Starting phenix.real_space_refine on Sat Mar 16 22:30:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z14_14440/03_2024/7z14_14440.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z14_14440/03_2024/7z14_14440.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z14_14440/03_2024/7z14_14440.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z14_14440/03_2024/7z14_14440.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z14_14440/03_2024/7z14_14440.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z14_14440/03_2024/7z14_14440.pdb" } resolution = 3.15 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= 0.001 sd= 0.058 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 95 5.16 5 C 10337 2.51 5 N 2515 2.21 5 O 2909 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 13": "OE1" <-> "OE2" Residue "A GLU 23": "OE1" <-> "OE2" Residue "A ASP 97": "OD1" <-> "OD2" Residue "A TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 172": "OE1" <-> "OE2" Residue "A GLU 175": "OE1" <-> "OE2" Residue "A PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 414": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 155": "OE1" <-> "OE2" Residue "B GLU 167": "OE1" <-> "OE2" Residue "B GLU 169": "OE1" <-> "OE2" Residue "B TYR 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 268": "OD1" <-> "OD2" Residue "B PHE 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 255": "OE1" <-> "OE2" Residue "C PHE 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 478": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 4": "OE1" <-> "OE2" Residue "D GLU 23": "OE1" <-> "OE2" Residue "D GLU 51": "OE1" <-> "OE2" Residue "D TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 129": "OE1" <-> "OE2" Residue "D TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 45": "OE1" <-> "OE2" Residue "E PHE 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 472": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 29": "OD1" <-> "OD2" Residue "G TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 15856 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 2892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 355, 2892 Classifications: {'peptide': 355} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 335} Chain breaks: 4 Chain: "B" Number of atoms: 3018 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 3018 Classifications: {'peptide': 373} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 350} Chain breaks: 2 Chain: "C" Number of atoms: 3046 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 3046 Classifications: {'peptide': 376} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 349} Chain breaks: 1 Chain: "D" Number of atoms: 2669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2669 Classifications: {'peptide': 328} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 311} Chain breaks: 1 Chain: "E" Number of atoms: 2945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2945 Classifications: {'peptide': 361} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 341} Chain breaks: 1 Chain: "F" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 471 Classifications: {'peptide': 60} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 55} Chain: "G" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 471 Classifications: {'peptide': 60} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 55} Chain: "H" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "L" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 64 Unusual residues: {'MAN': 2, 'NAG': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 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 Time building chain proxies: 8.54, per 1000 atoms: 0.54 Number of scatterers: 15856 At special positions: 0 Unit cell: (101.905, 129.385, 135.11, 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 95 16.00 O 2909 8.00 N 2515 7.00 C 10337 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 142 " distance=2.03 Simple disulfide: pdb=" SG CYS A 192 " - pdb=" SG CYS A 193 " distance=2.06 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 142 " distance=2.03 Simple disulfide: pdb=" SG CYS C 130 " - pdb=" SG CYS C 144 " distance=2.03 Simple disulfide: pdb=" SG CYS D 128 " - pdb=" SG CYS D 142 " distance=2.03 Simple disulfide: pdb=" SG CYS D 192 " - pdb=" SG CYS D 193 " distance=2.05 Simple disulfide: pdb=" SG CYS E 128 " - pdb=" SG CYS E 142 " distance=2.03 Simple disulfide: pdb=" SG CYS F 3 " - pdb=" SG CYS F 22 " distance=2.03 Simple disulfide: pdb=" SG CYS F 17 " - pdb=" SG CYS F 39 " distance=2.03 Simple disulfide: pdb=" SG CYS F 41 " - pdb=" SG CYS F 52 " distance=2.03 Simple disulfide: pdb=" SG CYS F 53 " - pdb=" SG CYS F 58 " distance=2.03 Simple disulfide: pdb=" SG CYS G 3 " - pdb=" SG CYS G 22 " distance=2.03 Simple disulfide: pdb=" SG CYS G 17 " - pdb=" SG CYS G 39 " distance=2.03 Simple disulfide: pdb=" SG CYS G 41 " - pdb=" SG CYS G 52 " distance=2.03 Simple disulfide: pdb=" SG CYS G 53 " - pdb=" SG CYS G 58 " 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 ALPHA1-2 " MAN H 5 " - " MAN H 6 " " MAN H 8 " - " MAN H 9 " " MAN K 5 " - " MAN K 6 " " MAN K 8 " - " MAN K 9 " ALPHA1-3 " BMA H 3 " - " MAN H 8 " " MAN H 4 " - " MAN H 7 " " BMA K 3 " - " MAN K 8 " " MAN K 4 " - " MAN K 7 " ALPHA1-6 " BMA H 3 " - " MAN H 4 " " MAN H 4 " - " MAN H 5 " " BMA K 3 " - " MAN K 4 " " MAN K 4 " - " MAN K 5 " " NAG L 3 " - " MAN L 4 " " MAN L 4 " - " MAN L 5 " BETA1-4 " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " NAG L 3 " NAG-ASN " NAG C 601 " - " ASN C 208 " " NAG H 1 " - " ASN D 141 " " NAG I 1 " - " ASN C 143 " " NAG J 1 " - " ASN B 141 " " NAG K 1 " - " ASN A 141 " " NAG L 1 " - " ASN E 141 " Time building additional restraints: 6.79 Conformation dependent library (CDL) restraints added in 2.8 seconds 3762 Ramachandran restraints generated. 1881 Oldfield, 0 Emsley, 1881 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3682 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 27 sheets defined 35.6% alpha, 24.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.75 Creating SS restraints... Processing helix chain 'A' and resid 1 through 12 Processing helix chain 'A' and resid 63 through 66 Processing helix chain 'A' and resid 81 through 85 removed outlier: 3.518A pdb=" N ASP A 84 " --> pdb=" O PRO A 81 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N VAL A 85 " --> pdb=" O SER A 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 81 through 85' Processing helix chain 'A' and resid 212 through 219 Processing helix chain 'A' and resid 219 through 230 removed outlier: 3.867A pdb=" N GLY A 230 " --> pdb=" O SER A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 235 Processing helix chain 'A' and resid 241 through 264 Processing helix chain 'A' and resid 272 through 300 Processing helix chain 'A' and resid 312 through 317 Processing helix chain 'A' and resid 320 through 324 removed outlier: 3.606A pdb=" N MET A 324 " --> pdb=" O PRO A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 426 removed outlier: 3.660A pdb=" N PHE A 426 " --> pdb=" O THR A 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 12 Processing helix chain 'B' and resid 68 through 72 Processing helix chain 'B' and resid 81 through 85 removed outlier: 3.587A pdb=" N VAL B 85 " --> pdb=" O SER B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 241 Proline residue: B 227 - end of helix removed outlier: 4.571A pdb=" N PHE B 239 " --> pdb=" O ALA B 235 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N TYR B 240 " --> pdb=" O ILE B 236 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU B 241 " --> pdb=" O LEU B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 246 Processing helix chain 'B' and resid 247 through 270 removed outlier: 4.093A pdb=" N ASP B 268 " --> pdb=" O LEU B 264 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N LYS B 269 " --> pdb=" O LEU B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 307 Processing helix chain 'B' and resid 315 through 323 removed outlier: 3.512A pdb=" N ARG B 319 " --> pdb=" O PRO B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 460 Processing helix chain 'C' and resid 3 through 13 Processing helix chain 'C' and resid 83 through 87 Processing helix chain 'C' and resid 226 through 232 Processing helix chain 'C' and resid 233 through 246 Processing helix chain 'C' and resid 247 through 249 No H-bonds generated for 'chain 'C' and resid 247 through 249' Processing helix chain 'C' and resid 255 through 276 removed outlier: 3.694A pdb=" N THR C 259 " --> pdb=" O GLU C 255 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLN C 276 " --> pdb=" O LEU C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 314 Processing helix chain 'C' and resid 443 through 476 Proline residue: C 463 - end of helix Processing helix chain 'D' and resid 2 through 12 removed outlier: 3.632A pdb=" N LEU D 12 " --> pdb=" O VAL D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 73 removed outlier: 4.136A pdb=" N GLY D 73 " --> pdb=" O ALA D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 85 Processing helix chain 'D' and resid 212 through 218 Processing helix chain 'D' and resid 218 through 230 removed outlier: 3.672A pdb=" N GLY D 230 " --> pdb=" O SER D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 235 Processing helix chain 'D' and resid 241 through 264 Processing helix chain 'D' and resid 272 through 300 Processing helix chain 'D' and resid 400 through 425 Processing helix chain 'E' and resid 2 through 13 removed outlier: 3.996A pdb=" N ARG E 6 " --> pdb=" O ASN E 2 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 66 removed outlier: 3.866A pdb=" N SER E 66 " --> pdb=" O TYR E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 72 Processing helix chain 'E' and resid 81 through 85 Processing helix chain 'E' and resid 131 through 135 removed outlier: 4.335A pdb=" N TYR E 134 " --> pdb=" O ALA E 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 219 through 226 removed outlier: 3.727A pdb=" N ILE E 223 " --> pdb=" O PRO E 219 " (cutoff:3.500A) Processing helix chain 'E' and resid 226 through 235 Processing helix chain 'E' and resid 236 through 242 removed outlier: 3.675A pdb=" N VAL E 240 " --> pdb=" O VAL E 237 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 271 removed outlier: 3.835A pdb=" N GLN E 271 " --> pdb=" O PHE E 267 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 309 Processing helix chain 'E' and resid 440 through 473 removed outlier: 3.763A pdb=" N TRP E 453 " --> pdb=" O LYS E 449 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ILE E 454 " --> pdb=" O ALA E 450 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASN E 473 " --> pdb=" O THR E 469 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 77 through 78 removed outlier: 4.140A pdb=" N LYS A 115 " --> pdb=" O ASP A 111 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ILE A 61 " --> pdb=" O ASP A 30 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ASP A 30 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N VAL A 29 " --> pdb=" O SER A 157 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N SER A 159 " --> pdb=" O VAL A 29 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ILE A 31 " --> pdb=" O SER A 159 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 37 through 44 removed outlier: 7.461A pdb=" N ILE A 38 " --> pdb=" O ARG A 55 " (cutoff:3.500A) removed outlier: 8.905A pdb=" N ARG A 55 " --> pdb=" O ILE A 38 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N LEU A 40 " --> pdb=" O ASN A 53 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ASN A 53 " --> pdb=" O LEU A 40 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 92 removed outlier: 4.474A pdb=" N ILE A 148 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N LEU A 199 " --> pdb=" O ILE A 148 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 90 through 92 removed outlier: 4.474A pdb=" N ILE A 148 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N LEU A 199 " --> pdb=" O ILE A 148 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ASP A 180 " --> pdb=" O ILE A 206 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N GLN A 208 " --> pdb=" O MET A 178 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N MET A 178 " --> pdb=" O GLN A 208 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 77 through 80 removed outlier: 4.367A pdb=" N ALA B 115 " --> pdb=" O GLN B 111 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 77 through 80 removed outlier: 4.367A pdb=" N ALA B 115 " --> pdb=" O GLN B 111 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N ASN B 53 " --> pdb=" O LEU B 40 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N LEU B 40 " --> pdb=" O ASN B 53 " (cutoff:3.500A) removed outlier: 8.407A pdb=" N PHE B 55 " --> pdb=" O THR B 38 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N THR B 38 " --> pdb=" O PHE B 55 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N ASN B 57 " --> pdb=" O THR B 36 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N THR B 36 " --> pdb=" O ASN B 57 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N ALA B 59 " --> pdb=" O GLY B 34 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N GLY B 34 " --> pdb=" O ALA B 59 " (cutoff:3.500A) removed outlier: 8.972A pdb=" N THR B 61 " --> pdb=" O ARG B 32 " (cutoff:3.500A) removed outlier: 9.668A pdb=" N ARG B 32 " --> pdb=" O THR B 61 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 90 through 92 Processing sheet with id=AA8, first strand: chain 'B' and resid 139 through 140 removed outlier: 7.109A pdb=" N GLN B 214 " --> pdb=" O ILE B 188 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N ILE B 188 " --> pdb=" O GLN B 214 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 80 through 82 removed outlier: 3.524A pdb=" N LEU C 82 " --> pdb=" O VAL C 110 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 80 through 82 removed outlier: 3.524A pdb=" N LEU C 82 " --> pdb=" O VAL C 110 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N THR C 51 " --> pdb=" O SER C 44 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N SER C 44 " --> pdb=" O THR C 51 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N THR C 53 " --> pdb=" O LEU C 42 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N LEU C 42 " --> pdb=" O THR C 53 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N ASN C 55 " --> pdb=" O SER C 40 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N TYR C 63 " --> pdb=" O ASN C 32 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ASN C 32 " --> pdb=" O TYR C 63 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 93 through 94 Processing sheet with id=AB3, first strand: chain 'C' and resid 141 through 143 removed outlier: 6.946A pdb=" N ILE C 220 " --> pdb=" O ILE C 193 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 164 through 166 Processing sheet with id=AB5, first strand: chain 'D' and resid 77 through 78 removed outlier: 4.334A pdb=" N LYS D 115 " --> pdb=" O ASP D 111 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 77 through 78 removed outlier: 4.334A pdb=" N LYS D 115 " --> pdb=" O ASP D 111 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N ILE D 49 " --> pdb=" O SER D 42 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N SER D 42 " --> pdb=" O ILE D 49 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N GLU D 51 " --> pdb=" O LEU D 40 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N LEU D 40 " --> pdb=" O GLU D 51 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N ASN D 53 " --> pdb=" O ILE D 38 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ILE D 61 " --> pdb=" O ASP D 30 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ASP D 30 " --> pdb=" O ILE D 61 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 90 through 92 removed outlier: 4.492A pdb=" N ILE D 148 " --> pdb=" O LEU D 199 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N LEU D 199 " --> pdb=" O ILE D 148 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 90 through 92 removed outlier: 4.492A pdb=" N ILE D 148 " --> pdb=" O LEU D 199 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N LEU D 199 " --> pdb=" O ILE D 148 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N THR D 196 " --> pdb=" O TYR D 190 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N TYR D 190 " --> pdb=" O THR D 196 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ASP D 180 " --> pdb=" O ILE D 206 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N GLN D 208 " --> pdb=" O MET D 178 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N MET D 178 " --> pdb=" O GLN D 208 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 57 through 59 removed outlier: 6.597A pdb=" N ILE E 29 " --> pdb=" O ASN E 157 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N GLN E 159 " --> pdb=" O ILE E 29 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N VAL E 31 " --> pdb=" O GLN E 159 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 37 through 44 removed outlier: 5.719A pdb=" N LEU E 37 " --> pdb=" O TRP E 55 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N TRP E 55 " --> pdb=" O LEU E 37 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N THR E 51 " --> pdb=" O ILE E 41 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N LEU E 43 " --> pdb=" O ALA E 49 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ALA E 49 " --> pdb=" O LEU E 43 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 78 through 80 Processing sheet with id=AC3, first strand: chain 'E' and resid 90 through 92 removed outlier: 5.135A pdb=" N SER E 148 " --> pdb=" O GLN E 207 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N GLN E 207 " --> pdb=" O SER E 148 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 139 through 142 removed outlier: 6.819A pdb=" N ILE E 214 " --> pdb=" O ARG E 187 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 162 through 163 Processing sheet with id=AC6, first strand: chain 'F' and resid 2 through 4 removed outlier: 3.889A pdb=" N CYS F 3 " --> pdb=" O LYS F 15 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 33 through 39 Processing sheet with id=AC8, first strand: chain 'G' and resid 2 through 4 Processing sheet with id=AC9, first strand: chain 'G' and resid 22 through 28 removed outlier: 3.665A pdb=" N TYR G 23 " --> pdb=" O GLY G 38 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLY G 38 " --> pdb=" O TYR G 23 " (cutoff:3.500A) 727 hydrogen bonds defined for protein. 2037 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: 4.85 Time building geometry restraints manager: 7.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.38: 5290 1.38 - 1.53: 9015 1.53 - 1.68: 1825 1.68 - 1.83: 141 1.83 - 1.98: 2 Bond restraints: 16273 Sorted by residual: bond pdb=" CB CYS A 192 " pdb=" SG CYS A 192 " ideal model delta sigma weight residual 1.808 1.634 0.174 3.30e-02 9.18e+02 2.79e+01 bond pdb=" CB CYS A 193 " pdb=" SG CYS A 193 " ideal model delta sigma weight residual 1.808 1.982 -0.174 3.30e-02 9.18e+02 2.78e+01 bond pdb=" CB CYS D 192 " pdb=" SG CYS D 192 " ideal model delta sigma weight residual 1.808 1.891 -0.083 3.30e-02 9.18e+02 6.36e+00 bond pdb=" CA CYS A 193 " pdb=" CB CYS A 193 " ideal model delta sigma weight residual 1.530 1.552 -0.022 1.22e-02 6.72e+03 3.24e+00 bond pdb=" CA CYS A 192 " pdb=" CB CYS A 192 " ideal model delta sigma weight residual 1.530 1.505 0.026 1.58e-02 4.01e+03 2.62e+00 ... (remaining 16268 not shown) Histogram of bond angle deviations from ideal: 97.35 - 107.31: 739 107.31 - 117.26: 11463 117.26 - 127.22: 9773 127.22 - 137.18: 234 137.18 - 147.14: 1 Bond angle restraints: 22210 Sorted by residual: angle pdb=" CA CYS A 192 " pdb=" CB CYS A 192 " pdb=" SG CYS A 192 " ideal model delta sigma weight residual 114.40 147.14 -32.74 2.30e+00 1.89e-01 2.03e+02 angle pdb=" C CYS A 192 " pdb=" CA CYS A 192 " pdb=" CB CYS A 192 " ideal model delta sigma weight residual 110.92 97.35 13.57 1.59e+00 3.96e-01 7.29e+01 angle pdb=" CA CYS A 193 " pdb=" CB CYS A 193 " pdb=" SG CYS A 193 " ideal model delta sigma weight residual 114.40 127.08 -12.68 2.30e+00 1.89e-01 3.04e+01 angle pdb=" CA CYS D 192 " pdb=" CB CYS D 192 " pdb=" SG CYS D 192 " ideal model delta sigma weight residual 114.40 122.90 -8.50 2.30e+00 1.89e-01 1.37e+01 angle pdb=" CA CYS A 192 " pdb=" C CYS A 192 " pdb=" N CYS A 193 " ideal model delta sigma weight residual 116.79 112.83 3.96 1.28e+00 6.10e-01 9.58e+00 ... (remaining 22205 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.37: 9345 21.37 - 42.74: 555 42.74 - 64.11: 66 64.11 - 85.48: 41 85.48 - 106.86: 16 Dihedral angle restraints: 10023 sinusoidal: 4364 harmonic: 5659 Sorted by residual: dihedral pdb=" CA CYS A 192 " pdb=" C CYS A 192 " pdb=" N CYS A 193 " pdb=" CA CYS A 193 " ideal model delta harmonic sigma weight residual -180.00 -111.65 -68.35 0 5.00e+00 4.00e-02 1.87e+02 dihedral pdb=" CB CYS C 130 " pdb=" SG CYS C 130 " pdb=" SG CYS C 144 " pdb=" CB CYS C 144 " ideal model delta sinusoidal sigma weight residual -86.00 -17.92 -68.08 1 1.00e+01 1.00e-02 6.02e+01 dihedral pdb=" CB CYS G 17 " pdb=" SG CYS G 17 " pdb=" SG CYS G 39 " pdb=" CB CYS G 39 " ideal model delta sinusoidal sigma weight residual 93.00 158.67 -65.67 1 1.00e+01 1.00e-02 5.64e+01 ... (remaining 10020 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 2251 0.062 - 0.123: 380 0.123 - 0.185: 30 0.185 - 0.247: 1 0.247 - 0.308: 3 Chirality restraints: 2665 Sorted by residual: chirality pdb=" C5 BMA H 3 " pdb=" C4 BMA H 3 " pdb=" C6 BMA H 3 " pdb=" O5 BMA H 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.58 0.31 2.00e-01 2.50e+01 2.38e+00 chirality pdb=" C5 BMA K 3 " pdb=" C4 BMA K 3 " pdb=" C6 BMA K 3 " pdb=" O5 BMA K 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.58 0.30 2.00e-01 2.50e+01 2.27e+00 chirality pdb=" C1 NAG K 1 " pdb=" ND2 ASN A 141 " pdb=" C2 NAG K 1 " pdb=" O5 NAG K 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-01 2.50e+01 1.62e+00 ... (remaining 2662 not shown) Planarity restraints: 2709 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL B 222 " -0.013 2.00e-02 2.50e+03 2.66e-02 7.06e+00 pdb=" C VAL B 222 " 0.046 2.00e-02 2.50e+03 pdb=" O VAL B 222 " -0.017 2.00e-02 2.50e+03 pdb=" N TYR B 223 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO B 327 " -0.034 5.00e-02 4.00e+02 5.15e-02 4.25e+00 pdb=" N PRO B 328 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO B 328 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 328 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 216 " -0.032 5.00e-02 4.00e+02 4.90e-02 3.84e+00 pdb=" N PRO B 217 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO B 217 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 217 " -0.027 5.00e-02 4.00e+02 ... (remaining 2706 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 285 2.68 - 3.24: 15343 3.24 - 3.79: 24956 3.79 - 4.35: 33829 4.35 - 4.90: 56492 Nonbonded interactions: 130905 Sorted by model distance: nonbonded pdb=" O TYR C 248 " pdb=" ND2 ASN D 297 " model vdw 2.128 2.520 nonbonded pdb=" NH2 ARG E 147 " pdb=" OE1 GLU E 208 " model vdw 2.139 2.520 nonbonded pdb=" OG SER A 239 " pdb=" NE2 HIS B 306 " model vdw 2.241 2.520 nonbonded pdb=" OH TYR F 23 " pdb=" OE2 GLU F 36 " model vdw 2.241 2.440 nonbonded pdb=" O VAL A 285 " pdb=" OG SER A 288 " model vdw 2.248 2.440 ... (remaining 130900 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 301 or resid 399 through 425)) selection = chain 'D' } ncs_group { reference = chain 'F' selection = chain 'G' } ncs_group { reference = chain 'H' selection = chain 'K' } ncs_group { reference = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.040 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: 4.600 Check model and map are aligned: 0.250 Set scattering table: 0.160 Process input model: 43.340 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 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 : 0.004 0.174 16273 Z= 0.270 Angle : 0.719 32.737 22210 Z= 0.338 Chirality : 0.046 0.308 2665 Planarity : 0.004 0.052 2703 Dihedral : 14.572 106.856 6296 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.20), residues: 1881 helix: 1.39 (0.21), residues: 576 sheet: -0.33 (0.26), residues: 437 loop : -0.86 (0.21), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 317 HIS 0.005 0.001 HIS D 408 PHE 0.028 0.001 PHE D 233 TYR 0.017 0.001 TYR C 218 ARG 0.007 0.000 ARG E 147 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3762 Ramachandran restraints generated. 1881 Oldfield, 0 Emsley, 1881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3762 Ramachandran restraints generated. 1881 Oldfield, 0 Emsley, 1881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 339 time to evaluate : 1.728 Fit side-chains REVERT: A 193 CYS cc_start: 0.5925 (m) cc_final: 0.5435 (m) REVERT: B 133 MET cc_start: 0.7195 (tmm) cc_final: 0.6614 (tmm) REVERT: B 320 GLN cc_start: 0.7043 (pp30) cc_final: 0.6756 (pp30) REVERT: C 46 LYS cc_start: 0.7598 (pptt) cc_final: 0.6692 (pptt) REVERT: C 247 PHE cc_start: 0.8205 (m-10) cc_final: 0.7796 (m-80) REVERT: D 80 LEU cc_start: 0.8741 (mt) cc_final: 0.8524 (mt) REVERT: D 175 GLU cc_start: 0.7549 (pm20) cc_final: 0.7165 (pm20) REVERT: D 227 PHE cc_start: 0.7968 (t80) cc_final: 0.7572 (t80) REVERT: D 238 ASP cc_start: 0.8408 (m-30) cc_final: 0.8167 (m-30) REVERT: D 415 MET cc_start: 0.7428 (mmp) cc_final: 0.6423 (ttt) REVERT: E 116 MET cc_start: 0.8436 (mmt) cc_final: 0.8088 (mmt) REVERT: E 130 ILE cc_start: 0.8883 (mm) cc_final: 0.8617 (mm) REVERT: E 199 LEU cc_start: 0.8366 (tt) cc_final: 0.8163 (tt) REVERT: E 236 LEU cc_start: 0.8903 (mt) cc_final: 0.8657 (mt) outliers start: 0 outliers final: 0 residues processed: 339 average time/residue: 0.2465 time to fit residues: 126.9274 Evaluate side-chains 268 residues out of total 1771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 268 time to evaluate : 1.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 159 optimal weight: 3.9990 chunk 143 optimal weight: 4.9990 chunk 79 optimal weight: 0.9980 chunk 48 optimal weight: 0.5980 chunk 96 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 chunk 148 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 90 optimal weight: 0.4980 chunk 110 optimal weight: 0.0570 chunk 171 optimal weight: 3.9990 overall best weight: 1.2300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 57 ASN F 10 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.1036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 16273 Z= 0.238 Angle : 0.609 8.634 22210 Z= 0.301 Chirality : 0.045 0.171 2665 Planarity : 0.004 0.047 2703 Dihedral : 9.944 76.063 2603 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 1.36 % Allowed : 8.13 % Favored : 90.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.20), residues: 1881 helix: 1.54 (0.21), residues: 580 sheet: -0.37 (0.26), residues: 438 loop : -0.76 (0.21), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 187 HIS 0.005 0.001 HIS C 60 PHE 0.027 0.001 PHE B 262 TYR 0.014 0.001 TYR D 234 ARG 0.003 0.000 ARG C 113 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3762 Ramachandran restraints generated. 1881 Oldfield, 0 Emsley, 1881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3762 Ramachandran restraints generated. 1881 Oldfield, 0 Emsley, 1881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 280 time to evaluate : 1.900 Fit side-chains revert: symmetry clash REVERT: A 179 LYS cc_start: 0.8671 (mmtp) cc_final: 0.8433 (mmtp) REVERT: A 324 MET cc_start: 0.4748 (tmm) cc_final: 0.3641 (mtt) REVERT: B 133 MET cc_start: 0.7387 (tmm) cc_final: 0.6295 (tmm) REVERT: B 253 ILE cc_start: 0.8628 (mm) cc_final: 0.8380 (mm) REVERT: C 171 ASP cc_start: 0.8289 (m-30) cc_final: 0.7292 (p0) REVERT: C 471 PHE cc_start: 0.7707 (t80) cc_final: 0.7437 (t80) REVERT: D 224 LEU cc_start: 0.8062 (tp) cc_final: 0.7858 (tp) REVERT: D 227 PHE cc_start: 0.7958 (t80) cc_final: 0.7638 (t80) REVERT: D 238 ASP cc_start: 0.8416 (m-30) cc_final: 0.8169 (m-30) REVERT: D 282 MET cc_start: 0.8417 (mmm) cc_final: 0.8191 (tmm) REVERT: D 415 MET cc_start: 0.7569 (mmp) cc_final: 0.6500 (ttt) REVERT: E 130 ILE cc_start: 0.8859 (mm) cc_final: 0.8611 (mm) REVERT: E 147 ARG cc_start: 0.8579 (ptt180) cc_final: 0.8290 (ptt180) REVERT: E 199 LEU cc_start: 0.8268 (tt) cc_final: 0.7987 (tt) REVERT: E 236 LEU cc_start: 0.8821 (mt) cc_final: 0.8563 (mt) REVERT: E 300 ASN cc_start: 0.7602 (t0) cc_final: 0.7379 (t0) outliers start: 24 outliers final: 15 residues processed: 292 average time/residue: 0.2531 time to fit residues: 112.8635 Evaluate side-chains 276 residues out of total 1771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 261 time to evaluate : 1.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 192 CYS Chi-restraints excluded: chain B residue 48 GLU Chi-restraints excluded: chain C residue 297 SER Chi-restraints excluded: chain D residue 7 LEU Chi-restraints excluded: chain D residue 193 CYS Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 413 VAL Chi-restraints excluded: chain E residue 44 ASN Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 446 VAL Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain G residue 17 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 95 optimal weight: 7.9990 chunk 53 optimal weight: 6.9990 chunk 142 optimal weight: 0.6980 chunk 116 optimal weight: 0.4980 chunk 47 optimal weight: 0.7980 chunk 171 optimal weight: 3.9990 chunk 185 optimal weight: 3.9990 chunk 153 optimal weight: 4.9990 chunk 170 optimal weight: 0.8980 chunk 58 optimal weight: 0.7980 chunk 137 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 214 GLN D 58 GLN ** E 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.1305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 16273 Z= 0.179 Angle : 0.560 9.192 22210 Z= 0.274 Chirality : 0.044 0.212 2665 Planarity : 0.004 0.045 2703 Dihedral : 8.122 69.250 2603 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.64 % Allowed : 11.24 % Favored : 87.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.20), residues: 1881 helix: 1.77 (0.21), residues: 575 sheet: -0.33 (0.25), residues: 444 loop : -0.77 (0.21), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 187 HIS 0.005 0.001 HIS C 60 PHE 0.018 0.001 PHE B 262 TYR 0.012 0.001 TYR C 218 ARG 0.002 0.000 ARG G 31 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3762 Ramachandran restraints generated. 1881 Oldfield, 0 Emsley, 1881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3762 Ramachandran restraints generated. 1881 Oldfield, 0 Emsley, 1881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 279 time to evaluate : 1.877 Fit side-chains revert: symmetry clash REVERT: A 117 MET cc_start: 0.7770 (tpt) cc_final: 0.7523 (tpt) REVERT: A 277 TYR cc_start: 0.8258 (t80) cc_final: 0.7929 (t80) REVERT: A 278 MET cc_start: 0.7344 (tmm) cc_final: 0.7120 (tpp) REVERT: A 324 MET cc_start: 0.4547 (tmm) cc_final: 0.3416 (mtt) REVERT: B 77 ASP cc_start: 0.8373 (p0) cc_final: 0.7932 (p0) REVERT: B 133 MET cc_start: 0.7497 (tmm) cc_final: 0.6237 (tmm) REVERT: B 253 ILE cc_start: 0.8551 (mm) cc_final: 0.8212 (mm) REVERT: B 429 GLN cc_start: 0.7568 (OUTLIER) cc_final: 0.6494 (mp10) REVERT: B 457 ASP cc_start: 0.8231 (t0) cc_final: 0.7994 (t0) REVERT: C 46 LYS cc_start: 0.7498 (pptt) cc_final: 0.7123 (pptt) REVERT: C 171 ASP cc_start: 0.8160 (m-30) cc_final: 0.7227 (p0) REVERT: C 471 PHE cc_start: 0.7708 (t80) cc_final: 0.7432 (t80) REVERT: D 224 LEU cc_start: 0.8120 (tp) cc_final: 0.7712 (tt) REVERT: D 227 PHE cc_start: 0.7765 (t80) cc_final: 0.7382 (t80) REVERT: D 238 ASP cc_start: 0.8386 (m-30) cc_final: 0.8144 (m-30) REVERT: D 243 MET cc_start: 0.8772 (mmm) cc_final: 0.8537 (tpp) REVERT: D 282 MET cc_start: 0.8386 (mmm) cc_final: 0.8123 (tmm) REVERT: E 116 MET cc_start: 0.8506 (mmt) cc_final: 0.8239 (mmt) REVERT: E 130 ILE cc_start: 0.8845 (mm) cc_final: 0.8575 (mm) REVERT: E 147 ARG cc_start: 0.8556 (ptt180) cc_final: 0.8268 (ptt180) REVERT: E 199 LEU cc_start: 0.8259 (tt) cc_final: 0.7947 (tt) REVERT: E 236 LEU cc_start: 0.8725 (mt) cc_final: 0.8509 (mt) REVERT: E 300 ASN cc_start: 0.7803 (t0) cc_final: 0.7344 (t0) REVERT: F 15 LYS cc_start: 0.8867 (ptpt) cc_final: 0.8265 (pttp) outliers start: 29 outliers final: 18 residues processed: 295 average time/residue: 0.2552 time to fit residues: 116.5675 Evaluate side-chains 273 residues out of total 1771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 254 time to evaluate : 1.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 192 CYS Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain B residue 48 GLU Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 429 GLN Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain C residue 297 SER Chi-restraints excluded: chain D residue 7 LEU Chi-restraints excluded: chain D residue 193 CYS Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 257 LEU Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 408 HIS Chi-restraints excluded: chain E residue 44 ASN Chi-restraints excluded: chain F residue 55 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 169 optimal weight: 4.9990 chunk 129 optimal weight: 5.9990 chunk 89 optimal weight: 4.9990 chunk 19 optimal weight: 0.6980 chunk 82 optimal weight: 4.9990 chunk 115 optimal weight: 0.7980 chunk 172 optimal weight: 5.9990 chunk 182 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 163 optimal weight: 0.7980 chunk 49 optimal weight: 3.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN ** E 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.1466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 16273 Z= 0.229 Angle : 0.567 10.023 22210 Z= 0.280 Chirality : 0.044 0.221 2665 Planarity : 0.004 0.047 2703 Dihedral : 7.666 65.528 2603 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 1.98 % Allowed : 13.27 % Favored : 84.75 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.20), residues: 1881 helix: 1.78 (0.21), residues: 583 sheet: -0.36 (0.25), residues: 443 loop : -0.73 (0.21), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 187 HIS 0.005 0.001 HIS A 204 PHE 0.012 0.001 PHE B 262 TYR 0.011 0.001 TYR C 172 ARG 0.002 0.000 ARG D 20 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3762 Ramachandran restraints generated. 1881 Oldfield, 0 Emsley, 1881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3762 Ramachandran restraints generated. 1881 Oldfield, 0 Emsley, 1881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 269 time to evaluate : 1.967 Fit side-chains revert: symmetry clash REVERT: A 179 LYS cc_start: 0.8650 (mmtp) cc_final: 0.8430 (mmtp) REVERT: A 277 TYR cc_start: 0.8347 (t80) cc_final: 0.7957 (t80) REVERT: A 278 MET cc_start: 0.7266 (tmm) cc_final: 0.6924 (tpt) REVERT: B 77 ASP cc_start: 0.8248 (p0) cc_final: 0.7828 (p0) REVERT: B 133 MET cc_start: 0.7657 (tmm) cc_final: 0.6424 (tmm) REVERT: B 253 ILE cc_start: 0.8608 (mm) cc_final: 0.8271 (mm) REVERT: B 429 GLN cc_start: 0.7566 (OUTLIER) cc_final: 0.6469 (mp10) REVERT: C 45 LEU cc_start: 0.7690 (OUTLIER) cc_final: 0.7376 (tt) REVERT: C 46 LYS cc_start: 0.7580 (pptt) cc_final: 0.7340 (pptt) REVERT: C 471 PHE cc_start: 0.7742 (t80) cc_final: 0.7446 (t80) REVERT: D 224 LEU cc_start: 0.8070 (tp) cc_final: 0.7625 (tp) REVERT: D 227 PHE cc_start: 0.7781 (t80) cc_final: 0.7389 (t80) REVERT: D 235 LEU cc_start: 0.8237 (mp) cc_final: 0.8011 (mt) REVERT: D 282 MET cc_start: 0.8398 (mmm) cc_final: 0.8164 (tmm) REVERT: D 415 MET cc_start: 0.7810 (mmp) cc_final: 0.6565 (ttt) REVERT: E 130 ILE cc_start: 0.8928 (mm) cc_final: 0.8682 (mm) REVERT: E 147 ARG cc_start: 0.8528 (ptt180) cc_final: 0.8261 (ptt180) REVERT: E 199 LEU cc_start: 0.8276 (tt) cc_final: 0.7938 (tt) REVERT: E 236 LEU cc_start: 0.8740 (mt) cc_final: 0.8525 (mt) REVERT: E 271 GLN cc_start: 0.8579 (OUTLIER) cc_final: 0.8319 (mt0) REVERT: E 300 ASN cc_start: 0.7619 (t0) cc_final: 0.7402 (t0) REVERT: F 15 LYS cc_start: 0.8869 (ptpt) cc_final: 0.8261 (pttp) outliers start: 35 outliers final: 22 residues processed: 287 average time/residue: 0.2450 time to fit residues: 108.3406 Evaluate side-chains 281 residues out of total 1771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 256 time to evaluate : 1.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 48 GLN Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 192 CYS Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain B residue 48 GLU Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 429 GLN Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 186 GLU Chi-restraints excluded: chain C residue 297 SER Chi-restraints excluded: chain D residue 7 LEU Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 408 HIS Chi-restraints excluded: chain E residue 44 ASN Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 271 GLN Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 55 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 152 optimal weight: 2.9990 chunk 103 optimal weight: 6.9990 chunk 2 optimal weight: 0.4980 chunk 136 optimal weight: 0.9980 chunk 75 optimal weight: 3.9990 chunk 155 optimal weight: 3.9990 chunk 126 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 93 optimal weight: 0.6980 chunk 163 optimal weight: 0.6980 chunk 46 optimal weight: 0.4980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 439 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 16273 Z= 0.181 Angle : 0.550 11.493 22210 Z= 0.271 Chirality : 0.044 0.227 2665 Planarity : 0.004 0.047 2703 Dihedral : 7.314 61.492 2603 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.26 % Allowed : 15.25 % Favored : 82.50 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.20), residues: 1881 helix: 1.82 (0.21), residues: 583 sheet: -0.35 (0.26), residues: 443 loop : -0.68 (0.21), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 187 HIS 0.004 0.000 HIS A 204 PHE 0.020 0.001 PHE B 262 TYR 0.011 0.001 TYR C 172 ARG 0.001 0.000 ARG C 113 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3762 Ramachandran restraints generated. 1881 Oldfield, 0 Emsley, 1881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3762 Ramachandran restraints generated. 1881 Oldfield, 0 Emsley, 1881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 273 time to evaluate : 1.851 Fit side-chains revert: symmetry clash REVERT: A 278 MET cc_start: 0.7254 (tmm) cc_final: 0.6987 (tpt) REVERT: B 77 ASP cc_start: 0.8194 (p0) cc_final: 0.7797 (p0) REVERT: B 133 MET cc_start: 0.7663 (tmm) cc_final: 0.6357 (tmm) REVERT: B 253 ILE cc_start: 0.8602 (mm) cc_final: 0.8230 (mm) REVERT: B 429 GLN cc_start: 0.7582 (OUTLIER) cc_final: 0.6418 (mp10) REVERT: C 45 LEU cc_start: 0.7616 (OUTLIER) cc_final: 0.7317 (tt) REVERT: C 46 LYS cc_start: 0.7537 (pptt) cc_final: 0.7312 (pptt) REVERT: C 471 PHE cc_start: 0.7722 (t80) cc_final: 0.7413 (t80) REVERT: D 13 GLU cc_start: 0.8110 (mm-30) cc_final: 0.7781 (pt0) REVERT: D 224 LEU cc_start: 0.8008 (tp) cc_final: 0.7663 (tp) REVERT: D 227 PHE cc_start: 0.7734 (t80) cc_final: 0.7363 (t80) REVERT: D 235 LEU cc_start: 0.8187 (mp) cc_final: 0.7949 (mt) REVERT: E 130 ILE cc_start: 0.8911 (mm) cc_final: 0.8653 (mm) REVERT: E 147 ARG cc_start: 0.8552 (ptt180) cc_final: 0.8292 (ptt180) REVERT: E 199 LEU cc_start: 0.8204 (tt) cc_final: 0.7875 (tt) REVERT: E 236 LEU cc_start: 0.8718 (mt) cc_final: 0.8500 (mt) REVERT: E 271 GLN cc_start: 0.8533 (OUTLIER) cc_final: 0.8285 (mt0) REVERT: E 295 MET cc_start: 0.7798 (mmm) cc_final: 0.7175 (ttp) REVERT: F 15 LYS cc_start: 0.8826 (ptpt) cc_final: 0.8186 (pttp) outliers start: 40 outliers final: 23 residues processed: 299 average time/residue: 0.2407 time to fit residues: 112.4011 Evaluate side-chains 278 residues out of total 1771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 252 time to evaluate : 1.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain B residue 48 GLU Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 429 GLN Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 186 GLU Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 297 SER Chi-restraints excluded: chain D residue 7 LEU Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 238 ASP Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 257 LEU Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 408 HIS Chi-restraints excluded: chain E residue 44 ASN Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 271 GLN Chi-restraints excluded: chain F residue 14 THR Chi-restraints excluded: chain F residue 55 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 61 optimal weight: 4.9990 chunk 164 optimal weight: 0.7980 chunk 36 optimal weight: 0.8980 chunk 107 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 182 optimal weight: 4.9990 chunk 151 optimal weight: 6.9990 chunk 84 optimal weight: 0.7980 chunk 15 optimal weight: 0.3980 chunk 60 optimal weight: 2.9990 chunk 96 optimal weight: 8.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 447 ASN ** E 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.101 16273 Z= 0.227 Angle : 0.570 12.696 22210 Z= 0.282 Chirality : 0.044 0.262 2665 Planarity : 0.004 0.048 2703 Dihedral : 7.278 71.076 2603 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 2.88 % Allowed : 15.92 % Favored : 81.20 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.20), residues: 1881 helix: 1.89 (0.21), residues: 579 sheet: -0.32 (0.26), residues: 443 loop : -0.73 (0.21), residues: 859 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 311 HIS 0.005 0.001 HIS C 60 PHE 0.022 0.001 PHE B 262 TYR 0.010 0.001 TYR C 218 ARG 0.002 0.000 ARG D 20 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3762 Ramachandran restraints generated. 1881 Oldfield, 0 Emsley, 1881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3762 Ramachandran restraints generated. 1881 Oldfield, 0 Emsley, 1881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 265 time to evaluate : 1.476 Fit side-chains revert: symmetry clash REVERT: A 278 MET cc_start: 0.7385 (tmm) cc_final: 0.7181 (tpp) REVERT: B 77 ASP cc_start: 0.8192 (p0) cc_final: 0.7793 (p0) REVERT: B 133 MET cc_start: 0.7710 (tmm) cc_final: 0.6341 (tmm) REVERT: B 253 ILE cc_start: 0.8620 (mm) cc_final: 0.8252 (mm) REVERT: C 121 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8754 (tt) REVERT: C 471 PHE cc_start: 0.7734 (t80) cc_final: 0.7433 (t80) REVERT: D 13 GLU cc_start: 0.8139 (mm-30) cc_final: 0.7796 (pt0) REVERT: D 224 LEU cc_start: 0.7996 (tp) cc_final: 0.7709 (tp) REVERT: D 227 PHE cc_start: 0.7721 (t80) cc_final: 0.7373 (t80) REVERT: D 235 LEU cc_start: 0.8191 (OUTLIER) cc_final: 0.7946 (mt) REVERT: D 243 MET cc_start: 0.8281 (tpp) cc_final: 0.7926 (mmm) REVERT: D 415 MET cc_start: 0.7868 (mmp) cc_final: 0.6569 (ttt) REVERT: E 130 ILE cc_start: 0.8931 (mm) cc_final: 0.8701 (mm) REVERT: E 147 ARG cc_start: 0.8544 (ptt180) cc_final: 0.8298 (ptt180) REVERT: E 199 LEU cc_start: 0.8236 (tt) cc_final: 0.7899 (tt) REVERT: E 236 LEU cc_start: 0.8711 (mt) cc_final: 0.8481 (mt) REVERT: E 271 GLN cc_start: 0.8545 (OUTLIER) cc_final: 0.8332 (mt0) REVERT: E 295 MET cc_start: 0.7799 (OUTLIER) cc_final: 0.7425 (ttp) REVERT: F 15 LYS cc_start: 0.8878 (ptpt) cc_final: 0.8265 (pttp) outliers start: 51 outliers final: 28 residues processed: 297 average time/residue: 0.2409 time to fit residues: 111.9463 Evaluate side-chains 289 residues out of total 1771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 257 time to evaluate : 1.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain B residue 48 GLU Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 297 SER Chi-restraints excluded: chain D residue 7 LEU Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 238 ASP Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 408 HIS Chi-restraints excluded: chain E residue 44 ASN Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 271 GLN Chi-restraints excluded: chain E residue 295 MET Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 14 THR Chi-restraints excluded: chain F residue 55 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 176 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 104 optimal weight: 2.9990 chunk 133 optimal weight: 3.9990 chunk 103 optimal weight: 0.0020 chunk 153 optimal weight: 0.8980 chunk 102 optimal weight: 0.9990 chunk 182 optimal weight: 0.9980 chunk 114 optimal weight: 4.9990 chunk 111 optimal weight: 3.9990 chunk 84 optimal weight: 0.7980 overall best weight: 0.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 214 GLN ** E 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.114 16273 Z= 0.201 Angle : 0.569 14.343 22210 Z= 0.281 Chirality : 0.044 0.270 2665 Planarity : 0.003 0.048 2703 Dihedral : 7.035 72.095 2603 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.37 % Allowed : 17.00 % Favored : 80.63 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.20), residues: 1881 helix: 1.85 (0.21), residues: 579 sheet: -0.25 (0.26), residues: 443 loop : -0.72 (0.21), residues: 859 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 311 HIS 0.005 0.001 HIS C 60 PHE 0.018 0.001 PHE B 262 TYR 0.018 0.001 TYR C 172 ARG 0.001 0.000 ARG A 209 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3762 Ramachandran restraints generated. 1881 Oldfield, 0 Emsley, 1881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3762 Ramachandran restraints generated. 1881 Oldfield, 0 Emsley, 1881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 275 time to evaluate : 1.822 Fit side-chains revert: symmetry clash REVERT: B 77 ASP cc_start: 0.8163 (p0) cc_final: 0.7777 (p0) REVERT: B 133 MET cc_start: 0.7715 (tmm) cc_final: 0.6261 (tmm) REVERT: B 253 ILE cc_start: 0.8596 (mm) cc_final: 0.8212 (mm) REVERT: C 471 PHE cc_start: 0.7662 (t80) cc_final: 0.7368 (t80) REVERT: D 13 GLU cc_start: 0.8074 (mm-30) cc_final: 0.7708 (pt0) REVERT: D 224 LEU cc_start: 0.8045 (tp) cc_final: 0.7426 (tp) REVERT: D 227 PHE cc_start: 0.7669 (t80) cc_final: 0.7263 (t80) REVERT: D 235 LEU cc_start: 0.8168 (OUTLIER) cc_final: 0.7960 (mt) REVERT: D 243 MET cc_start: 0.8271 (tpp) cc_final: 0.7950 (mmm) REVERT: E 130 ILE cc_start: 0.8913 (mm) cc_final: 0.8682 (mm) REVERT: E 147 ARG cc_start: 0.8529 (ptt180) cc_final: 0.8251 (ptt180) REVERT: E 183 GLU cc_start: 0.7626 (tt0) cc_final: 0.7323 (tt0) REVERT: E 199 LEU cc_start: 0.8194 (tt) cc_final: 0.7855 (tt) REVERT: E 236 LEU cc_start: 0.8703 (mt) cc_final: 0.8481 (mt) REVERT: E 295 MET cc_start: 0.7799 (OUTLIER) cc_final: 0.7245 (mmm) REVERT: F 15 LYS cc_start: 0.8880 (ptpt) cc_final: 0.8189 (pttp) outliers start: 42 outliers final: 27 residues processed: 300 average time/residue: 0.2269 time to fit residues: 107.0178 Evaluate side-chains 283 residues out of total 1771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 254 time to evaluate : 2.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain B residue 48 GLU Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 297 SER Chi-restraints excluded: chain D residue 7 LEU Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 238 ASP Chi-restraints excluded: chain D residue 257 LEU Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 408 HIS Chi-restraints excluded: chain E residue 44 ASN Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain E residue 295 MET Chi-restraints excluded: chain F residue 14 THR Chi-restraints excluded: chain F residue 55 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 112 optimal weight: 0.8980 chunk 72 optimal weight: 0.9980 chunk 108 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 35 optimal weight: 6.9990 chunk 115 optimal weight: 2.9990 chunk 124 optimal weight: 0.0370 chunk 90 optimal weight: 5.9990 chunk 16 optimal weight: 0.8980 chunk 143 optimal weight: 1.9990 chunk 165 optimal weight: 0.0670 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.142 16273 Z= 0.206 Angle : 0.580 16.745 22210 Z= 0.286 Chirality : 0.044 0.293 2665 Planarity : 0.003 0.048 2703 Dihedral : 6.854 74.721 2603 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.20 % Allowed : 18.01 % Favored : 79.79 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.20), residues: 1881 helix: 1.92 (0.21), residues: 579 sheet: -0.15 (0.26), residues: 443 loop : -0.70 (0.21), residues: 859 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 311 HIS 0.005 0.000 HIS C 60 PHE 0.018 0.001 PHE B 262 TYR 0.010 0.001 TYR A 277 ARG 0.001 0.000 ARG G 31 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3762 Ramachandran restraints generated. 1881 Oldfield, 0 Emsley, 1881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3762 Ramachandran restraints generated. 1881 Oldfield, 0 Emsley, 1881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 267 time to evaluate : 1.916 Fit side-chains revert: symmetry clash REVERT: B 77 ASP cc_start: 0.8068 (p0) cc_final: 0.7712 (p0) REVERT: B 133 MET cc_start: 0.7746 (tmm) cc_final: 0.6243 (tmm) REVERT: B 253 ILE cc_start: 0.8519 (mm) cc_final: 0.8194 (mm) REVERT: C 471 PHE cc_start: 0.7652 (t80) cc_final: 0.7371 (t80) REVERT: D 13 GLU cc_start: 0.8058 (mm-30) cc_final: 0.7688 (pt0) REVERT: D 224 LEU cc_start: 0.8044 (tp) cc_final: 0.7426 (tp) REVERT: D 227 PHE cc_start: 0.7707 (t80) cc_final: 0.7284 (t80) REVERT: D 235 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.8016 (mt) REVERT: E 130 ILE cc_start: 0.8908 (mm) cc_final: 0.8676 (mm) REVERT: E 147 ARG cc_start: 0.8511 (ptt180) cc_final: 0.8243 (ptt180) REVERT: E 183 GLU cc_start: 0.7626 (tt0) cc_final: 0.7322 (tt0) REVERT: E 199 LEU cc_start: 0.8180 (tt) cc_final: 0.7845 (tt) REVERT: E 236 LEU cc_start: 0.8708 (mt) cc_final: 0.8497 (mt) REVERT: E 295 MET cc_start: 0.7723 (OUTLIER) cc_final: 0.7298 (mmm) REVERT: F 15 LYS cc_start: 0.8812 (ptpt) cc_final: 0.8094 (pttp) outliers start: 39 outliers final: 26 residues processed: 295 average time/residue: 0.2229 time to fit residues: 103.6168 Evaluate side-chains 287 residues out of total 1771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 259 time to evaluate : 2.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain B residue 48 GLU Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 297 SER Chi-restraints excluded: chain C residue 461 ILE Chi-restraints excluded: chain D residue 7 LEU Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 238 ASP Chi-restraints excluded: chain D residue 257 LEU Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 408 HIS Chi-restraints excluded: chain E residue 44 ASN Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain E residue 295 MET Chi-restraints excluded: chain F residue 55 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 174 optimal weight: 0.8980 chunk 159 optimal weight: 8.9990 chunk 169 optimal weight: 0.4980 chunk 102 optimal weight: 0.8980 chunk 73 optimal weight: 0.0470 chunk 133 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 153 optimal weight: 0.5980 chunk 160 optimal weight: 0.9980 chunk 111 optimal weight: 0.9990 chunk 179 optimal weight: 4.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN ** E 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.126 16273 Z= 0.206 Angle : 0.581 14.676 22210 Z= 0.287 Chirality : 0.044 0.304 2665 Planarity : 0.003 0.048 2703 Dihedral : 6.754 76.661 2603 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.43 % Allowed : 18.29 % Favored : 79.28 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.20), residues: 1881 helix: 1.97 (0.21), residues: 579 sheet: -0.13 (0.26), residues: 443 loop : -0.69 (0.21), residues: 859 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 311 HIS 0.005 0.001 HIS C 60 PHE 0.018 0.001 PHE E 267 TYR 0.008 0.001 TYR C 218 ARG 0.001 0.000 ARG A 55 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3762 Ramachandran restraints generated. 1881 Oldfield, 0 Emsley, 1881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3762 Ramachandran restraints generated. 1881 Oldfield, 0 Emsley, 1881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 268 time to evaluate : 1.900 Fit side-chains revert: symmetry clash REVERT: B 77 ASP cc_start: 0.8065 (p0) cc_final: 0.7727 (p0) REVERT: B 133 MET cc_start: 0.7778 (tmm) cc_final: 0.6024 (tmm) REVERT: B 253 ILE cc_start: 0.8498 (mm) cc_final: 0.8156 (mm) REVERT: C 471 PHE cc_start: 0.7644 (t80) cc_final: 0.7378 (t80) REVERT: D 13 GLU cc_start: 0.8019 (mm-30) cc_final: 0.7657 (pt0) REVERT: D 224 LEU cc_start: 0.8040 (tp) cc_final: 0.7423 (tp) REVERT: D 227 PHE cc_start: 0.7768 (t80) cc_final: 0.7426 (t80) REVERT: D 235 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.8037 (mt) REVERT: E 130 ILE cc_start: 0.8906 (mm) cc_final: 0.8705 (mm) REVERT: E 147 ARG cc_start: 0.8518 (ptt180) cc_final: 0.8259 (ptt180) REVERT: E 199 LEU cc_start: 0.8174 (tt) cc_final: 0.7840 (tt) REVERT: E 236 LEU cc_start: 0.8699 (mt) cc_final: 0.8488 (mt) REVERT: E 295 MET cc_start: 0.7753 (OUTLIER) cc_final: 0.7314 (mmm) outliers start: 43 outliers final: 34 residues processed: 297 average time/residue: 0.2326 time to fit residues: 108.5723 Evaluate side-chains 294 residues out of total 1771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 258 time to evaluate : 2.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 48 GLN Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain B residue 48 GLU Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 297 SER Chi-restraints excluded: chain C residue 461 ILE Chi-restraints excluded: chain D residue 7 LEU Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 192 CYS Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 238 ASP Chi-restraints excluded: chain D residue 257 LEU Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 408 HIS Chi-restraints excluded: chain E residue 44 ASN Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain E residue 215 ILE Chi-restraints excluded: chain E residue 295 MET Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 14 THR Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain G residue 50 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 109 optimal weight: 6.9990 chunk 85 optimal weight: 0.0020 chunk 124 optimal weight: 0.0770 chunk 188 optimal weight: 2.9990 chunk 173 optimal weight: 0.9980 chunk 149 optimal weight: 0.3980 chunk 15 optimal weight: 7.9990 chunk 115 optimal weight: 0.8980 chunk 91 optimal weight: 6.9990 chunk 119 optimal weight: 5.9990 chunk 159 optimal weight: 8.9990 overall best weight: 0.4746 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN C 447 ASN C 451 GLN ** E 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.151 16273 Z= 0.214 Angle : 0.599 14.594 22210 Z= 0.294 Chirality : 0.044 0.309 2665 Planarity : 0.003 0.048 2703 Dihedral : 6.673 77.964 2603 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.20 % Allowed : 18.86 % Favored : 78.94 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.20), residues: 1881 helix: 2.00 (0.21), residues: 579 sheet: -0.14 (0.26), residues: 443 loop : -0.70 (0.21), residues: 859 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 311 HIS 0.006 0.001 HIS C 60 PHE 0.017 0.001 PHE B 262 TYR 0.023 0.001 TYR C 172 ARG 0.001 0.000 ARG G 31 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3762 Ramachandran restraints generated. 1881 Oldfield, 0 Emsley, 1881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3762 Ramachandran restraints generated. 1881 Oldfield, 0 Emsley, 1881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 262 time to evaluate : 1.801 Fit side-chains revert: symmetry clash REVERT: B 77 ASP cc_start: 0.8041 (p0) cc_final: 0.7717 (p0) REVERT: B 133 MET cc_start: 0.7766 (tmm) cc_final: 0.6021 (tmm) REVERT: B 253 ILE cc_start: 0.8482 (mm) cc_final: 0.8120 (mm) REVERT: C 471 PHE cc_start: 0.7662 (t80) cc_final: 0.7389 (t80) REVERT: D 13 GLU cc_start: 0.8018 (mm-30) cc_final: 0.7660 (pt0) REVERT: D 224 LEU cc_start: 0.8049 (tp) cc_final: 0.7413 (tp) REVERT: D 227 PHE cc_start: 0.7767 (t80) cc_final: 0.7428 (t80) REVERT: D 235 LEU cc_start: 0.8250 (OUTLIER) cc_final: 0.8033 (mt) REVERT: E 147 ARG cc_start: 0.8516 (ptt180) cc_final: 0.8267 (ptt180) REVERT: E 199 LEU cc_start: 0.8176 (tt) cc_final: 0.7843 (tt) REVERT: E 295 MET cc_start: 0.7749 (OUTLIER) cc_final: 0.7316 (mmm) outliers start: 39 outliers final: 31 residues processed: 287 average time/residue: 0.2406 time to fit residues: 108.3999 Evaluate side-chains 287 residues out of total 1771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 254 time to evaluate : 1.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 48 GLN Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain B residue 48 GLU Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 297 SER Chi-restraints excluded: chain C residue 447 ASN Chi-restraints excluded: chain C residue 461 ILE Chi-restraints excluded: chain D residue 7 LEU Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 192 CYS Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 238 ASP Chi-restraints excluded: chain D residue 257 LEU Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 408 HIS Chi-restraints excluded: chain E residue 215 ILE Chi-restraints excluded: chain E residue 295 MET Chi-restraints excluded: chain E residue 296 LEU Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain F residue 14 THR Chi-restraints excluded: chain F residue 55 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 45 optimal weight: 6.9990 chunk 138 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 150 optimal weight: 0.6980 chunk 62 optimal weight: 0.7980 chunk 154 optimal weight: 0.0270 chunk 19 optimal weight: 0.7980 chunk 27 optimal weight: 6.9990 chunk 131 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN C 451 GLN ** E 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.125600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.105356 restraints weight = 23540.979| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 2.65 r_work: 0.3164 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3173 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3173 r_free = 0.3173 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3172 r_free = 0.3172 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3172 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.152 16273 Z= 0.220 Angle : 0.606 14.580 22210 Z= 0.295 Chirality : 0.045 0.313 2665 Planarity : 0.003 0.048 2703 Dihedral : 6.653 77.907 2603 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.09 % Allowed : 18.97 % Favored : 78.94 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.20), residues: 1881 helix: 2.02 (0.21), residues: 579 sheet: -0.12 (0.26), residues: 444 loop : -0.65 (0.22), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 311 HIS 0.010 0.001 HIS C 60 PHE 0.016 0.001 PHE B 262 TYR 0.009 0.001 TYR A 277 ARG 0.003 0.000 ARG G 31 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3377.56 seconds wall clock time: 61 minutes 41.77 seconds (3701.77 seconds total)