi-restraints excluded: chain K residue 164 VAL Chi-restraints excluded: chain K residue 300 VAL Chi-restraints excluded: chain K residue 360 VAL Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 84 ASN Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 99 LEU Chi-restraints excluded: chain N residue 103 VAL Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 53 SER Chi-restraints excluded: chain O residue 77 ASN Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 83 ILE Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 90 GLN Chi-restraints excluded: chain P residue 36 THR Chi-restraints excluded: chain Q residue 66 GLU Chi-restraints excluded: chain Q residue 99 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 130 optimal weight: 10.0000 chunk 72 optimal weight: 4.9990 chunk 194 optimal weight: 1.9990 chunk 159 optimal weight: 3.9990 chunk 64 optimal weight: 0.6980 chunk 234 optimal weight: 9.9990 chunk 253 optimal weight: 4.9990 chunk 209 optimal weight: 4.9990 chunk 232 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 188 optimal weight: 0.8980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 183 ASN D 37 HIS G 74 ASN I 6 GLN K 227 ASN K 284 GLN ** L 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 90 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.1268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 21126 Z= 0.247 Angle : 0.571 10.672 28647 Z= 0.298 Chirality : 0.044 0.164 3330 Planarity : 0.004 0.054 3630 Dihedral : 4.994 52.291 2944 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 5.33 % Allowed : 17.65 % Favored : 77.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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: -1.99 (0.16), residues: 2652 helix: 0.01 (0.28), residues: 375 sheet: -0.83 (0.18), residues: 900 loop : -2.08 (0.15), residues: 1377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 314 HIS 0.004 0.002 HIS D 37 PHE 0.013 0.001 PHE A 237 TYR 0.020 0.001 TYR R 86 ARG 0.008 0.000 ARG N 85 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5304 Ramachandran restraints generated. 2652 Oldfield, 0 Emsley, 2652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5304 Ramachandran restraints generated. 2652 Oldfield, 0 Emsley, 2652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 2349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 323 time to evaluate : 2.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 396 MET cc_start: 0.7828 (ptm) cc_final: 0.7590 (ptp) REVERT: D 90 GLN cc_start: 0.7949 (pp30) cc_final: 0.7704 (pp30) REVERT: F 79 LEU cc_start: 0.6349 (OUTLIER) cc_final: 0.5937 (tt) REVERT: L 32 TYR cc_start: 0.8596 (m-80) cc_final: 0.8387 (m-80) REVERT: O 103 THR cc_start: 0.8516 (t) cc_final: 0.8184 (m) REVERT: H 90 GLN cc_start: 0.8070 (pp30) cc_final: 0.7659 (pp30) outliers start: 125 outliers final: 86 residues processed: 413 average time/residue: 0.2854 time to fit residues: 188.5739 Evaluate side-chains 397 residues out of total 2349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 310 time to evaluate : 2.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 84 ASN Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 51 TYR Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 32 ASN Chi-restraints excluded: chain F residue 59 ILE Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 98 THR Chi-restraints excluded: chain F residue 106 ASP Chi-restraints excluded: chain G residue 84 ASN Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 32 LEU Chi-restraints excluded: chain I residue 34 ILE Chi-restraints excluded: chain I residue 71 ILE Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 96 ILE Chi-restraints excluded: chain J residue 103 THR Chi-restraints excluded: chain K residue 164 VAL Chi-restraints excluded: chain K residue 245 THR Chi-restraints excluded: chain K residue 300 VAL Chi-restraints excluded: chain K residue 344 ASP Chi-restraints excluded: chain K residue 360 VAL Chi-restraints excluded: chain K residue 396 MET Chi-restraints excluded: chain K residue 398 SER Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 84 ASN Chi-restraints excluded: chain L residue 96 CYS Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 20 VAL Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 71 ILE Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 99 LEU Chi-restraints excluded: chain N residue 103 VAL Chi-restraints excluded: chain N residue 108 LEU Chi-restraints excluded: chain O residue 3 VAL Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 59 ILE Chi-restraints excluded: chain O residue 68 SER Chi-restraints excluded: chain O residue 79 LEU Chi-restraints excluded: chain O residue 96 ILE Chi-restraints excluded: chain H residue 10 SER Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 93 ASN Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 85 THR Chi-restraints excluded: chain P residue 36 THR Chi-restraints excluded: chain P residue 64 ILE Chi-restraints excluded: chain Q residue 66 GLU Chi-restraints excluded: chain Q residue 67 ASN Chi-restraints excluded: chain Q residue 99 SER Chi-restraints excluded: chain Q residue 100 THR Chi-restraints excluded: chain R residue 29 THR Chi-restraints excluded: chain R residue 64 ILE Chi-restraints excluded: chain R residue 95 LEU Chi-restraints excluded: chain R residue 99 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 231 optimal weight: 4.9990 chunk 176 optimal weight: 4.9990 chunk 121 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 112 optimal weight: 7.9990 chunk 157 optimal weight: 0.9980 chunk 235 optimal weight: 4.9990 chunk 249 optimal weight: 3.9990 chunk 123 optimal weight: 0.8980 chunk 223 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 183 ASN D 37 HIS G 74 ASN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 24 GLN ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 90 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.1494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 21126 Z= 0.275 Angle : 0.587 8.678 28647 Z= 0.304 Chirality : 0.044 0.166 3330 Planarity : 0.004 0.055 3630 Dihedral : 5.174 57.425 2944 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 5.84 % Allowed : 18.97 % Favored : 75.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.16), residues: 2652 helix: -0.01 (0.28), residues: 375 sheet: -0.79 (0.18), residues: 897 loop : -2.14 (0.15), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 314 HIS 0.005 0.001 HIS M 49 PHE 0.011 0.002 PHE G 68 TYR 0.021 0.001 TYR R 86 ARG 0.009 0.001 ARG I 85 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5304 Ramachandran restraints generated. 2652 Oldfield, 0 Emsley, 2652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5304 Ramachandran restraints generated. 2652 Oldfield, 0 Emsley, 2652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 2349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 323 time to evaluate : 2.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 396 MET cc_start: 0.7641 (ptm) cc_final: 0.7439 (ptp) REVERT: D 90 GLN cc_start: 0.8137 (pp30) cc_final: 0.7801 (pp30) REVERT: F 79 LEU cc_start: 0.6459 (OUTLIER) cc_final: 0.6122 (tt) REVERT: G 56 GLU cc_start: 0.8326 (mp0) cc_final: 0.7789 (mp0) REVERT: K 289 MET cc_start: 0.7342 (OUTLIER) cc_final: 0.7071 (tmm) REVERT: K 367 CYS cc_start: 0.6179 (m) cc_final: 0.5712 (m) REVERT: L 58 THR cc_start: 0.8533 (OUTLIER) cc_final: 0.8293 (p) REVERT: O 103 THR cc_start: 0.8438 (t) cc_final: 0.8058 (m) REVERT: H 90 GLN cc_start: 0.8148 (pp30) cc_final: 0.7672 (pp30) REVERT: M 90 GLN cc_start: 0.8431 (OUTLIER) cc_final: 0.8036 (pp30) outliers start: 137 outliers final: 102 residues processed: 417 average time/residue: 0.2955 time to fit residues: 197.8374 Evaluate side-chains 415 residues out of total 2349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 309 time to evaluate : 2.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 84 ASN Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 290 SER Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 51 TYR Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 99 LEU Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 32 ASN Chi-restraints excluded: chain F residue 59 ILE Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 98 THR Chi-restraints excluded: chain F residue 106 ASP Chi-restraints excluded: chain G residue 84 ASN Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 32 LEU Chi-restraints excluded: chain I residue 34 ILE Chi-restraints excluded: chain I residue 71 ILE Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 111 ASP Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 96 ILE Chi-restraints excluded: chain J residue 103 THR Chi-restraints excluded: chain J residue 106 ASP Chi-restraints excluded: chain K residue 142 LEU Chi-restraints excluded: chain K residue 144 VAL Chi-restraints excluded: chain K residue 164 VAL Chi-restraints excluded: chain K residue 245 THR Chi-restraints excluded: chain K residue 289 MET Chi-restraints excluded: chain K residue 300 VAL Chi-restraints excluded: chain K residue 335 THR Chi-restraints excluded: chain K residue 344 ASP Chi-restraints excluded: chain K residue 349 VAL Chi-restraints excluded: chain K residue 360 VAL Chi-restraints excluded: chain K residue 396 MET Chi-restraints excluded: chain K residue 398 SER Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 96 CYS Chi-restraints excluded: chain N residue 20 VAL Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 71 ILE Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 99 LEU Chi-restraints excluded: chain N residue 103 VAL Chi-restraints excluded: chain N residue 108 LEU Chi-restraints excluded: chain O residue 3 VAL Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 59 ILE Chi-restraints excluded: chain O residue 68 SER Chi-restraints excluded: chain O residue 79 LEU Chi-restraints excluded: chain O residue 96 ILE Chi-restraints excluded: chain O residue 106 ASP Chi-restraints excluded: chain H residue 10 SER Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 93 ASN Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 85 THR Chi-restraints excluded: chain M residue 90 GLN Chi-restraints excluded: chain P residue 29 THR Chi-restraints excluded: chain P residue 36 THR Chi-restraints excluded: chain P residue 64 ILE Chi-restraints excluded: chain Q residue 29 THR Chi-restraints excluded: chain Q residue 46 SER Chi-restraints excluded: chain Q residue 66 GLU Chi-restraints excluded: chain Q residue 67 ASN Chi-restraints excluded: chain Q residue 99 SER Chi-restraints excluded: chain Q residue 100 THR Chi-restraints excluded: chain R residue 29 THR Chi-restraints excluded: chain R residue 64 ILE Chi-restraints excluded: chain R residue 99 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 207 optimal weight: 4.9990 chunk 141 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 185 optimal weight: 2.9990 chunk 102 optimal weight: 9.9990 chunk 212 optimal weight: 6.9990 chunk 172 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 127 optimal weight: 8.9990 chunk 223 optimal weight: 0.0170 chunk 62 optimal weight: 2.9990 overall best weight: 1.3822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 183 ASN D 37 HIS ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 24 GLN ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.1541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21126 Z= 0.212 Angle : 0.567 10.350 28647 Z= 0.292 Chirality : 0.043 0.163 3330 Planarity : 0.004 0.054 3630 Dihedral : 5.053 58.290 2944 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 5.75 % Allowed : 19.99 % Favored : 74.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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: -1.96 (0.16), residues: 2652 helix: 0.12 (0.28), residues: 375 sheet: -0.88 (0.18), residues: 903 loop : -2.02 (0.15), residues: 1374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 314 HIS 0.005 0.001 HIS D 37 PHE 0.015 0.001 PHE E 59 TYR 0.018 0.001 TYR A 342 ARG 0.009 0.000 ARG N 85 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5304 Ramachandran restraints generated. 2652 Oldfield, 0 Emsley, 2652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5304 Ramachandran restraints generated. 2652 Oldfield, 0 Emsley, 2652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 2349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 321 time to evaluate : 2.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 505 PHE cc_start: 0.8384 (OUTLIER) cc_final: 0.8080 (t80) REVERT: B 77 ASN cc_start: 0.8192 (OUTLIER) cc_final: 0.7754 (p0) REVERT: C 396 MET cc_start: 0.7666 (ptm) cc_final: 0.7457 (ptp) REVERT: D 90 GLN cc_start: 0.8231 (pp30) cc_final: 0.7759 (pp30) REVERT: D 93 ASN cc_start: 0.6938 (m-40) cc_final: 0.6701 (m110) REVERT: F 79 LEU cc_start: 0.6444 (OUTLIER) cc_final: 0.6092 (tt) REVERT: G 83 MET cc_start: 0.6924 (mtm) cc_final: 0.6179 (mtm) REVERT: K 144 VAL cc_start: 0.9155 (OUTLIER) cc_final: 0.8954 (t) REVERT: K 289 MET cc_start: 0.7275 (OUTLIER) cc_final: 0.6726 (tmm) REVERT: K 367 CYS cc_start: 0.6203 (m) cc_final: 0.5776 (m) REVERT: L 58 THR cc_start: 0.8522 (OUTLIER) cc_final: 0.8305 (p) REVERT: L 72 ARG cc_start: 0.8555 (ttt90) cc_final: 0.8340 (ttt90) REVERT: O 103 THR cc_start: 0.8508 (t) cc_final: 0.8191 (m) REVERT: H 73 LEU cc_start: 0.8207 (OUTLIER) cc_final: 0.7948 (tt) REVERT: H 90 GLN cc_start: 0.8183 (pp30) cc_final: 0.7643 (pp30) REVERT: R 49 ARG cc_start: 0.7650 (tmm160) cc_final: 0.7429 (tmm160) outliers start: 135 outliers final: 103 residues processed: 415 average time/residue: 0.3008 time to fit residues: 198.6872 Evaluate side-chains 423 residues out of total 2349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 313 time to evaluate : 2.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 237 PHE Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 289 MET Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 505 PHE Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 77 ASN Chi-restraints excluded: chain B residue 84 ASN Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 290 SER Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain C residue 360 VAL Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 51 TYR Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 99 LEU Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 110 ILE Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 32 ASN Chi-restraints excluded: chain F residue 59 ILE Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 98 THR Chi-restraints excluded: chain F residue 106 ASP Chi-restraints excluded: chain G residue 84 ASN Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 32 LEU Chi-restraints excluded: chain I residue 34 ILE Chi-restraints excluded: chain I residue 71 ILE Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 111 ASP Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 96 ILE Chi-restraints excluded: chain J residue 106 ASP Chi-restraints excluded: chain K residue 142 LEU Chi-restraints excluded: chain K residue 144 VAL Chi-restraints excluded: chain K residue 164 VAL Chi-restraints excluded: chain K residue 245 THR Chi-restraints excluded: chain K residue 289 MET Chi-restraints excluded: chain K residue 300 VAL Chi-restraints excluded: chain K residue 335 THR Chi-restraints excluded: chain K residue 344 ASP Chi-restraints excluded: chain K residue 349 VAL Chi-restraints excluded: chain K residue 360 VAL Chi-restraints excluded: chain K residue 396 MET Chi-restraints excluded: chain K residue 398 SER Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 84 ASN Chi-restraints excluded: chain L residue 96 CYS Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 20 VAL Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 71 ILE Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 99 LEU Chi-restraints excluded: chain N residue 103 VAL Chi-restraints excluded: chain N residue 108 LEU Chi-restraints excluded: chain O residue 3 VAL Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 59 ILE Chi-restraints excluded: chain O residue 68 SER Chi-restraints excluded: chain O residue 79 LEU Chi-restraints excluded: chain O residue 96 ILE Chi-restraints excluded: chain O residue 106 ASP Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 73 LEU Chi-restraints excluded: chain P residue 27 ASN Chi-restraints excluded: chain P residue 29 THR Chi-restraints excluded: chain P residue 36 THR Chi-restraints excluded: chain P residue 64 ILE Chi-restraints excluded: chain Q residue 27 ASN Chi-restraints excluded: chain Q residue 29 THR Chi-restraints excluded: chain Q residue 66 GLU Chi-restraints excluded: chain Q residue 67 ASN Chi-restraints excluded: chain Q residue 99 SER Chi-restraints excluded: chain R residue 27 ASN Chi-restraints excluded: chain R residue 29 THR Chi-restraints excluded: chain R residue 36 THR Chi-restraints excluded: chain R residue 46 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 83 optimal weight: 0.0980 chunk 224 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 146 optimal weight: 0.4980 chunk 61 optimal weight: 5.9990 chunk 249 optimal weight: 2.9990 chunk 207 optimal weight: 3.9990 chunk 115 optimal weight: 7.9990 chunk 20 optimal weight: 0.7980 chunk 82 optimal weight: 0.9980 chunk 131 optimal weight: 10.0000 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 183 ASN D 37 HIS ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21126 Z= 0.182 Angle : 0.549 8.793 28647 Z= 0.283 Chirality : 0.043 0.161 3330 Planarity : 0.004 0.055 3630 Dihedral : 4.907 57.499 2944 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 6.22 % Allowed : 19.86 % Favored : 73.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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: -1.80 (0.16), residues: 2652 helix: 0.54 (0.28), residues: 360 sheet: -0.83 (0.18), residues: 903 loop : -1.95 (0.15), residues: 1389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 314 HIS 0.005 0.001 HIS D 37 PHE 0.010 0.001 PHE E 59 TYR 0.018 0.001 TYR A 342 ARG 0.011 0.000 ARG I 85 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5304 Ramachandran restraints generated. 2652 Oldfield, 0 Emsley, 2652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5304 Ramachandran restraints generated. 2652 Oldfield, 0 Emsley, 2652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 2349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 338 time to evaluate : 2.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 505 PHE cc_start: 0.8196 (OUTLIER) cc_final: 0.7830 (t80) REVERT: B 71 SER cc_start: 0.8354 (t) cc_final: 0.7675 (p) REVERT: B 77 ASN cc_start: 0.8184 (OUTLIER) cc_final: 0.7772 (p0) REVERT: C 396 MET cc_start: 0.7705 (ptm) cc_final: 0.7480 (ptp) REVERT: D 23 CYS cc_start: 0.7874 (t) cc_final: 0.6791 (p) REVERT: D 90 GLN cc_start: 0.8248 (pp30) cc_final: 0.7796 (pp30) REVERT: D 93 ASN cc_start: 0.6853 (OUTLIER) cc_final: 0.6621 (m110) REVERT: E 6 GLN cc_start: 0.8308 (mm-40) cc_final: 0.7650 (mm110) REVERT: F 79 LEU cc_start: 0.6454 (OUTLIER) cc_final: 0.6109 (tt) REVERT: G 83 MET cc_start: 0.6981 (mtm) cc_final: 0.6267 (mtm) REVERT: K 289 MET cc_start: 0.7251 (OUTLIER) cc_final: 0.6880 (tmm) REVERT: L 58 THR cc_start: 0.8578 (OUTLIER) cc_final: 0.8342 (p) REVERT: N 6 GLN cc_start: 0.8190 (mm-40) cc_final: 0.7906 (mm110) REVERT: O 103 THR cc_start: 0.8587 (t) cc_final: 0.8259 (m) REVERT: H 65 ARG cc_start: 0.8086 (ttm110) cc_final: 0.7674 (ttp-110) REVERT: H 73 LEU cc_start: 0.8232 (OUTLIER) cc_final: 0.7932 (tt) REVERT: H 90 GLN cc_start: 0.8250 (pp30) cc_final: 0.7683 (pp30) REVERT: R 49 ARG cc_start: 0.7625 (tmm160) cc_final: 0.7378 (tmm160) outliers start: 146 outliers final: 110 residues processed: 440 average time/residue: 0.2876 time to fit residues: 200.9874 Evaluate side-chains 436 residues out of total 2349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 319 time to evaluate : 2.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 237 PHE Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 289 MET Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 505 PHE Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 77 ASN Chi-restraints excluded: chain B residue 84 ASN Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 183 ASN Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 290 SER Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain C residue 360 VAL Chi-restraints excluded: chain C residue 423 THR Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 93 ASN Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 51 TYR Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 99 LEU Chi-restraints excluded: chain E residue 110 ILE Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 32 ASN Chi-restraints excluded: chain F residue 38 GLN Chi-restraints excluded: chain F residue 59 ILE Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 98 THR Chi-restraints excluded: chain F residue 106 ASP Chi-restraints excluded: chain G residue 84 ASN Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 32 LEU Chi-restraints excluded: chain I residue 34 ILE Chi-restraints excluded: chain I residue 71 ILE Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 96 ILE Chi-restraints excluded: chain J residue 106 ASP Chi-restraints excluded: chain K residue 142 LEU Chi-restraints excluded: chain K residue 164 VAL Chi-restraints excluded: chain K residue 245 THR Chi-restraints excluded: chain K residue 261 ILE Chi-restraints excluded: chain K residue 289 MET Chi-restraints excluded: chain K residue 335 THR Chi-restraints excluded: chain K residue 344 ASP Chi-restraints excluded: chain K residue 349 VAL Chi-restraints excluded: chain K residue 360 VAL Chi-restraints excluded: chain K residue 396 MET Chi-restraints excluded: chain K residue 398 SER Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain L residue 84 ASN Chi-restraints excluded: chain L residue 96 CYS Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 20 VAL Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 71 ILE Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 99 LEU Chi-restraints excluded: chain N residue 103 VAL Chi-restraints excluded: chain N residue 108 LEU Chi-restraints excluded: chain O residue 3 VAL Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 59 ILE Chi-restraints excluded: chain O residue 68 SER Chi-restraints excluded: chain O residue 76 ILE Chi-restraints excluded: chain O residue 79 LEU Chi-restraints excluded: chain O residue 96 ILE Chi-restraints excluded: chain O residue 106 ASP Chi-restraints excluded: chain H residue 24 GLN Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 29 ILE Chi-restraints excluded: chain P residue 27 ASN Chi-restraints excluded: chain P residue 29 THR Chi-restraints excluded: chain P residue 36 THR Chi-restraints excluded: chain Q residue 29 THR Chi-restraints excluded: chain Q residue 66 GLU Chi-restraints excluded: chain Q residue 67 ASN Chi-restraints excluded: chain Q residue 99 SER Chi-restraints excluded: chain R residue 27 ASN Chi-restraints excluded: chain R residue 29 THR Chi-restraints excluded: chain R residue 36 THR Chi-restraints excluded: chain R residue 61 LEU Chi-restraints excluded: chain R residue 64 ILE Chi-restraints excluded: chain R residue 99 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 240 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 142 optimal weight: 2.9990 chunk 182 optimal weight: 1.9990 chunk 141 optimal weight: 9.9990 chunk 210 optimal weight: 9.9990 chunk 139 optimal weight: 0.8980 chunk 248 optimal weight: 0.9990 chunk 155 optimal weight: 5.9990 chunk 151 optimal weight: 0.0670 chunk 114 optimal weight: 5.9990 overall best weight: 0.9722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 183 ASN D 37 HIS ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21126 Z= 0.174 Angle : 0.559 9.512 28647 Z= 0.284 Chirality : 0.043 0.160 3330 Planarity : 0.004 0.054 3630 Dihedral : 4.844 56.560 2944 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 5.88 % Allowed : 21.06 % Favored : 73.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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: -1.72 (0.16), residues: 2652 helix: 0.66 (0.28), residues: 360 sheet: -0.65 (0.18), residues: 873 loop : -1.99 (0.15), residues: 1419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 314 HIS 0.005 0.001 HIS D 37 PHE 0.010 0.001 PHE E 59 TYR 0.019 0.001 TYR B 53 ARG 0.012 0.000 ARG N 85 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5304 Ramachandran restraints generated. 2652 Oldfield, 0 Emsley, 2652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5304 Ramachandran restraints generated. 2652 Oldfield, 0 Emsley, 2652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 2349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 321 time to evaluate : 2.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 505 PHE cc_start: 0.7939 (OUTLIER) cc_final: 0.7485 (t80) REVERT: B 71 SER cc_start: 0.8364 (t) cc_final: 0.7683 (p) REVERT: B 77 ASN cc_start: 0.8171 (OUTLIER) cc_final: 0.7787 (p0) REVERT: C 396 MET cc_start: 0.7690 (ptm) cc_final: 0.7428 (ptp) REVERT: D 23 CYS cc_start: 0.7882 (t) cc_final: 0.6755 (p) REVERT: D 90 GLN cc_start: 0.8286 (pp30) cc_final: 0.7802 (pp30) REVERT: D 93 ASN cc_start: 0.6493 (OUTLIER) cc_final: 0.6288 (m110) REVERT: E 6 GLN cc_start: 0.8269 (mm-40) cc_final: 0.7944 (mm110) REVERT: F 79 LEU cc_start: 0.6461 (OUTLIER) cc_final: 0.6114 (tt) REVERT: G 83 MET cc_start: 0.6976 (mtm) cc_final: 0.6270 (mtm) REVERT: K 289 MET cc_start: 0.7073 (OUTLIER) cc_final: 0.6713 (tmm) REVERT: L 58 THR cc_start: 0.8576 (OUTLIER) cc_final: 0.8352 (p) REVERT: N 6 GLN cc_start: 0.8166 (mm-40) cc_final: 0.7880 (mm110) REVERT: O 103 THR cc_start: 0.8582 (t) cc_final: 0.8257 (m) REVERT: H 73 LEU cc_start: 0.8227 (OUTLIER) cc_final: 0.7943 (tt) REVERT: H 90 GLN cc_start: 0.8271 (pp30) cc_final: 0.7706 (pp30) outliers start: 138 outliers final: 113 residues processed: 414 average time/residue: 0.2869 time to fit residues: 189.2308 Evaluate side-chains 435 residues out of total 2349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 315 time to evaluate : 2.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 237 PHE Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 289 MET Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 505 PHE Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 77 ASN Chi-restraints excluded: chain B residue 84 ASN Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 290 SER Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain C residue 360 VAL Chi-restraints excluded: chain C residue 423 THR Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 93 ASN Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 51 TYR Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 32 ASN Chi-restraints excluded: chain F residue 59 ILE Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 98 THR Chi-restraints excluded: chain F residue 106 ASP Chi-restraints excluded: chain G residue 84 ASN Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 32 LEU Chi-restraints excluded: chain I residue 34 ILE Chi-restraints excluded: chain I residue 71 ILE Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 111 ASP Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 96 ILE Chi-restraints excluded: chain J residue 106 ASP Chi-restraints excluded: chain K residue 142 LEU Chi-restraints excluded: chain K residue 164 VAL Chi-restraints excluded: chain K residue 245 THR Chi-restraints excluded: chain K residue 261 ILE Chi-restraints excluded: chain K residue 289 MET Chi-restraints excluded: chain K residue 300 VAL Chi-restraints excluded: chain K residue 335 THR Chi-restraints excluded: chain K residue 344 ASP Chi-restraints excluded: chain K residue 349 VAL Chi-restraints excluded: chain K residue 360 VAL Chi-restraints excluded: chain K residue 396 MET Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain L residue 84 ASN Chi-restraints excluded: chain L residue 96 CYS Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 20 VAL Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 29 LEU Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 71 ILE Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 99 LEU Chi-restraints excluded: chain N residue 103 VAL Chi-restraints excluded: chain N residue 108 LEU Chi-restraints excluded: chain O residue 3 VAL Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 59 ILE Chi-restraints excluded: chain O residue 68 SER Chi-restraints excluded: chain O residue 76 ILE Chi-restraints excluded: chain O residue 79 LEU Chi-restraints excluded: chain O residue 96 ILE Chi-restraints excluded: chain O residue 106 ASP Chi-restraints excluded: chain H residue 10 SER Chi-restraints excluded: chain H residue 24 GLN Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 93 ASN Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 29 ILE Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain P residue 27 ASN Chi-restraints excluded: chain P residue 29 THR Chi-restraints excluded: chain P residue 36 THR Chi-restraints excluded: chain P residue 64 ILE Chi-restraints excluded: chain Q residue 27 ASN Chi-restraints excluded: chain Q residue 29 THR Chi-restraints excluded: chain Q residue 66 GLU Chi-restraints excluded: chain Q residue 67 ASN Chi-restraints excluded: chain Q residue 99 SER Chi-restraints excluded: chain R residue 27 ASN Chi-restraints excluded: chain R residue 29 THR Chi-restraints excluded: chain R residue 36 THR Chi-restraints excluded: chain R residue 61 LEU Chi-restraints excluded: chain R residue 64 ILE Chi-restraints excluded: chain R residue 94 GLN Chi-restraints excluded: chain R residue 99 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 153 optimal weight: 5.9990 chunk 99 optimal weight: 10.0000 chunk 148 optimal weight: 5.9990 chunk 74 optimal weight: 4.9990 chunk 48 optimal weight: 6.9990 chunk 158 optimal weight: 0.6980 chunk 169 optimal weight: 0.5980 chunk 122 optimal weight: 7.9990 chunk 23 optimal weight: 0.4980 chunk 195 optimal weight: 5.9990 chunk 226 optimal weight: 5.9990 overall best weight: 2.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 84 ASN C 208 ASN D 37 HIS G 84 ASN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 79 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 21126 Z= 0.339 Angle : 0.637 9.617 28647 Z= 0.329 Chirality : 0.046 0.190 3330 Planarity : 0.004 0.059 3630 Dihedral : 5.323 59.441 2944 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.14 % Favored : 91.86 % Rotamer: Outliers : 6.05 % Allowed : 20.80 % Favored : 73.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.16), residues: 2652 helix: 0.09 (0.28), residues: 375 sheet: -0.85 (0.18), residues: 900 loop : -2.13 (0.15), residues: 1377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 314 HIS 0.006 0.002 HIS M 49 PHE 0.014 0.002 PHE E 95 TYR 0.026 0.002 TYR Q 86 ARG 0.012 0.001 ARG N 85 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5304 Ramachandran restraints generated. 2652 Oldfield, 0 Emsley, 2652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5304 Ramachandran restraints generated. 2652 Oldfield, 0 Emsley, 2652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 2349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 320 time to evaluate : 2.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 505 PHE cc_start: 0.7990 (OUTLIER) cc_final: 0.7499 (t80) REVERT: B 77 ASN cc_start: 0.8372 (OUTLIER) cc_final: 0.8079 (p0) REVERT: C 396 MET cc_start: 0.7776 (ptm) cc_final: 0.7496 (ptm) REVERT: D 90 GLN cc_start: 0.8517 (pp30) cc_final: 0.8058 (pp30) REVERT: E 6 GLN cc_start: 0.8106 (mm-40) cc_final: 0.7582 (mm110) REVERT: E 51 TYR cc_start: 0.7581 (OUTLIER) cc_final: 0.6826 (t80) REVERT: F 79 LEU cc_start: 0.6880 (OUTLIER) cc_final: 0.6616 (tt) REVERT: G 83 MET cc_start: 0.6602 (mtm) cc_final: 0.6000 (mtm) REVERT: K 289 MET cc_start: 0.7536 (OUTLIER) cc_final: 0.7306 (tmm) REVERT: L 58 THR cc_start: 0.8497 (OUTLIER) cc_final: 0.8204 (p) REVERT: N 6 GLN cc_start: 0.8164 (mm-40) cc_final: 0.7844 (mm110) REVERT: O 103 THR cc_start: 0.8428 (t) cc_final: 0.8053 (m) REVERT: H 65 ARG cc_start: 0.8109 (ttm110) cc_final: 0.7672 (ttp-110) REVERT: H 73 LEU cc_start: 0.8239 (OUTLIER) cc_final: 0.7906 (tt) REVERT: H 90 GLN cc_start: 0.8332 (pp30) cc_final: 0.7805 (pp30) REVERT: M 39 LYS cc_start: 0.7386 (mtmt) cc_final: 0.6918 (mtmt) outliers start: 142 outliers final: 119 residues processed: 421 average time/residue: 0.2893 time to fit residues: 194.9638 Evaluate side-chains 437 residues out of total 2349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 311 time to evaluate : 2.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 289 MET Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 505 PHE Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 77 ASN Chi-restraints excluded: chain B residue 84 ASN Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 290 SER Chi-restraints excluded: chain C residue 333 CYS Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 51 TYR Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 110 ILE Chi-restraints excluded: chain E residue 111 ASP Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 32 ASN Chi-restraints excluded: chain F residue 59 ILE Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain F residue 98 THR Chi-restraints excluded: chain F residue 106 ASP Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 32 LEU Chi-restraints excluded: chain I residue 34 ILE Chi-restraints excluded: chain I residue 71 ILE Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 110 ILE Chi-restraints excluded: chain I residue 111 ASP Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 96 ILE Chi-restraints excluded: chain J residue 106 ASP Chi-restraints excluded: chain K residue 142 LEU Chi-restraints excluded: chain K residue 164 VAL Chi-restraints excluded: chain K residue 245 THR Chi-restraints excluded: chain K residue 261 ILE Chi-restraints excluded: chain K residue 289 MET Chi-restraints excluded: chain K residue 300 VAL Chi-restraints excluded: chain K residue 335 THR Chi-restraints excluded: chain K residue 344 ASP Chi-restraints excluded: chain K residue 349 VAL Chi-restraints excluded: chain K residue 360 VAL Chi-restraints excluded: chain K residue 396 MET Chi-restraints excluded: chain K residue 398 SER Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 77 ASN Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain L residue 84 ASN Chi-restraints excluded: chain L residue 96 CYS Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 20 VAL Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 29 LEU Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 99 LEU Chi-restraints excluded: chain N residue 103 VAL Chi-restraints excluded: chain N residue 108 LEU Chi-restraints excluded: chain O residue 3 VAL Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 59 ILE Chi-restraints excluded: chain O residue 68 SER Chi-restraints excluded: chain O residue 76 ILE Chi-restraints excluded: chain O residue 79 LEU Chi-restraints excluded: chain O residue 96 ILE Chi-restraints excluded: chain O residue 106 ASP Chi-restraints excluded: chain H residue 10 SER Chi-restraints excluded: chain H residue 24 GLN Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 93 ASN Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 73 LEU Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 85 THR Chi-restraints excluded: chain P residue 27 ASN Chi-restraints excluded: chain P residue 29 THR Chi-restraints excluded: chain P residue 36 THR Chi-restraints excluded: chain P residue 46 SER Chi-restraints excluded: chain P residue 64 ILE Chi-restraints excluded: chain P residue 99 SER Chi-restraints excluded: chain Q residue 27 ASN Chi-restraints excluded: chain Q residue 29 THR Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 66 GLU Chi-restraints excluded: chain Q residue 67 ASN Chi-restraints excluded: chain Q residue 99 SER Chi-restraints excluded: chain Q residue 100 THR Chi-restraints excluded: chain R residue 27 ASN Chi-restraints excluded: chain R residue 29 THR Chi-restraints excluded: chain R residue 36 THR Chi-restraints excluded: chain R residue 46 SER Chi-restraints excluded: chain R residue 61 LEU Chi-restraints excluded: chain R residue 64 ILE Chi-restraints excluded: chain R residue 99 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 238 optimal weight: 3.9990 chunk 217 optimal weight: 6.9990 chunk 231 optimal weight: 0.0980 chunk 139 optimal weight: 0.8980 chunk 100 optimal weight: 3.9990 chunk 181 optimal weight: 3.9990 chunk 71 optimal weight: 6.9990 chunk 209 optimal weight: 0.8980 chunk 219 optimal weight: 9.9990 chunk 230 optimal weight: 1.9990 chunk 152 optimal weight: 0.0980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 37 HIS ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21126 Z= 0.165 Angle : 0.574 9.549 28647 Z= 0.292 Chirality : 0.043 0.163 3330 Planarity : 0.004 0.054 3630 Dihedral : 4.999 58.433 2944 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 4.86 % Allowed : 22.21 % Favored : 72.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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: -1.73 (0.16), residues: 2652 helix: 0.72 (0.29), residues: 357 sheet: -0.79 (0.18), residues: 894 loop : -1.93 (0.15), residues: 1401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 314 HIS 0.005 0.001 HIS D 37 PHE 0.010 0.001 PHE O 84 TYR 0.018 0.001 TYR B 53 ARG 0.014 0.000 ARG N 85 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5304 Ramachandran restraints generated. 2652 Oldfield, 0 Emsley, 2652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5304 Ramachandran restraints generated. 2652 Oldfield, 0 Emsley, 2652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 2349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 323 time to evaluate : 2.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 505 PHE cc_start: 0.7947 (OUTLIER) cc_final: 0.7398 (t80) REVERT: B 71 SER cc_start: 0.8458 (t) cc_final: 0.7710 (p) REVERT: B 77 ASN cc_start: 0.8296 (OUTLIER) cc_final: 0.7975 (p0) REVERT: C 396 MET cc_start: 0.7783 (ptm) cc_final: 0.7538 (ptm) REVERT: D 23 CYS cc_start: 0.7831 (t) cc_final: 0.6670 (p) REVERT: D 90 GLN cc_start: 0.8370 (pp30) cc_final: 0.7855 (pp30) REVERT: E 6 GLN cc_start: 0.8049 (mm-40) cc_final: 0.7532 (mm110) REVERT: F 79 LEU cc_start: 0.6722 (OUTLIER) cc_final: 0.6416 (tt) REVERT: G 83 MET cc_start: 0.6930 (mtm) cc_final: 0.6238 (mtm) REVERT: K 289 MET cc_start: 0.7214 (OUTLIER) cc_final: 0.6876 (tmm) REVERT: L 58 THR cc_start: 0.8577 (OUTLIER) cc_final: 0.8349 (p) REVERT: N 6 GLN cc_start: 0.8162 (mm-40) cc_final: 0.7838 (mm110) REVERT: O 103 THR cc_start: 0.8562 (t) cc_final: 0.8247 (m) REVERT: H 65 ARG cc_start: 0.8083 (ttm110) cc_final: 0.7599 (ttp-110) REVERT: H 73 LEU cc_start: 0.8217 (OUTLIER) cc_final: 0.7880 (tt) REVERT: H 90 GLN cc_start: 0.8368 (pp30) cc_final: 0.7773 (pp30) outliers start: 114 outliers final: 91 residues processed: 400 average time/residue: 0.2841 time to fit residues: 180.9566 Evaluate side-chains 414 residues out of total 2349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 317 time to evaluate : 2.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 PHE Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 289 MET Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 505 PHE Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 77 ASN Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 333 CYS Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain C residue 423 THR Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 110 ILE Chi-restraints excluded: chain E residue 111 ASP Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 59 ILE Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 98 THR Chi-restraints excluded: chain F residue 106 ASP Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 32 LEU Chi-restraints excluded: chain I residue 34 ILE Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 111 ASP Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 38 GLN Chi-restraints excluded: chain J residue 96 ILE Chi-restraints excluded: chain J residue 106 ASP Chi-restraints excluded: chain K residue 142 LEU Chi-restraints excluded: chain K residue 164 VAL Chi-restraints excluded: chain K residue 245 THR Chi-restraints excluded: chain K residue 289 MET Chi-restraints excluded: chain K residue 300 VAL Chi-restraints excluded: chain K residue 335 THR Chi-restraints excluded: chain K residue 344 ASP Chi-restraints excluded: chain K residue 349 VAL Chi-restraints excluded: chain K residue 360 VAL Chi-restraints excluded: chain K residue 396 MET Chi-restraints excluded: chain K residue 398 SER Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain L residue 84 ASN Chi-restraints excluded: chain L residue 96 CYS Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 20 VAL Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 29 LEU Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 99 LEU Chi-restraints excluded: chain N residue 108 LEU Chi-restraints excluded: chain O residue 3 VAL Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 59 ILE Chi-restraints excluded: chain O residue 68 SER Chi-restraints excluded: chain O residue 79 LEU Chi-restraints excluded: chain O residue 96 ILE Chi-restraints excluded: chain O residue 106 ASP Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain P residue 29 THR Chi-restraints excluded: chain P residue 64 ILE Chi-restraints excluded: chain Q residue 27 ASN Chi-restraints excluded: chain Q residue 29 THR Chi-restraints excluded: chain Q residue 66 GLU Chi-restraints excluded: chain Q residue 67 ASN Chi-restraints excluded: chain R residue 27 ASN Chi-restraints excluded: chain R residue 29 THR Chi-restraints excluded: chain R residue 36 THR Chi-restraints excluded: chain R residue 61 LEU Chi-restraints excluded: chain R residue 64 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 245 optimal weight: 6.9990 chunk 149 optimal weight: 0.0060 chunk 116 optimal weight: 2.9990 chunk 170 optimal weight: 2.9990 chunk 257 optimal weight: 0.8980 chunk 236 optimal weight: 0.9990 chunk 204 optimal weight: 0.4980 chunk 21 optimal weight: 1.9990 chunk 158 optimal weight: 0.8980 chunk 125 optimal weight: 1.9990 chunk 162 optimal weight: 1.9990 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 HIS ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 79 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 21126 Z= 0.155 Angle : 0.562 10.836 28647 Z= 0.285 Chirality : 0.043 0.160 3330 Planarity : 0.004 0.056 3630 Dihedral : 4.726 54.136 2944 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 4.56 % Allowed : 22.80 % Favored : 72.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.16), residues: 2652 helix: 0.86 (0.29), residues: 360 sheet: -0.77 (0.18), residues: 909 loop : -1.85 (0.15), residues: 1383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 314 HIS 0.006 0.001 HIS D 37 PHE 0.014 0.001 PHE N 59 TYR 0.019 0.001 TYR C 342 ARG 0.014 0.000 ARG N 85 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5304 Ramachandran restraints generated. 2652 Oldfield, 0 Emsley, 2652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5304 Ramachandran restraints generated. 2652 Oldfield, 0 Emsley, 2652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 2349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 335 time to evaluate : 2.316 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 367 CYS cc_start: 0.6616 (m) cc_final: 0.6282 (m) REVERT: A 505 PHE cc_start: 0.7935 (OUTLIER) cc_final: 0.7470 (t80) REVERT: B 71 SER cc_start: 0.8506 (t) cc_final: 0.7754 (p) REVERT: B 77 ASN cc_start: 0.8172 (OUTLIER) cc_final: 0.7912 (p0) REVERT: C 396 MET cc_start: 0.7791 (ptm) cc_final: 0.7547 (ptm) REVERT: D 23 CYS cc_start: 0.7786 (t) cc_final: 0.6617 (p) REVERT: D 90 GLN cc_start: 0.8412 (pp30) cc_final: 0.7870 (pp30) REVERT: E 6 GLN cc_start: 0.8099 (mm-40) cc_final: 0.7552 (mm110) REVERT: F 79 LEU cc_start: 0.6493 (OUTLIER) cc_final: 0.6142 (tt) REVERT: G 83 MET cc_start: 0.6928 (mtm) cc_final: 0.6316 (mtm) REVERT: K 289 MET cc_start: 0.6943 (OUTLIER) cc_final: 0.6648 (tmm) REVERT: L 58 THR cc_start: 0.8564 (OUTLIER) cc_final: 0.8342 (p) REVERT: O 103 THR cc_start: 0.8529 (t) cc_final: 0.8234 (m) REVERT: H 65 ARG cc_start: 0.8030 (ttm110) cc_final: 0.7566 (ttp-110) REVERT: H 73 LEU cc_start: 0.8208 (OUTLIER) cc_final: 0.7897 (tt) REVERT: H 90 GLN cc_start: 0.8293 (pp30) cc_final: 0.7741 (pp30) REVERT: Q 29 THR cc_start: 0.8354 (OUTLIER) cc_final: 0.8085 (m) outliers start: 107 outliers final: 90 residues processed: 410 average time/residue: 0.2846 time to fit residues: 185.4598 Evaluate side-chains 418 residues out of total 2349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 321 time to evaluate : 2.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 PHE Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 289 MET Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 505 PHE Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 77 ASN Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 290 SER Chi-restraints excluded: chain C residue 333 CYS Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain C residue 423 THR Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 110 ILE Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 38 GLN Chi-restraints excluded: chain F residue 59 ILE Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 98 THR Chi-restraints excluded: chain F residue 106 ASP Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 32 LEU Chi-restraints excluded: chain I residue 34 ILE Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 111 ASP Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 106 ASP Chi-restraints excluded: chain K residue 142 LEU Chi-restraints excluded: chain K residue 164 VAL Chi-restraints excluded: chain K residue 245 THR Chi-restraints excluded: chain K residue 289 MET Chi-restraints excluded: chain K residue 300 VAL Chi-restraints excluded: chain K residue 335 THR Chi-restraints excluded: chain K residue 344 ASP Chi-restraints excluded: chain K residue 349 VAL Chi-restraints excluded: chain K residue 360 VAL Chi-restraints excluded: chain K residue 396 MET Chi-restraints excluded: chain K residue 398 SER Chi-restraints excluded: chain L residue 37 VAL Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 77 ASN Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 20 VAL Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 99 LEU Chi-restraints excluded: chain N residue 108 LEU Chi-restraints excluded: chain O residue 3 VAL Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 13 LEU Chi-restraints excluded: chain O residue 59 ILE Chi-restraints excluded: chain O residue 68 SER Chi-restraints excluded: chain O residue 76 ILE Chi-restraints excluded: chain O residue 79 LEU Chi-restraints excluded: chain O residue 96 ILE Chi-restraints excluded: chain O residue 106 ASP Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 29 ILE Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain P residue 27 ASN Chi-restraints excluded: chain P residue 29 THR Chi-restraints excluded: chain Q residue 29 THR Chi-restraints excluded: chain Q residue 66 GLU Chi-restraints excluded: chain Q residue 67 ASN Chi-restraints excluded: chain R residue 27 ASN Chi-restraints excluded: chain R residue 29 THR Chi-restraints excluded: chain R residue 36 THR Chi-restraints excluded: chain R residue 61 LEU Chi-restraints excluded: chain R residue 64 ILE Chi-restraints excluded: chain R residue 99 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 218 optimal weight: 0.0470 chunk 62 optimal weight: 2.9990 chunk 188 optimal weight: 7.9990 chunk 30 optimal weight: 5.9990 chunk 56 optimal weight: 0.8980 chunk 205 optimal weight: 10.0000 chunk 85 optimal weight: 9.9990 chunk 210 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 37 optimal weight: 7.9990 chunk 179 optimal weight: 4.9990 overall best weight: 2.1884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 37 HIS ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 84 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.145958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.123418 restraints weight = 30649.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.124750 restraints weight = 20720.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.126067 restraints weight = 15074.079| |-----------------------------------------------------------------------------| r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 21126 Z= 0.304 Angle : 0.635 10.989 28647 Z= 0.325 Chirality : 0.045 0.171 3330 Planarity : 0.004 0.059 3630 Dihedral : 5.196 58.178 2944 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.88 % Favored : 92.12 % Rotamer: Outliers : 4.94 % Allowed : 22.51 % Favored : 72.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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: -1.86 (0.16), residues: 2652 helix: 0.30 (0.28), residues: 375 sheet: -0.82 (0.18), residues: 921 loop : -1.99 (0.15), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 314 HIS 0.008 0.002 HIS B 35 PHE 0.014 0.002 PHE D 71 TYR 0.023 0.002 TYR R 86 ARG 0.014 0.001 ARG I 85 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4159.42 seconds wall clock time: 76 minutes 44.50 seconds (4604.50 seconds total)