Starting phenix.real_space_refine on Sun Dec 10 23:15:01 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z14_14440/12_2023/7z14_14440.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z14_14440/12_2023/7z14_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_14440/12_2023/7z14_14440.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z14_14440/12_2023/7z14_14440.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z14_14440/12_2023/7z14_14440.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z14_14440/12_2023/7z14_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: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 6 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: 6 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: 9 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: 8.47, per 1000 atoms: 0.53 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: 6.69 Conformation dependent library (CDL) restraints added in 2.7 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: 1.74 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: 5.28 Time building geometry restraints manager: 7.20 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 - 17.06: 8836 17.06 - 34.12: 708 34.12 - 51.18: 127 51.18 - 68.24: 36 68.24 - 85.30: 12 Dihedral angle restraints: 9719 sinusoidal: 4060 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 9716 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: 1.000 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: 0.010 Extract box with map and model: 4.450 Check model and map are aligned: 0.220 Set scattering table: 0.150 Process input model: 43.760 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.290 ------------------------------------------------------------------------------- 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 : 13.042 85.303 5992 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 : 1.712 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 339 average time/residue: 0.2568 time to fit residues: 132.9708 Evaluate side-chains 263 residues out of total 1771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 263 time to evaluate : 1.900 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5327 ------------------------------------------------------------------------------- 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: 8.9990 chunk 143 optimal weight: 4.9990 chunk 79 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 96 optimal weight: 7.9990 chunk 76 optimal weight: 3.9990 chunk 148 optimal weight: 4.9990 chunk 57 optimal weight: 0.6980 chunk 90 optimal weight: 4.9990 chunk 110 optimal weight: 0.0970 chunk 171 optimal weight: 3.9990 overall best weight: 1.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 57 ASN ** B 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 58 GLN F 10 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.1168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 16273 Z= 0.292 Angle : 0.622 9.371 22210 Z= 0.308 Chirality : 0.045 0.189 2665 Planarity : 0.004 0.048 2703 Dihedral : 6.714 56.855 2299 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 1.47 % Allowed : 9.20 % Favored : 89.33 % 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: 1.49 (0.21), residues: 581 sheet: -0.44 (0.26), residues: 436 loop : -0.81 (0.21), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 187 HIS 0.005 0.001 HIS C 60 PHE 0.027 0.001 PHE B 262 TYR 0.013 0.001 TYR D 234 ARG 0.003 0.000 ARG D 20 *********************** 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 300 residues out of total 1771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 274 time to evaluate : 2.009 Fit side-chains revert: symmetry clash outliers start: 26 outliers final: 15 residues processed: 287 average time/residue: 0.2611 time to fit residues: 115.0185 Evaluate side-chains 263 residues out of total 1771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 248 time to evaluate : 1.820 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1445 time to fit residues: 6.4595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 95 optimal weight: 0.4980 chunk 53 optimal weight: 0.5980 chunk 142 optimal weight: 3.9990 chunk 116 optimal weight: 0.9980 chunk 47 optimal weight: 0.5980 chunk 171 optimal weight: 0.9980 chunk 185 optimal weight: 6.9990 chunk 153 optimal weight: 2.9990 chunk 170 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 137 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 214 GLN E 225 ASN ** 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: 0.7736 moved from start: 0.1306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 16273 Z= 0.177 Angle : 0.564 9.782 22210 Z= 0.278 Chirality : 0.043 0.205 2665 Planarity : 0.004 0.045 2703 Dihedral : 6.227 55.496 2299 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.24 % Allowed : 11.80 % Favored : 86.96 % 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: 0.12 (0.20), residues: 1881 helix: 1.70 (0.21), residues: 581 sheet: -0.36 (0.25), residues: 444 loop : -0.77 (0.21), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 187 HIS 0.004 0.001 HIS C 60 PHE 0.016 0.001 PHE B 262 TYR 0.013 0.001 TYR C 218 ARG 0.002 0.000 ARG C 113 *********************** 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 298 residues out of total 1771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 276 time to evaluate : 1.798 Fit side-chains revert: symmetry clash outliers start: 22 outliers final: 11 residues processed: 286 average time/residue: 0.2505 time to fit residues: 112.1006 Evaluate side-chains 257 residues out of total 1771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 246 time to evaluate : 1.703 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 11 outliers final: 1 residues processed: 11 average time/residue: 0.1469 time to fit residues: 5.2949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 169 optimal weight: 1.9990 chunk 129 optimal weight: 0.8980 chunk 89 optimal weight: 0.0010 chunk 19 optimal weight: 0.8980 chunk 82 optimal weight: 6.9990 chunk 115 optimal weight: 0.5980 chunk 172 optimal weight: 5.9990 chunk 182 optimal weight: 3.9990 chunk 90 optimal weight: 4.9990 chunk 163 optimal weight: 6.9990 chunk 49 optimal weight: 3.9990 overall best weight: 0.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 447 ASN E 159 GLN ** E 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 439 ASN F 10 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.1454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 16273 Z= 0.196 Angle : 0.570 10.598 22210 Z= 0.280 Chirality : 0.043 0.236 2665 Planarity : 0.004 0.046 2703 Dihedral : 6.034 57.547 2299 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 1.41 % Allowed : 13.89 % Favored : 84.70 % 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: 0.17 (0.20), residues: 1881 helix: 1.76 (0.21), residues: 583 sheet: -0.33 (0.25), residues: 449 loop : -0.77 (0.21), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 187 HIS 0.004 0.001 HIS A 204 PHE 0.026 0.001 PHE B 262 TYR 0.017 0.001 TYR C 172 ARG 0.002 0.000 ARG C 113 *********************** 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 282 residues out of total 1771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 257 time to evaluate : 1.788 Fit side-chains revert: symmetry clash outliers start: 25 outliers final: 10 residues processed: 270 average time/residue: 0.2467 time to fit residues: 104.3998 Evaluate side-chains 257 residues out of total 1771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 247 time to evaluate : 1.764 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1385 time to fit residues: 5.0951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 152 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 2 optimal weight: 0.1980 chunk 136 optimal weight: 0.0570 chunk 75 optimal weight: 4.9990 chunk 155 optimal weight: 4.9990 chunk 126 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 93 optimal weight: 0.9980 chunk 163 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 159 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: 0.7725 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 16273 Z= 0.174 Angle : 0.564 12.744 22210 Z= 0.274 Chirality : 0.043 0.264 2665 Planarity : 0.004 0.047 2703 Dihedral : 5.763 61.217 2299 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 1.02 % Allowed : 15.53 % Favored : 83.46 % 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: 1.85 (0.22), residues: 583 sheet: -0.29 (0.25), residues: 449 loop : -0.72 (0.21), residues: 849 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 0.019 0.001 PHE B 262 TYR 0.012 0.001 TYR C 172 ARG 0.002 0.000 ARG A 57 *********************** 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 294 residues out of total 1771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 276 time to evaluate : 1.840 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 7 residues processed: 288 average time/residue: 0.2588 time to fit residues: 116.4104 Evaluate side-chains 253 residues out of total 1771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 246 time to evaluate : 1.795 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1519 time to fit residues: 4.6801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 61 optimal weight: 0.6980 chunk 164 optimal weight: 1.9990 chunk 36 optimal weight: 0.4980 chunk 107 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 182 optimal weight: 0.6980 chunk 151 optimal weight: 4.9990 chunk 84 optimal weight: 0.6980 chunk 15 optimal weight: 0.2980 chunk 60 optimal weight: 0.8980 chunk 96 optimal weight: 8.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 159 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: 0.7718 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.097 16273 Z= 0.174 Angle : 0.557 13.496 22210 Z= 0.273 Chirality : 0.043 0.260 2665 Planarity : 0.004 0.047 2703 Dihedral : 5.621 63.171 2299 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 1.41 % Allowed : 16.32 % Favored : 82.27 % Cbeta Deviations : 0.05 % 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: 0.29 (0.20), residues: 1881 helix: 1.88 (0.21), residues: 583 sheet: -0.22 (0.26), residues: 449 loop : -0.73 (0.21), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 311 HIS 0.003 0.000 HIS A 204 PHE 0.035 0.001 PHE B 262 TYR 0.011 0.001 TYR E 241 ARG 0.007 0.000 ARG E 187 *********************** 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 294 residues out of total 1771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 269 time to evaluate : 1.803 Fit side-chains revert: symmetry clash outliers start: 25 outliers final: 9 residues processed: 288 average time/residue: 0.2284 time to fit residues: 104.7782 Evaluate side-chains 258 residues out of total 1771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 249 time to evaluate : 1.878 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1446 time to fit residues: 5.1059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 176 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 chunk 133 optimal weight: 0.3980 chunk 103 optimal weight: 1.9990 chunk 153 optimal weight: 1.9990 chunk 102 optimal weight: 0.8980 chunk 182 optimal weight: 3.9990 chunk 114 optimal weight: 5.9990 chunk 111 optimal weight: 2.9990 chunk 84 optimal weight: 0.3980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 214 GLN E 159 GLN E 300 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.122 16273 Z= 0.228 Angle : 0.586 15.775 22210 Z= 0.287 Chirality : 0.044 0.290 2665 Planarity : 0.004 0.048 2703 Dihedral : 5.642 64.631 2299 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 0.96 % Allowed : 17.56 % Favored : 81.48 % Cbeta Deviations : 0.05 % 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: 0.25 (0.20), residues: 1881 helix: 1.88 (0.22), residues: 579 sheet: -0.23 (0.26), residues: 449 loop : -0.77 (0.21), residues: 853 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 0.021 0.001 PHE B 262 TYR 0.012 0.001 TYR E 241 ARG 0.006 0.000 ARG E 187 *********************** 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 279 residues out of total 1771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 262 time to evaluate : 1.827 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 9 residues processed: 273 average time/residue: 0.2283 time to fit residues: 99.5952 Evaluate side-chains 261 residues out of total 1771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 252 time to evaluate : 1.724 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1402 time to fit residues: 4.7498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 112 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 108 optimal weight: 0.9990 chunk 54 optimal weight: 4.9990 chunk 35 optimal weight: 6.9990 chunk 115 optimal weight: 4.9990 chunk 124 optimal weight: 0.5980 chunk 90 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 143 optimal weight: 4.9990 chunk 165 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.124 16273 Z= 0.246 Angle : 0.601 15.808 22210 Z= 0.293 Chirality : 0.044 0.296 2665 Planarity : 0.004 0.048 2703 Dihedral : 5.659 64.235 2299 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 0.79 % Allowed : 18.29 % Favored : 80.91 % Cbeta Deviations : 0.05 % 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: 0.23 (0.20), residues: 1881 helix: 1.89 (0.21), residues: 579 sheet: -0.27 (0.26), residues: 441 loop : -0.79 (0.21), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 311 HIS 0.006 0.001 HIS C 60 PHE 0.020 0.001 PHE B 262 TYR 0.013 0.001 TYR E 241 ARG 0.005 0.000 ARG E 187 *********************** 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 273 residues out of total 1771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 259 time to evaluate : 2.168 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 7 residues processed: 269 average time/residue: 0.2442 time to fit residues: 105.0067 Evaluate side-chains 253 residues out of total 1771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 246 time to evaluate : 1.864 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1523 time to fit residues: 4.6600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 174 optimal weight: 7.9990 chunk 159 optimal weight: 6.9990 chunk 169 optimal weight: 0.7980 chunk 102 optimal weight: 4.9990 chunk 73 optimal weight: 0.6980 chunk 133 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 153 optimal weight: 0.8980 chunk 160 optimal weight: 4.9990 chunk 111 optimal weight: 0.0980 chunk 179 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.146 16273 Z= 0.206 Angle : 0.603 16.919 22210 Z= 0.292 Chirality : 0.043 0.289 2665 Planarity : 0.004 0.048 2703 Dihedral : 5.571 64.722 2299 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 0.56 % Allowed : 18.97 % Favored : 80.46 % Cbeta Deviations : 0.05 % 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: 0.26 (0.20), residues: 1881 helix: 1.89 (0.21), residues: 579 sheet: -0.23 (0.26), residues: 443 loop : -0.77 (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 0.020 0.001 PHE B 262 TYR 0.009 0.001 TYR E 241 ARG 0.005 0.000 ARG E 187 *********************** 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 266 residues out of total 1771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 256 time to evaluate : 1.980 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 5 residues processed: 262 average time/residue: 0.2420 time to fit residues: 100.6556 Evaluate side-chains 250 residues out of total 1771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 245 time to evaluate : 1.888 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1522 time to fit residues: 3.9182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0070 chunk 124 optimal weight: 2.9990 chunk 188 optimal weight: 0.7980 chunk 173 optimal weight: 1.9990 chunk 149 optimal weight: 0.6980 chunk 15 optimal weight: 0.1980 chunk 115 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 119 optimal weight: 0.5980 chunk 159 optimal weight: 5.9990 overall best weight: 0.4598 ------------------------------------------------------------------------------- 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 159 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.137 16273 Z= 0.192 Angle : 0.590 16.025 22210 Z= 0.287 Chirality : 0.043 0.285 2665 Planarity : 0.004 0.048 2703 Dihedral : 5.489 65.195 2299 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.17 % Allowed : 19.59 % Favored : 80.24 % Cbeta Deviations : 0.05 % 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: 0.31 (0.20), residues: 1881 helix: 1.90 (0.22), residues: 577 sheet: -0.19 (0.26), residues: 448 loop : -0.72 (0.22), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 311 HIS 0.007 0.001 HIS C 60 PHE 0.021 0.001 PHE E 267 TYR 0.011 0.001 TYR A 277 ARG 0.005 0.000 ARG E 187 ********************** 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 258 residues out of total 1771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 255 time to evaluate : 1.926 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 257 average time/residue: 0.2374 time to fit residues: 96.6652 Evaluate side-chains 248 residues out of total 1771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 247 time to evaluate : 1.883 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1430 time to fit residues: 3.1295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 45 optimal weight: 0.5980 chunk 138 optimal weight: 5.9990 chunk 22 optimal weight: 0.0980 chunk 41 optimal weight: 0.9990 chunk 150 optimal weight: 0.9990 chunk 62 optimal weight: 0.0870 chunk 154 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 131 optimal weight: 1.9990 chunk 8 optimal weight: 0.0980 overall best weight: 0.3558 ------------------------------------------------------------------------------- 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 159 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.125977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.105862 restraints weight = 23548.783| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 2.65 r_work: 0.3174 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3168 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3168 r_free = 0.3168 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 = 0.3167 r_free = 0.3167 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3167 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.155 16273 Z= 0.195 Angle : 0.601 18.015 22210 Z= 0.290 Chirality : 0.043 0.282 2665 Planarity : 0.004 0.048 2703 Dihedral : 5.415 64.126 2299 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.28 % Allowed : 19.88 % Favored : 79.84 % Cbeta Deviations : 0.05 % 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: 0.33 (0.20), residues: 1881 helix: 1.91 (0.21), residues: 583 sheet: -0.16 (0.26), residues: 456 loop : -0.73 (0.22), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 311 HIS 0.006 0.000 HIS C 60 PHE 0.020 0.001 PHE B 262 TYR 0.008 0.001 TYR C 218 ARG 0.005 0.000 ARG E 187 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3346.69 seconds wall clock time: 61 minutes 51.92 seconds (3711.92 seconds total)